title: ChIP_Input_WT_rep2

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

institute: The University of Oxford

description: Genome-wide library of Immunoprecipitated fragments

data_processing:
Mapping : bowtie -m 2 --maxIns 350, hg9
For un-mapping reads : trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks
Genome_build: hg19
Supplementary_files_format_and_content: bigWig : (DEEPtools) bamCoverage converison of filtered fragments (reconstructed, duplicate-filtered fragments : see above) from bam to bigwig,  (--binSize 10 --normalizeUsingRPKM --minMappingQuality 30)

growth_protocol: Cells were maintained in the expansion phase using StemSpan SFEM medium (Stem Cell Technologies) supplemented with: hSCF (50 ng/ml, Peprotech), erythropoietin (3 IU/ml, OUH hospital pharmacy), dexamethasone (10^-6M, OUH Hospital pharmacy), glutamine (2mM, Life Technologies), Penicillin/Streptomycin (P/S, 100IU/ml, Life Technologies) and doxycycline (2μg/ml, Sigma-Aldrich) at 37°C with 5% CO2 incubation. Cell concentration was maintained between 0.5 and 1x10^6 cells/ml with media change every 48 hours.  Cells were kept for a maxmimum of 3 weeks.  To induce differentiation, cells were transferred to IMDM (Life Technologies) supplemented with: Solvent/Detergent pooled AB plasma (2.5%, NHSBT), hSCF (50ng/μl), Epo (3IU/ml) holotransferrin (330μg/ml, Sigma-Aldrich), insulin (10 μg/ml, Sigma-Aldrich), heparin (2IU/ml, JR hospital pharmacy), P/S (100IU/ml) glutamine (2mM) and doxycycline (2μg/ml) at 37ÅãC with 5% CO2 incubation. Media was changed every 48 hours. Cell concentration was maintained between 0.5 and 1x10^6 cells/ml. After seven days, doxycycline was removed from the media and cells were then cultured for a further 3 days prior to experiments. Adequate differentiation wasconfirmed using flow cytometry and cytospin.

extract_protocol:
[isolation protocol]  Chromatin immunoprecipitation (ChIP) was performed on 3-5x10^6 cells per replicate using the ChIP Assay Kit (Cat. No. 17-295, Millipore).  All stages beyond the fixation stage used kit solutions as per the manufacturer’s instructions.  A single 10 minute 1% formaldehyde fixation was used for all antibodies.  The cross-linking reaction was quenched by addition of glycine (Sigma-Aldrich) to a final concentration of 130mM), then washed once in PBS and snap frozen.  Samples were stored at -80C prior to further processing. Cells were lysed in SDS lysis buffer with Complete Proteinase Inhibitor Cocktail (PIC, Roche).  Samples were then fragmented using the Covaris S220 Focused ultra-sonicator with the following settings (Duty Cycle: 2%, Intensity: 3.0, Cycles/burst: 200, Power mode: Freq. Sweeping, Duration: 120s, Temp: 6C, Batches: 4).  Sonicated chromatin samples were diluted 1:10 in ChIP dilution buffer containing PIC to 2mL.  Before addition of the antibody, 100 μL was taken from each 2mL sample to be used as a 5% input.  The chromatin was pre-cleared with Protein A agarose for 30 min before immunoprecipitation overnight at 4C rotating (the volumes added are also shown).  Protein A agarose beads were added the next morning for 60 min at 4C, after which the beads were sequentially washed in Low Salt Buffer (1x), High Salt Buffer (1x), LiCl Buffer (1x) and TE Buffer (2x) with the final TE buffer wash at room temperature.  Bound chromatin fragments were eluted from beads in elution buffer (1% SDS, 0.1M NaHCO3), de-crosslinked by incubating samples at 65C for 5 hours, then proteinase K treated for one hour at 55C.  DNA was precipitated using phenol/chloroform extraction and ethanol precipitation with GlycoBlue (15mg/mL) (Thermo Scientific) to visualise the pellet prior to dissolving in 55 μL of H2O.
DNA was purified by phenol-chloroform extraction with PhaseLock tubes (5Prime) and ethanol precipitation with NaOAc, and 2 µl GlycoBlue (Invitrogen). ChIP enrichment was determined by RT-qPCR
NEBNext Ultra II DNA Library Prep kit for Illumina (New England Biolabs).

tag: chip antibody

value: WT

tag: time

value: Day 10 Differentiation


title: ChIP_Input_WT_rep1

status: Public on Apr 28 2021

type: SRA

country: United Kingdom

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: treatment

tag: genotype


title: 26304_5: WT-REC-anti-IL-2 RNA-seq

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

country: USA

institute: City of Hope National Medical Center

description: WT C57BL/6 donor CD4+ T cells in the spleen of HCT recipients given anti-IL-2 treatment

library_source: transcriptomic

data_processing:
Reads were aligned to mm10 Genome Assembly using Tophat2 with default settings
Gene expression level of UCSC known genes were quantified using HTseq-count v0.9.1
Annotaton file used was TxDb.Mmusculus.UCSC.mm10.knownGene (downloaded 8/30/2018)
Genome_build: mm10
Supplementary_files_format_and_content: text files containing raw gene level counts

molecule: total RNA

organism: Mus musculus

source_name: T cells from Spleen

growth_protocol: spleen and bone marrow cell from WT C57BL/6 mice were harvested and intravenus injection into the lethally irradiated WT BALB/C mice, then given the control IgG or anti-IL-2 mAb to the recipients every other day from day 0 to day 6 after injection, on day 7 after injection, spleen and colon were harvested from recipients,and WT C57BL/6 type CD4+ T or CD8+ T cells were purify by FACS sorting

extract_protocol:
RNA extracted by using miRNeasy mini kit (QIAGEN) ,RNA concentration was mesuared by NanoDrop 1000 (Thermo Fisher Scientific, Waltham Massachusetts, US) and RNA integrity was determined using Bioanalyzer (Agilent).
Library construction of 280 ng total RNA for each sample was made using KAPA Stranded mRNA-Seq Kit (Illumina Platforms) (Kapa Biosystems, Wilmington, USA). and the size distribution assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).
Using 10 cycles of PCR amplification. Libraries were purified using AxyPrep Mag PCR Clean-up kit (Thermo Fisher Scientific). Each library was quantified using a Qubit fluorometer (Life Technologies)

treatment_protocol: the cells were freshly isolated from spleen and colon tissue by FACS sorting

tag: cell type

value: CD4  T Cells

tag: tissue

value: Spleen

tag: strain

value: WT C57BL/6

tag: batch


title: ChIP_Input_LRFKO

value: CRISPR/Cas9 Edited

value: LRFKO


title: LV_GPR3_LowTiter

city: Odense M

first: Lasse Kruse

last: Markussen

address: Campusvej 55

department: BMB

country: Denmark

institute: University of Southern Denmark

data_processing:
RNA-sequencing (RNA-seq) (TruSeq2, Illumina) was performed according to the instructions by the manufacturer using 1µg of RNA for preparation of cDNA libraries.
Sequencing reads were mapped to the mouse genome using STAR (Dobin et al., 2013).
Tag counts were summarized at the gene level using HOMER (Heinz et al., 2010).
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: patient-derived non-immortalized brown adipocytes

growth_protocol: Human preadipocytes were cultured in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin. Media was changed every 2nd day. On the day of confluece, cells were induced to differentiate with DMEM supplemented with 10% FBS, 1% penicillin/streptomycin, biotin (33uM), insulin (0.5uM), pantothenate (17uM), dexamethasone (0.1uM), T3 (2nM), IBMX (500 uM), indomethacin (30uM), rosiglitazone (1uM). Media was changed every 2nd day throughout differentiation.

extract_protocol:
Cells were harvested on day 14 of differentiation. Cells were immediatly lysed using Qiazol, and subequently isolated using Rneasy Mini Kit according to manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: On day 9 og differentiation, cells were transduced with serial dilutions of sterile-filtered virus-containing supernatant (in DMEM + 0.1% polybrene).

tag: lv treatment

value: GPR3 ORF, LowTiter


title: LV_GPR3_HighTiter

value: patient-derived non-immortalized brown adipocytes

value: GPR3 ORF, HighTiter


title: HFD_WT_BAT_rep 1

data_processing:
RNA-sequencing (RNA-seq) (TruSeq2, Illumina) was performed according to the instructions by the manufacturer using 1µg of RNA for preparation of cDNA libraries.
Sequencing reads were mapped to the mouse genome using STAR (Dobin et al., 2013).
Tag counts were summarized at the gene level using HOMER (Heinz et al., 2010).
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Brown adipose tissue

extract_protocol:
BAT was removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Control

tag: injection scheme

tag: diet

value: 7 days HFD

value: BAT


title: African American TNBC 12

city: Birmingham

first: Sooryanarayana

last: Varambally

state: Alabama

address: 1824 6th Avenue S

department: Pathology

institute: University of Alabama

data_processing:
The raw sequence reads obtained as FASTQ files were trimmed using Trim Galore (v0.4.1) [http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/] to remove adapter sequences and low quality reads.
After performing the quality control analysis using FastQC (v0.11.5) [http://www.bioinformatics.babraham.ac.uk/projects/fastqc/], the trimmed reads were mapped to human genome (GRCh38/hg38) using TopHat v2.1.0.
The aligned reads were sorted via samtools (Version: 1.3.1). HTSeq-count (version 0.6.0) was used to obtain raw read counts for each annotated human gene. Differential expression analysis and read count normalization was carried out using DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text file include normalized read counts for each sample from DESeq.

source_name: triple negative breast cancer tumor (FFPE)

extract_protocol:
RNA were extracted from FFPE sections using Qiagen All Prep DNA/RNA FFPE Kit (cat # 80234)
RNA sequencing libraries were prepared for Illumina using manufacturer’s instructions.

tag: age in years

tag: Stage

value: Stage III

tag: race

value: African American


title: ChIP_Input_BCL11AKO


title: Chow_C-3BO_BAT_rep 5

value: Chow


title: African American TNBC 11

value: triple negative breast cancer tumor (FFPE)

value: Stage II


title: Chow_C-3BO_BAT_rep 4


title: LV_EV_LowTiter

value: EV, LowTiter


title: 26300_1: WT-REC-IgG RNA-seq

description: WT C57BL/6 donor CD4+ T cells in the spleen of HCT recipients given IgG treatment

value: CD4  T Cells

value: REC-IgG


title: mRNA Ctrl 2

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

institute: The Babraham Institute

data_processing:
Quality of all libraries was checked by FastQC (v0.11.8) and FastqScreen (v0.13.0)
For mRNA-seq, Ribo-seq and 4sU-seq: reads were trimmed for poor quality and adaptor sequences using Trim Galore (0.5.0 dev) with default parameters, then mapped to the mouse GRCm38 genome build using Hisat2 (--dta --sp 1000,1000, including known-splicesite-infile).
Mapped reads were imported into Seqmonk (v1.44.0), and raw read counts were generated for the GRCm38 v90 annotation release over mRNA features assuming opposing strand specificity (mRNA-seq and 4sU-seq), or over CDS features assuming same strand specificity.
For iCLIP datasets: fastq files were uploaded to the Genialis iMaps platform (without first demultiplexing), demultiplexed based on the first three bases, deduplicated based on their random 5' barcode (next four bases), and analysed using the iCount (v2.0.1.dev) demulitplex and analyse pipeline with default paramters to identify cross-link sites (see König et al, Nat Struct Mol Biol, 2010, DOI: 10.1038/nsmb.1838 for details). For iCLIP BRF1/2 1, where RNA from low and high molecular weight protein:RNA complexes were sequenced separately, fastq files for these were merged prior to analysis.
Cross-link sites for the three replicates for iCLIP with each antibody were then merged before calling peaks using iCount (v2.0.1.dev). These were then filtered to include only sites with FDR < 0.05, and annotated in R (using biomaRt and GenomicRanges packages) to indicate genes whose 3'UTR overlaps each site, considering only transcript isoforms with a CCDS.
Genome_build: GRCm38
Supplementary_files_format_and_content: For mRNA-seq, Ribo-seq and 4sU-seq, tab-delimited text files show gene names together with raw read counts generated over mRNA (mRNA-seq and 4sU-seq) or CDS (Ribo-seq) features for each sample. For iCLIP, position and strand of significant crosslink sites (FDR < 0.05) for merged replicates (separate file for each antibody) are shown together the number of detected crosslinks and FDR, and a comma-separated list of genes whose 3'UTR overlaps with the site, considering only isoforms with a CCDS.

source_name: Activated CD4+ T cells

growth_protocol: Naïve CD4+ T cells were isolated from pooled peripheral and mesenteric lymph nodes and spleen using the Miltenyi Biotech CD4+ CD62L+ T Cell Isolation Kit

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen).
Libraries were prepared using the TruSeq stranded mRNA sample prep kit, and sequenced on the HiSeq 2000.

treatment_protocol: T cells were cultured in RPMI1640 containing 10% FCS RPMI media with 10% FCS, 50 µM β-mercaptoethanol, 2mM Glutamine, penicillin/streptomycin and activated by crosslinking CD3ε on 2C11 monoclonal antibody coated tissue culture wells (10µg/ml), together with the 37.51 anti-CD28 monoclonal antibody as a hybridoma supernatant or purified antibody at 10µg/ml

value: Zfp36fl/fl Zfp36l1fl/fl control

tag: age of mice

value: 7 weeks

tag: sex of mice

value: Mix of male/female

tag: number of mice

value: Spleen, peripheral and mesenteric LN

value: CD4+ T cells


title: African American TNBC 10


title: Chow_C-3BO_BAT_rep 3


title: LV_EV_HighTiter

value: patient-derived non-immortalized brown adipocytes

value: EV, HighTiter


title: African American TNBC 9


title: ChIP_H3K4me3_WT_rep2

tag: chip antibody

value: H3K4me3, Abcm ab8580

value: WT

tag: time

value: Day 10 Differentiation


title: ChIP_H3K4me3_WT_rep1

tag: cell line

tag: treatment


title: African American TNBC 8

value: African American


title: Chow_C-3BO_BAT_rep 2

tag: genotype

value: Chow

value: BAT


title: Chow_C-3BO_BAT_rep 1

tag: tissue


title: Chow_WT_BAT_rep 5

value: Control


title: African American TNBC 6

value: triple negative breast cancer tumor (FFPE)

value: Stage II


title: African American TNBC 7


title: ChIP_H3K4me3_LRFKO

value: CRISPR/Cas9 Edited

value: LRFKO


title: ChIP_H3K4me3_BCL11AKO


title: Chow_WT_BAT_rep 4


title: African American TNBC 5

value: Stage III


title: ChIP_H3K27ac_WT_rep1

value: H3K27ac, Abcam  ab4729


title: ChIP_H3K27ac_LRFKO


title: Chow_WT_BAT_rep 3


title: African American TNBC 4


title: Chow_WT_BAT_rep 2


title: African American TNBC 3


title: ChIP_H3K27ac_BCL11AKO


title: siKD_Ctrl._rep 1

growth_protocol: Human supraclavicular BAT cells were cultured in DMEM/F-12 supplemented with 10% FBS, 1% P/S, and FGF1. Two days past confluence, cells were induced to differentiate with DMEM/F-12 supplemented with 1% P/S, dexamethansone (0.1uM), insulin (100nM), T3 (2nM), transferrin (10ug/mL), rosiglitazone (200nM), and IBMX (540uM). On day 3 of differentiation, media was changed and IBMX was omitted from the differentiation media. Thereafter, media was refreshed on day 6 and 9 and at both times, IBMX and rosiglitazone were omitted from the media. On day 9 of differentiation, cells were forward transfected (20 nM of siRNA). Cells were harrvested on day 12 of differentiation.

extract_protocol:
Cells were immediatly lysed using Qiazol, and subequently isolated using Rneasy Mini Kit according to manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

tag: sirna

value: siControl


title: siKD_GPR3_rep 1


title: siKD_Ctrl._rep 2


title: siKD_GPR3_rep 3


title: siKD_Ctrl._rep 3


title: siKD_GPR3_rep 2


title: CRISPR_GPR3_rep 3

molecule: polyA RNA

source_name: human fat stromal vascular fraction cells

growth_protocol: CRISPR-GPR3-OE preadipocytes were cultured in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin. Media was changed every 2nd day. On the day of confluence, cells were induced to differentiate with DMEM supplemented with 10% FBS, 1% penicillin/streptomycin, biotin (33uM), insulin (0.5uM), pantothenate (17uM), dexamethasone (0.1uM), T3 (2nM), IBMX (500 uM), indomethacin (30uM), rosiglitazone (1uM). Media was changed every 2nd day throughout differentiation.

value: fat stromal vascular fraction cells

tag: sgrna


title: M18_20_CTL3_NRF2

city: Boston

first: John

middle: N

last: Hutchinson

state: Massachusetts

address: 201 Wachusett Street

institute: Diamond Age Data Science

description: 030817B Best1 GFP

data_processing:
All samples were processed using an RNA-seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org/en/latest/). Raw reads were examined for quality issues using FastQC. (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to ensure library generation and sequencing were suitable for further analysis.
Quasimapping and quantification of raw reads was achieved using Salmon (0.9.1) with transcript information from Ensembl release 91. The same samples from different sequencing runs were aggregated at the counts level.
Genome_build: Mapped to the transcriptome - Ensembl release 91
Supplementary_files_format_and_content: nrf2_rd1_all_samples_raw_counts.csv - matrix table in comma separated value format (csv) with raw gene counts for every gene and every sample

source_name: rd1 RPE cells

extract_protocol:
The retina was removed and the eyecup was quickly cleaned of connective tissue and placed in RNA Protect (Qiagen, Hilden, Germany).  The supernatant was  collected and purified with a RNAeasy micro column (Qiagen) adapting the protocol introduce by Xing-Zhao Wang et al.
Purified RPE RNA was then amplified with a Ultra Low v4 kit (Clontech/Takara Bio) and libraries were prepared for sequencing using standard Illumina protocols. Samples were run on two separate sequencing runs.

treatment_protocol: Each mouse had one eye injected with AAV Best1 Nrf2 and AAV Best1 GFP, and the contralateral eye injected with AAV Best1 GFP only.  Immediately after sacrifice, the eye was enucleated and complete GFP infection was verified.

value: retinal pigment epithelial cells (RPE)

tag: age

tag: individual


title: African American TNBC 2

tag: age in years


title: CRISPR_GPR3_rep 2


title: ATAC_WT_P7_rep4

description: Genome-wide library of tagmented fragments

data_processing:
Library Strategy: ATAC-seq
Mapping : bowtie -m 2 --maxIns 350, hg9
For un-mapping reads : trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks
Genome_build: hg19
Supplementary_files_format_and_content: bigWig : (DEEPtools) bamCoverage converison of filtered fragments (reconstructed, duplicate-filtered fragments : see above) from bam to bigwig,  (--binSize 10 --normalizeUsingRPKM --minMappingQuality 30)

source_name: WT Rep 4 proerythroblast

growth_protocol: Cells were maintained in the expansion phase using StemSpan SFEM medium (Stem Cell Technologies) supplemented with: hSCF (50 ng/ml, Peprotech), erythropoietin (3 IU/ml, OUH hospital pharmacy), dexamethasone (10^-6M, OUH Hospital pharmacy), glutamine (2mM, Life Technologies), Penicillin/Streptomycin (P/S, 100IU/ml, Life Technologies) and doxycycline (2μg/ml, Sigma-Aldrich) at 37°C with 5% CO2 incubation. Cell concentration was maintained between 0.5 and 1x10^6 cells/ml with media change every 48 hours.  Cells were kept for a maxmimum of 3 weeks.  To induce differentiation, cells were transferred to IMDM (Life Technologies) supplemented with: Solvent/Detergent pooled AB plasma (2.5%, NHSBT), hSCF (50ng/μl), Epo (3IU/ml) holotransferrin (330μg/ml, Sigma-Aldrich), insulin (10 μg/ml, Sigma-Aldrich), heparin (2IU/ml, JR hospital pharmacy), P/S (100IU/ml) glutamine (2mM) and doxycycline (2μg/ml) at 37C with 5% CO2 incubation. Media was changed every 48 hours. Cell concentration was maintained between 0.5 and 1x10^6 cells/ml. After seven days, doxycycline was removed from the media and cells were then cultured for a further 3 days prior to experiments. Adequate differentiation wasconfirmed using flow cytometry and cytospin.

extract_protocol:
ATAC-seq was performed as published (Buenrostro et al., 2013). 10,000-50,000 cells were used per biological replicate where possible; if cells numbered less than 10,000 an optimized low cell number protocol was used. Cells were spun at 500g for 10 min, then lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl 3 mM MgCl2, 0.1% IGEPAL CA-630). Transposition was then performed with Tn5 transposase (Nextera, Illumina) for 30 min at 37ÅãC following the reaction volumes as published. DNA was purified using the Qiagen MinElute kit following the manufacturer’s instructions, then eluted in 20μl of elution buffer; samples could be stored at this point at -20ÅãC. Libraries were amplified and barcoded using the NEBNext 2xMastermix kit with custom primers as published (Buenrostro et al., 2013). ATAC-seq library profiles were visualized using the D1000 tape on the Agilent Tapestation to ensure correct tagmentation. Libraries were quantified using the universal library quantification kit (KAPA Biosystems) prior to massively parallel sequencing using a standard Illumina protocol (NextSeq High Output v2 75 cycle sequencing kit). The low cell number protocol uses proportionally less lysis buffer and Tn5 transposase (Corces et al., 2017). After spinning at 500g for 10 min and removing the supernatant, cells were permeabilised and tagmented with Dig-transposition buffer (25 μL 2x TD buffer [Illumina], 2.5 μL Tn5 Transposase, 0.5 μL 1% digitonin and 22 μL H2O) for 30 min. After the transposition step, samples were processed as per larger cell numbers.
Libraries were amplified and barcoded using the NEBNext 2xMastermix (NEB) and the custom primers as published in Buenrostro et al., 2013. ATAC-Seq libraries profiles were visualized using D1000 tape on the Tapestation (Agilent). The libraries were quantified using the universal library quantification kit (KAPA Biosystems).

value: proerythroblast


title: ChIP_H3K27ac_WT_rep2


title: ATAC_WT_P7_rep3

source_name: WT Rep 3 proerythroblast


title: African American TNBC 1

tag: Stage


title: CRISPR_GPR3_rep 1


title: ATAC_WT_P7_rep2

source_name: WT Rep 2 proerythroblast


title: Mtb transcriptome - Hspx Low_3

city: Ithaca

first: Davide

last: Pisu

state: NY

address: 930 Campus Road

department: Microbiology and Immunology

institute: Cornell University

description:
Dual Rna-seq of hspx-low infected lung cells
Dual Rna-seq
mtb_transcriptome_matrix.tsv
mtb_transcriptome_counts_normalized.csv

data_processing:
scRNA-seq: Raw sequencing reads from each run were processed using the software CellRanger (v.3.0) from 10X for the mRNA libraries and CITE-Seq-Count (v. 1.4.3) (https://hoohm.github.io/CITE-seq-Count/ ) for the ADT and HTO libraries, to generate raw count matrices for both mRNA and proteins.  Downstream analysis of the datasets was performed in Seurat (v. 3.1.4) as previously described.(Stuart et al., 2019)  Briefly, we first filtered out cells with  < 200 unique genes/cell and with very-high mitochondrial content (> 30% mitochondrial reads), then multiplexed samples were demultiplexed using the MULTIseqDemux function in Seurat ((McGinnis et al., 2019)), doublets and empty droplets were identified and removed, and the correct identity assigned to each sample. scRNA-seq datasets for each sample were pre-processed using the regularized negative binomial regression in Seurat (regressing out both the number of counts and percentage of mitochondrial reads) (Hafemeister and Satija, 2019) and analyzed to identify myeloid cell subsets. Myeloid cell subsets from the different samples were then merged to generate an annotated object containing information from all the different datasets. Subsequently, the RNA slot (containing the raw counts) of the merged object was used as an input for Harmony, as previously described (Korsunsky et al., 2019). Briefly, raw counts were log-normalized and the first 3000 highly variable genes identified. The expression of these genes was scaled and centered, PCA was computed on the scaled expression values and data integration with Harmony was performed using both “Batch” and “Infection Status” as covariates for the murine datasets and “Batch” for the human datasets. The aligned Harmony embeddings were then used to perform graph-based cluster detection using PCs (principal components) that were identified as statistically significant by the jackstraw method. (Chung and Storey, 2015) The Louvain algorithm was used for community detection. (Blondel, 2008) We annotated clusters of cell types by reference-based and canonical marker genes analysis, as described in the text. Trajectory and pseudotime analysis was performed in Monocle (v3.0), using the SeuratWrappers package in R (v. 0.2.0) to convert the integrated Seurat object. For unbiased trajectory and pseudotime analysis of the macrophage populations in both murine and human datasets, all cells previously classified as macrophages were assigned to the same partition and trajectory/pseudotime analysis was conducted as previously described.(Qiu et al., 2017)  Pathway enrichment analysis was performed in g:Profiler, using an ordered by fold change list of genes as a query, using the g:SCS method for multiple testing correction and the Reactome database as a data source. Only pathways enriched with FDR <0.05 were considered statistically significative.
Dual RNA-seq: Data analysis for the Dual RNA-seq datasets was performed as previously described. (Pisu et al., 2020a; Pisu et al., 2020b) Briefly, low quality reads and Illumina adapters were removed using FlexBar (v. 3.4) (Roehr et al., 2017) while remaining rRNA reads were removed using Bowtie2 (-sensitive mode) (Langmead and Salzberg, 2012) and a custom GTF file. The filtered fastq files were split using Bowtie2 (–very-sensitive mode) into species-specific files using the two reference genomes, GRCm38.94 for Mus musculus and NCBI assembly GCA_00668235.1 for Mtb Erdman. Hisat2 (v. 2.1.0) (Kim et al., 2015) was then used to align Mtb reads to the M.tuberculosis transcriptome and raw read counts for each sample were obtained using HTSeq. (v. 0.11.0)(Anders et al., 2015) The raw read count matrices obtained in this study (hspx-high and hspx-low) were then combined with the matrices obtained from samples of a previous study (Mtb in AM and Mtb in IM) (Pisu et al., 2020a) to compare bacterial responses belonging to ontogeny vs activation of the host immune cell. Exploratory, visualization and differential gene expression analysis was then carried out in R using DESeq2 and APEGLM for LFC estimation, as previously described (Pisu et al., 2020a). Genes with less than 10 raw counts across all samples were excluded from downstream analysis. The protein-protein interaction network for the Mtb genes was created in Cytoscape using the String app. (v. 1.4.1) . Only high-confidence interactions (co-expression, experiments, neighborhood, co-occurrence with a score > 0.7) relative to query proteins were considered.
ATAC-seq: Paired-end sequencing reads of length 2 x 42 bp were trimmed to remove adapter sequences using cutadapt (ver. 2.5) (Martin, 2011) and quality checked using FASTQC. The reads were aligned to the mm10 (GRCm38) mouse reference genome using bwa (ver. 0.7.17) (Li and Durbin, 2009). Low quality alignments (MAPQ < 30), secondary alignments, unmapped reads and reads with unmapped mate were discarded using samtools. For reads with multiple alignments only five best alignments were retained. PCR duplicates were removed using Picard MarkDuplicates. The remaining clean alignments were analysed for fragment length distribution using the ATACseqQC R/Bioconductor library (Ou et al., 2018). Read alignments to the positive strand were shifted 4 bp downstream and alignments to the negative strand were shifted 5bp upstream to centre the reads on the transposon binding events. Subsequently, peaks were called using macs2 (ver. 2.1.1.20160309) callpeak command with the parameters “-p 0.01 --shift -75 --extsize 150 --nomodel -B --SPMR --keep-dup all --call-summits”. Fold enrichment and p-value tracks normalized to input were produced using macs2 bdgcmp command (options -m FE and -m ppois respectively). Peaks with a q-value < 0.01 were shortlisted. Peaks in the blacklisted regions specified by ENCODE project were removed. For each of the four sample groups, viz. Uninfected AM, Infected AM, Uninfected IM and Infected IM, pooled samples were generated by pooling together reads from all individual replicates of the same group. These pooled samples were also analysed in the same manner as above. Peaks called in the pooled samples were compared against peaks called in the individual samples of the same condition using irreproducible discovery rate (IDR) framework. High quality reproducible peaks were shortlisted based on IDR < 0.05. Subsequently, the IDR peaks from the four groups were merged using “bedtools merge” to generate a final set of peaks (n = 127,513). Counts of reads aligned at each peak interval in each sample was determined using summarizeOverlaps function of the GenomicAlignments R/Bioconductor package (Lawrence et al., 2013) and TMM normalized using edgeR (Robinson et al., 2010).
Genome_build: Mus Musculus: GRCm38.94 / Homo Sapiens: GRCh38.98 / M.tuberculosis: GCA_00668235.1
Supplementary_files_format_and_content: TSV files: contains raw count matrices to import in R for downstream analysis
Supplementary_files_format_and_content: CSV files: contains raw or normalized count data, they were generated from the integrated Seurat objects and contain count data from all datasets
Supplementary_files_format_and_content: RDS file: Integrated Seurat objects that contain all datasets, metadata, dimensional reductions and cluster informations described in the manuscript

source_name: Lung infected cells

extract_protocol:
Single cell suspensions from mice infected with hspx’::GFP/smyc’::mCherry (n=3, 3 batches, total of 9 mice) have been prepared as described previously (Pisu et al, 2020). The two different populations of infected host-cells (hspx-high and hspx-low) have been sorted (Figure S1A) and collected directly in Trizol, as previously described.(Pisu et al., 2020a)
Dual RNA extraction has been performed as we previously reported (Pisu et al., 2020a). rRNA depletion has been performed using a 1:1 mix of depletion solutions from the Ribo-Zero H/M/R and Ribo-Zero Gram+ kits (Illumina) and a modified protocol previously described. (Pisu et al., 2020b) The rRNA-depleted samples were purified by ethanol precipitation. Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). Libraries were sequenced on a Novaseq 6000 S4 (Illumina) in multiple rounds until the desired sequencing depth for bacterial reads was reached (target 1M 2x150nt PE reads).

value: lung

tag: timepoint

value: 3 weeks

tag: disease state

value: Infected

tag: strain

tag: pathogen


title: CRISPR_EV_rep 3

value: EV


title: ATAC_WT_P7_rep1

source_name: WT Rep 1 proerythroblast

value: WT


title: Mtb transcriptome - Hspx Low_2


title: Kenyan TNBC 15

source_name: TNBC Tumor (FFPE)

extract_protocol:
RNA were extracted from FFPE sections using Qiagen All Prep DNA/RNA FFPE Kit (cat # 80234)
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA).

value: TNBC Tumor (FFPE)


title: CRISPR_EV_rep 2


title: Kenyan TNBC 14


title: Chow_WT_BAT_rep 1

value: Control

tag: injection scheme

tag: diet

value: Chow

value: BAT


title: Kenyan TNBC 13

value: Stage IIIA


title: CRISPR_EV_rep 1


title: ATAC_WT_P6_rep2

source_name: WT Rep 2 polychromatic erythroblast

tag: cell line

value: polychromatic erythroblast


title: Kenyan TNBC 12


title: Kenyan TNBC 10

value: Stage IIA


title: ATAC_WT_P5_rep3

source_name: WT Rep 3 normoblast

tag: treatment

value: normoblast


title: Kenyan TNBC 9


title: ATAC_WT_P6_rep1

source_name: WT Rep 1 polychromatic erythroblast

tag: genotype


title: Mtb transcriptome - Hspx High_2

description:
Dual Rna-seq of hspx-high infected lung cells
Dual Rna-seq
mtb_transcriptome_matrix.tsv
mtb_transcriptome_counts_normalized.csv

tag: tissue


title: Kenyan TNBC 11


title: ATAC_WT_P5_rep2

source_name: WT Rep 2 normoblast

tag: cell type


title: Mtb transcriptome - Hspx High_3


title: Mtb transcriptome - Hspx High_1


title: Kenyan TNBC 8

value: Stage IIIB


title: ATAC_WT_P5_rep1

source_name: WT Rep 1 normoblast


title: Kenyan TNBC 7


title: Mtb transcriptome - Hspx Low_1


title: ATAC_LRFKO_P5_rep4

source_name: Differentiation Rep 4 normoblast LRFKO

value: CRISPR/Cas9 Edited

value: LRFKO


title: Kenyan TNBC 6

value: Stage IIIC


title: ATAC_LRFKO_P5_rep3

source_name: Differentiation Rep 3 normoblast LRFKO


title: ATAC_LRFKO_P5_rep2

source_name: Differentiation Rep 2 normoblast LRFKO


title: ATAC_WT_P6_rep3

source_name: WT Rep 3 polychromatic erythroblast


title: ATAC_LRFKO_P5_rep1

source_name: Differentiation Rep 1 normoblast LRFKO


title: Pneumocystis uninfection (single-cell BCR Seq)

city: Beijing

first: Zhaohui

last: Tong

state: Beijing

address: NO. 8, Gong Ti South Road

department: Department of Respiratory and Critical Care Medicine

country: China

institute: Beijing Chaoyang Hospital

data_processing:
Library strategy: BCR Seq
The Cell Ranger software was obtained from 10x Genomics website https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest. Alignment, filtering, barcode counting, and UMI counting were performed with cellranger count module to generate feature-barcode matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle compoments were used to generate clusters by K-means algorithm and graph-based algorithm, respectively.
The other clustering method is Seurat 3.0(R package). Cells whose gene number was less than 200, or gene number ranked in the top 1%, or mitochondrial gene ratio was more than 25% were regarded as abnormal and filtered out. Dimensionality reduction was performed using PCA, and visualization was realized by TSNE and UMAP.
GO enrichment, KEGG enrichment, Reactome enrichment and Disease enrichment (human only) of cluster markers were performed using KOBAS software with Benjamini-Hochberg multiple testing adjustment, using top 20 markers gene of cluster. The results were visualized using R package
Protein-protein interaction was obtained from STRING database with combine_score >=400. For each cluster, the interaction of top 20 marker genes was extracted from the database and the results were visualized using Cytoscape software, respectively.
Transcription Factors were predicted within 2000 bp upstream and 500 bp downstream of TSS for top 20 marker genes of each cluster using TFBSTools and JASPAR database. The gene and TF network for each cluster was visualized using Cytoscape software.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung CD45+ cells

extract_protocol:
Single cell suspensions were isolated from mouse lungs by collagenase digestion.
CD45+ cells were sorted by BD FACS ARIA II cell sorter from lung cell suspensions. Full-length BCR V(D)J segments were generated by using the Chromium Single-Cell V(D)J Enrichment kit following the manufacturer’s protocol.

treatment_protocol: For Pneumocystis infection, 1×10e6 Pneumocystis cysts contained in 100μl PBS were injected through trachea of each mouse. Control mice were transtracheally injected with 100μl PBS.

value: Lung-derived CD45+ cells

value: 6-8 week

tag: infection

value: uninfected

tag: time (duration of infection)


title: Pneumocystis infection 3W (single-cell BCR Seq)

tag: age

value: Pneumocystis

value: 3 weeks


title: Pneumocystis infection 2W (single-cell BCR Seq)

value: 2 weeks


title: Kenyan TNBC 4

value: TNBC Tumor (FFPE)


title: Kenyan TNBC 3

value: Stage IIB


title: Pneumocystis infection 4W (single-cell BCR Seq)

value: 4 weeks


title: ATAC_DoubleKO_P5_rep2

source_name: Differentiation Rep 2 normoblast BCL11A/LRF KO

value: BCL11A/LRF KO


title: ATAC_DoubleKO_P5_rep1

source_name: Differentiation Rep 1 normoblast BCL11A/LRF KO


title: Kenyan TNBC 2


title: ATAC_BCL11AKO_P5_rep3

source_name: Differentiation Rep 3 normoblast BCL11AKO


title: Kenyan TNBC 1


title: 33_S29: Pure sporozoite sample

city: Utrecht

first: Arnar Kari

last: Sigurdarson Sandholt

address: Yalelaan 2

department: IRAS

country: Netherlands

institute: Utrecht University

data_processing:
Base calling with Illumina basecaller
Reads were trimmed to get rid of adapters and low-quality parts with Trimmomatic v. 0.36, using the standard Illumina adapter library, SLIDINGWINDOW:4:20 and MINLEN:50
Reads were mapped to a merged version of the reference genomes (effectively mapping to both at the same time as if they were a single genome) with STAR v. 2.7.2b, using default settings
Reads mapping to features were counted using HTSeq v. 0.9.1, with strandedness set on reverse, i.e. -s reverse, and otherwise default settings
Read counts loaded into R and, using edgeR, each sample was CPM normalized with regards to library size and genes filtered out that had few/no reads mapping to them across samples
Genome_build: GRCg6a/Eth001
Supplementary_files_format_and_content: comma separated text files containing raw gene counts for each gene and sample, one for the chicken data and one for E. tenella
Supplementary_files_format_and_content: comma separated text files containing CPM normalized read counts for each organism, with low expressed genes across time points filtered out along with samples without chicken data, for the chicken dataset, and samples without E. tenella data, for the E. tenella dataset

organism: Eimeria tenella

source_name: Eimeria tenella sporozoite culturre

growth_protocol: The immortalised chicken macrophage cell-line HD11 (Beug et al., 1979) was maintained in growth medium, i.e. RPMI 1640 (National Veterinary Institute) supplemented with 200 IU penicillin/ml, 100 µg streptomycin/ml, 2mM L glutamine, and 5% FCS. Before infection HD11 cells were trypsinised and live cells were counted by trypan blue exclusion. Cells were seeded at 5.6 x105 cells per well in flat-bottomed 6-well tissue culture plates (Nunc™, ThermoFisher Scientific) in 2 ml of growth medium and at 0.35 x105 cells per well in flat-bottomed 96-well tissue culture plates (Nunc™, ThermoFisher Scientific) in 100 µl of growth medium. Plates were incubated at 40°C, 5.2% CO2 in air at a humid atmosphere for 24 h after which the HD11 cells were approx. 50-70 % confluent in the wells. Cryopreserved E. tenella sporozoites were thawed into RPMI 1640 medium with 15% FCS, centrifuged down at 910 x g for 7 min, resuspended in growth medium and viable sporozoites were counted by trypan blue exclusion

extract_protocol:
For RNA isolation 1 ml of HD11 cell lysate in TRIzol was used and RNA was extracted using chloroform according to the TRIzol manufacturer’s protocol. The Isolated RNA was subsequently treated with DNAse (TURBO™ DNase, 2U/ul, ThermoFisher Scientific) according to the manufacturers protocol and further purified using reagents and the “RNA cleanup” protocol of the RNeasy Mini kit (Qiagen) protocol. RNA concentration and quality was then assessed using the Agilent RNA 6000 Nano kit on a 2100 Bioanalyzer Instrument (Agilent) and the RNA stored at -70°C until further analysis.
Sequencing libraries were prepared from 0.12 – 0.5 μg total RNA using the TruSeq stranded mRNA library preparation kit (Cat# RS-122-2101/2102, Illumina Inc.) including polyA selection. The library preparation was performed according to the manufacturers’ protocol (#15031047). Sequencing: HiSeq2500, paired-end 125bp read length, v4 sequencing chemistry.

treatment_protocol: At infection, 4.5 x106 sporozoites per well in 6-well plates and 0.28 x106 sporozoites per well in 96-well plates were added to the cultures aiming at a ratio of 4 sporozoites per HD11 cell. The same volume of growth medium without parasites was added to uninfected control cultures. Plates were then cultured until RNA harvest up to 72 h and for plates cultured longer than 24 h, growth medium was removed at 24 h, cultures washed with phosphate buffered saline (PBS; without Ca2+ and Mg2+ at pH 7) to remove loose sporozoites and fresh growth medium was added to the wells before culture was continued.

tag: infection status

tag: sample time post-infection [hours]

tag: chicken cell line

tag: e. tenella strain

value: Houghton


title: ATAC_BCL11AKO_P5_rep2

source_name: Differentiation Rep 2 normoblast BCL11A KO

value: BCL11A KO


title: Mice housed at 29°C without posterior hair rep5

city: Ann Arbor

first: Ormond

middle: A.

last: MacDougald

state: MI

address: 2800 Plymouth Rd

department: Molecular & Integrative Physiology

institute: University of Michigan

data_processing:
DNBSEQ-G400 platform
Read files were downloaded and quality of raw read data was checked using FastQC (version v0.11.30) to identify features of the data that may indicate quality problems (i.e. low-quality scores, over-represented sequences, inappropriate GC content).
Reads were aligned to the UCSC reference genome using STAR (version 2.7.5a). FastQC was used for the second round of quality control post-alignment to ensure that only high-quality data was input to expression quantitation and differential expression analysis.
Differential expression analysis was done using featureCounts/DESeq2, using GRCm39 as the reference genome sequence.
Genome_build: GRCm39
Supplementary_files_format_and_content: Matrix table (CSV file) with normalized abundance measurements of genes (rlog normalized counts) from DESeq2. Each sample is represented by a column in the table.
Supplementary_files_format_and_content: Matrix table (CSV file) with raw gene counts for every gene and every sample

source_name: white adipose tissue (WAT) 13 weeks of age

extract_protocol:
Total RNA was prepared from cells by using RNA Stat60 according to the manufacturer’s protocol (Tel-Test Inc.).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were housed from birth to 13 weeks of age at 22°C or 29°C. After weaning, posterior hair was removed.

value: Gluteal WAT


title: Pneumocystis infection 1W (single-cell BCR Seq)

value: 1 week


title: Mice housed at 29°C without posterior hair rep3


title: YTK

city: Xi'an

first: Yusi

last: Zhang

address: No.169 Changle West Road

department: Immunology

institute: Fourth Military Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 20%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes

source_name: PBMC

growth_protocol: freshly isolated PBMCs. Did not growth in vitro.

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3' Reagent Kit v3 (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ Library Gel Bead Kit V3 and prepared for sequencing using standard Illumina protocols

treatment_protocol: Did not treat in vitro.

tag: disease state

value: normal health control

tag: Sex

value: male


title: RM_samples_MULTI-seq

city: Toronto

first: Curtis

middle: William

last: McCloskey

state: ON

address: 101 College Street, PMCRT, Room 13-303

department: Medical Biophysics

country: Canada

institute: University Health Network

data_processing:
Raw sequencing reads were aligned using CellRanger 3.1.0
MULTI-seq sample barcode libraries were trimmed to 28bp using Trimmomatic v0.36 prior to demultiplexing.
MULTIseq sample barcode alignment and classification were performed using the deMULTIplex R package (https://github.com/chris-mcginnis-ucsf/MULTI-seq)
Further doublet removal and QC was performed as described in the paper, count matrix file supplied here is post-doublet removal and QC
Genome_build: GRCh38-3.0.0 Human genome
Supplementary_files_format_and_content: Expression libraries: gene-cell matrix provided as raw UMI counts post-demultiplexing, doublet removal and QC as described in the paper, along with metadata for each cell. Raw fastq files not supplied as this data is derived from multiplexed samples over mutliple runs as indicated in the RM_count_matrix_metadata.csv file

source_name: human mammary tissue from reduction mammoplasty

extract_protocol:
Cells were lysed in droplets in the 10x Chromium system
10x Genomics Single Cell 3' Reagent Kit (v3 chemistry)

tag: source

value: human primary reduction mammoplasty


title: YYZ

value: female


title: Kenyan TNBC 5

source_name: TNBC Tumor (FFPE)

tag: age in years

tag: Stage

value: Stage IIA


title: Mice housed at 29°C without posterior hair rep4

tag: strain


title: Y26

value: HFRS fever stage


title: Mice housed at 29°C without posterior hair rep1


title: Mice housed at 22°C without posterior hair rep7


title: Patient MFX238 osteoblasts transfected with MALAT1 LNA1

first: Archana

last: Sharma-Oates

address: Haworth Building

department: Centre for Computational Biology

institute: University of Birmingham

description:
MFX238-M-1-2-3_S9
End-stage
GeneCountsperSample.txt

data_processing:
Quantseq 3' RNA sequencing (Lexogen).
Fastq reads were mapped to hg38 whole genome using Star-Aligner v2.5.2b the following parameters: --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: GeneCountsperSample.txt: Tab-delimited text file includes ENSEMBL gene identifiers and read counts for each sample.

growth_protocol: Subchondral bone chips cultured in media (DMEM, 10% FBS, 100Units/mL Penicillin, 100ug/mL Streptomycin, 1% Non-essential amino acids, L-glutamine 2mM, ascorbic acid 50ug/ml, Dexamethasone 10nM, and beta-glycerophosphate 2mM).

extract_protocol:
Qiagen RNeasy columns.
Libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (#SKU: 015.96).

treatment_protocol: 24 h transfection with Locked Nucleic Acids using Lipofectamine 3000.

tag: patient

tag: diagnosis

value: Osteoarthritis

value: Subchondral bone osteoblasts

tag: treatment

value: MALAT1 LNA1


title: Patient MFX238 osteoblasts transfected with control (NC) LNA

description:
MFX238-NC2-2_S7
End-stage
GeneCountsperSample.txt

tag: cell type

value: Control (NC) LNA


title: Patient MFX238 osteoblasts transfected with MALAT1 LNA2

description:
MFX238-M-1-1-3_S8
End-stage
GeneCountsperSample.txt

value: MALAT1 LNA2


title: Patient MFX225 osteoblasts transfected with control (NC) LNA

description:
MFX225-NC2-3_S4
End-stage
GeneCountsperSample.txt


title: Mice housed at 22°C without posterior hair rep6


title: Patient MFX225 osteoblasts transfected with MALAT1 LNA1

description:
MFX225-M-1-2-2_S6
End-stage
GeneCountsperSample.txt


title: Y15


title: Y16


title: Mice housed at 29°C without posterior hair rep6


title: Patient MFX224 osteoblasts transfected with MALAT1 LNA2

description:
MFX224-M--1-2-3_S3
End-stage
GeneCountsperSample.txt


title: Patient MFX224 osteoblasts transfected with MALAT1 LNA1

description:
MFX224-M-1-1-2_S2
End-stage
GeneCountsperSample.txt


title: Patient MFX224 osteoblasts transfected with control (NC) LNA

description:
MFX224-M-NC2-1_S1
End-stage
GeneCountsperSample.txt


title: ATAC_BCL11AKO_P5_rep1

source_name: Differentiation Rep 1 normoblast BCL11AKO

tag: cell line

value: CRISPR/Cas9 Edited

value: normoblast

tag: genotype


title: Y07

tag: age


title: Mice housed at 22°C without posterior hair rep4


title: Y06


title: Y04


title: BAL - Subject_2_3

description:
Subject 2 and 3 for the human integrated dataset - HTO barcoded
scRNA-seq
bal_integrated.csv
bal_integrated.RDS

source_name: BAL - healthy volunteers

extract_protocol:
Bronchoscopy and BAL were performed as described previously (Mwandumba HC et al., J Immunol 2004; 172:4592-4598; Jambo KC et al., Thorax 2011; 66:375-382). A cell suspension containing 5 x106 BAC was centrifuged at 500g for 8 min at 4oC, the supernatant was discarded, and the cells were resuspended in 1mL of chilled 90% methanol (Merck Life Science, Dorset, UK).
Fixed BAL samples were equilibrated on ice for 15’, washed twice in rehydration buffer to remove residual methanol, stained with different HTO antibodies for 30’ at 4C (as described above), and washed twice in cell staining buffer + 0.5U/ul of Rnase inhibitor (Sigma). Subsequently, the amount of cells recovered from each sample has been quantified and different samples were mixed together in a 1:1 ratio and multiplexed into the same 10X run. Libraries were generated using the same modifications described for mouse scRNA-seq samples.

tag: tissue

value: lung

tag: timepoint

value: Uninfected

tag: pathogen


title: Mice housed at 29°C without posterior hair rep2

value: Gluteal WAT


title: Mice housed at 22°C without posterior hair rep3


title: BAL - Subject_1

description:
Subject 1 for the human integrated dataset
scRNA-seq
bal_integrated.csv
bal_integrated.RDS


title: Patient MFX225 osteoblasts transfected with MALAT1 LNA2

description:
MFX225-M-1-1-3_S5
End-stage
GeneCountsperSample.txt


title: Mice housed at 22°C without posterior hair rep1


title: inp-Myb_3

city: Oslo

first: Roza Berhanu

last: Lemma

address: Blindernveien 31

department: Department of Biosciences

country: Norway

institute: University of Oslo

description: Myb Input

data_processing:
Low quality reads and adaptors were removed using TrimGalore v0.3.3
Illumina spike-in PhiX were removed using BBMap v37.4
clean reads in fastq format were aligned to the human genome build hg19 using bwa mem v0.7.5a with default parameters
reads with mapq<20, improperly aligned reads and reads aligning to mitochondrial chromosome were filtered using SAMtools v0.1.19
peak calling was performed using MACS2 v2.1.0 with “-g hs -m 5 50 --bw 150 --fix-bimodal --extsize 100 --call-summits -p 0.01” as parameters
resulting peaks were refined using the bdgcmp function of MACS2 v2.1.0 with the 'ppois' method
bedGraph files containing refined peaks were converted to bigWig format using the tool, bedGraphToBigWig v4
Genome_build: hg19
Supplementary_files_format_and_content: tracks (peaks) in bigWig file format

source_name: human erythroleukemic cell line

growth_protocol: K-562 cells were cultivated in IMDM (ThermoFisher Scientific) supplemented with 10% Fetal Bovine Serum and 1% Penicillin/Streptamycin. Selection of stable cell lines was achieved with the addition of 200 µg/ml G418 to the medium.

extract_protocol:
Nuclei from stable K-562 cell lines was isolated after crosslinking followed by sonication and immunoprecipitation of sonicated chromatin with a mouse monoclonal anti-TY1 antibody. DNA from eluted chromatin was purified using a 'ChIP DNA clean concentrator KIT' (Zymo research #D5205).
ThruPLEXⓇ low-input sample-prep

treatment_protocol: No treatment

tag: stable expression

tag: chip antibody

value: No


title: inp-Myb_2

description: Myb Input


title: Mice housed at 22°C without posterior hair rep5


title: Mice housed at 22°C without posterior hair rep2


title: Non-responded W3

city: Guangzhou

first: Chao

address: Zhongshan Er Road

department: Thoracic Oncology

institute: Guangdong Lung Cancer Institute

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 20%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: Lung cancer

treatment_protocol: All included samples were collected after three cycles of induction checkpoint inhibitors

value: Lung

tag: tumor stage

value: stage IA

value: EGFR exon21 L858R/exon20 R77H


title: Responded W2

value: KRAS exon2 G12C


title: inp-Myb_1

description: Myb Input


title: inp-Ctrl_1

description: control Input


title: 14_S13: Infected 72h replicate 1

organism:
Eimeria tenella
Gallus gallus

source_name: Chicken macrophage cell culture

tag: infection status

value: Infected

tag: sample time post-infection [hours]

tag: chicken cell line

value: Macrophage HD-11

tag: e. tenella strain

value: Houghton


title: Non-responded W1

value: EGFR exon21 L858R


title: 17_Mabs_B9_PE

city: Seattle

first: Eliza

last: Peterson

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

description: Planktonic Early_t1

data_processing:
Illumina RiboZero bacteria kit was used for rRNA depletion. Samples were sequenced on the NextSeq sequencing instrumetn in mid output 150 v2 flow cell. Paired-end 75 bp reads were checked for technical artifacts using FastQC following Illumina default quality filtering steps. Raw FASTQ read data were processed using the R package DuffyNGS.
Genome_build: Mycobacterium abscessus ASM6918
Supplementary_files_format_and_content: tab-delimited text file includes read counts for each sample

organism: Mycobacteroides abscessus ATCC 19977

source_name: Planktonic Early_t1

growth_protocol: planktonic samples grown in Saunton's minimal media supplemented with 0.05% Tyloxapol at 37 degrees C with shaking (180 rpm)

extract_protocol:
In five independent experiments, colonies of M. absecssus were resuspended in sterile 1x PBS and diluted in Sauton's minimal media to an OD of 0.05 and grown in a 75cm2 cap-vented culture flask, in a 37 degrees C static incubator for 5 (T1) or 7 (t2) days. After harvesting at 5 or 7 days, cells pellets were spun down and immediately frozen at -80 degrees C until RNA isolation . Cell pellets in TRIzol were transferred to a tube containing Lysing Matrix B, and vigorously shaken at max speed for 30 s in a FastPrep 120 homogenizer three times. This mixture was centrifuged at max speed for 1 min and the supernatant was transferred to a fresh tube. RNA was isolated using phenol-chloroform extraction method, followed by DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: pellicle samples grown in Saunton's minimal media without tyloxapol at 37 degrees C stationary in 75 cm2 culture flasks

tag: strain

value: bacterial culture

value: 24 hour


title: 20_Mabs_B9_BL

description: Biofilm Late_T2

source_name: Biofilm Late_T2

value: 7 day


title: 18_Mabs_B9_PL

description: Planktonie Late_t2

source_name: Planktonie Late_t2

value: 48 hour


title: 19_Mabs_B9_BE

description: Biofilm Early_T1

source_name: Biofilm Early_T1

value: 5 day


title: 8_S8: Infected 72h replicate 3


title: inp-Ctrl_2

description: control Input


title: inp-Ctrl_3

description: control Input


title: 20_S17: Infected 72h replicate 2


title: aIL2: anti-IL-2 scRNA-seq

description: WT C57BL/6 donor cells in the spleen of HCT recipients given anti-IL-2 treatment

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline (version 3.1.0) to generate FASTQ files and aligned to mm10 genome to gene expression count
The subsequent data analysis was performed using “Seurat” package and R scripts
Data were scaled and log2 transformed within Seurat.
Genome_build: mm10

source_name: spleen cell

growth_protocol: spleen and bone marrow cell from WT C57BL/6 mice were harvested and intravenus injection into the lethally irradiated WT BALB/C mice, then given the Tacrolimus or anti-IL-2 mAb to the recipients  from day 0 to day 6 after injection, on day 6 after injection,  isolate single cells from spleen of the recipients

extract_protocol:
Library preparation for single cell RNA-seq and TCR-seq was done with the Chromium Single Cell 5' Reagent Kits from 10× Genomics according to manufacturer's protocol. Cellular suspensions were loaded on a Chromium Controller instrument (10x Genomics) to generate single-cell gel bead-in-emulsions (GEMs). GEM-reverse transcriptions (GEM-RTs) were performed in a Veriti 96-well thermal cycler (Thermo Fisher Scientific). After RT, GEMs were harvested and the cDNAs were amplified and cleaned up with the SPRIselect Reagent Kit (Beckman Coulter).
Indexed sequencing single cell RNA-seq libraries were constructed using the Chromium Single-Cell 5′ Library Kit  for enzymatic fragmentation, end-repair, A-tailing, adaptor ligation, ligation cleanup, sample index PCR, and PCR cleanup. The purity and library size were validated by capillary electrophoresis using 2,100 Bioanalyzer (Agilent Technologies). The quantity was measured fluorometrically using Qubit dsDNA HS Assay Kit from Invitrogen. Sequencing libraries were loaded on a NextSeq500 (Illumina).

treatment_protocol: the cells were freshly isolated from spleen

value: T cell

value: Spleen

value: WT C57BL/6


title: 15_Mabs_B8_BE

description: Biofilm Early_T1


title: 6_S6: Infected 48h replicate 3


title: TAC: Tacrolimus scRNA-seq

description: WT C57BL/6 donor cells in the spleen of HCT recipients given Tacrolimus treatment


title: 12_S11: Infected 48h replicate 1


title: SMH_g3_1

city: Santa Barbara

first: Delany

last: Rodriguez

address: Biological Science Building  RM1201 University of California Santa Barbara

department: Molecular Cellular and Developmental Biology

institute: University of California Santa Barbara

data_processing:
For sequencing libraries were diluted to 16 pM then applied to a V3 flowcell using the Illumina cBot according to manufacturer’s instructions.   Sequencing was carried out on the Hi-Seq 2000 using HSCS v 1.5.15.1.  Image analysis and basecalling were carried out using RTA 1.13.48.0, and deconvolution and fastq file production were performed with CASAVA 1.8.2.
Sequenced reads were trimmed for adaptor sequenceusing FastQC
Mapped to EST database "Bot_asmb assembly (04.05.2011, A. Gracey)" using bowtie v0.12.7
The number of reads mapping to each EST were obtained with Sam2Counts (Samtools version 0.1.18)
Differential expression analysis was performed with DESeq 1.10.1
Genome_build: http://octopus.obs-vlfr.fr/public/botryllus/blast_botryllus.php  (Note: use EST: *Bot_asmb assembly (04.05.2011, A. Gracey)*).
Supplementary_files_format_and_content: DESeq_g1_g3_all3x.csv reports foldChange.

organism: Botryllus schlosseri

source_name: Whole colony

growth_protocol: Botryllus schlosseri raised in the lab

extract_protocol:
Total RNA was extracted with Nucleo Spin RNA II kit from MN
The standard protocol for library construction began with 1 ug of total RNA.  Since the protocol utilized was based on polyA capture, RNA was visualized on a BIoRad Experion to insure RNA Quality Index values were greater than 8.  For library construction the illumina TruSeq v2 mRNA kit was utilized.  The protocol was followed according to manufacturer’s instructions except the final number of PCR cycles was 12 and not 15.  Following construction, libraries were visualized by Bioanalyzer (Agilent) using the High Sensitivity Chip and quantified for pooling and sequencing using Kapa Biosystems qPCR quantitation kit according to manufacturer’s instructions.

value: 4 months old


title: SMH_g3_2


title: SMH_g3_3


title: 29_S25: Infected 12h replicate 3


title: 4_S4: Infected 24h replicate 3


title: 11_Mabs_B6_BE

description: Biofilm Early_T1


title: 14_Mabs_B8_PL

description: Planktonie Late_t2


title: 13_Mabs_B8_PE

description: Planktonic Early_t1


title: 09_Mabs_B6_PE

description: Planktonic Early_t1


title: SMH_g1_3

value: 3 years old


title: Ctrl_1

description: control ChIP

value: TY1 (In house, TY1-BB2 hybridoma derived)


title: SMH_g2_2

value: 2 years old


title: 12_Mabs_B6_BL

description: Biofilm Late_T2


title: Myb_3

description: Myb ChIP


title: Myb_1

description: Myb ChIP


title: 18_S15: Infected 48h replicate 2


title: Ctrl_2

description: control ChIP


title: SMH_g2_3


title: Ctrl_3

description: control ChIP


title: 2_S2: Infected 4h replicate 3


title: Myb_2

description: Myb ChIP


title: 28_S24: Infected 12h replicate 2


title: 10_Mabs_B6_PL

description: Planktonie Late_t2


title: 07_Mabs_B3_BE

description: Biofilm Early_T1


title: 16_Mabs_B8_BL

description: Biofilm Late_T2


title: SMH_g1_2


title: SMH_g2_1


title: 27_S23: Infected 12h replicate 1


title: SMH_g1_1


title: 08_Mabs_B3_BL

description: Biofilm Late_T2


title: 06_Mabs_B3_PL

description: Planktonie Late_t2


title: 05_Mabs_B3_PE

description: Planktonic Early_t1


title: SMG_g3_1


title: 24_S20: Infected 2h replicate 3


title: SMG_g2_3


title: 23_S19: Infected 2h replicate 2


title: PB-Ctrl-gxx

type: RNA

first: Jinghua

last: Yang

address: 32 North Third Ring Road West, Haidian District, Beijing

institute: Beijing Zhiyun data technology co. LTD

hyb_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

data_processing: Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Hierarchical Clustering and combined analysis were performed using in-house scripts.

source_name: Peripheral Blood, Control,gxx

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions.

value: left ventricle tissue

tag: gender

value: female

value: 31 years


title: 4_S20: Infected 24h replicate 2

value: Infected

value: Macrophage HD-11

value: Houghton


title: SMG_g2_2


title: 6_S22: Infected 2h replicate 1


title: SMG_g3_3


title: Md5-3 input

city: Zhengzhou

first: ZHU Xiaojing

middle: Xiaojing

last: ZHU

state: Henan

address: 15 Longzihu University Park, Zhengdong New District

institute: Henan Agricultural University

description: Md5-3 input

data_processing:
Basecalls performed using CASAVA version 1.8
clean reads of input libraries were aligned to reference genome (Gallus_gallus-5.0,GaHV-2) by STAR software.
circRNAs were identified by DCC software using the STAR alignment results.
clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of LncRNA and circRNA were figured out and chosen by home-made scripts.
GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes, the associated genes of differentially methylated LncRNAs and the source genes of differentially methylated circRNAs separately.
Genome_build: Gallus_gallus-5.0,GaHV-2
Supplementary_files_format_and_content: Number of raw junction read

organism: Gallus gallus

source_name: chicken embryo fibroblast cells

growth_protocol: Specific pathogen-free (SPF) eggs (Boehringer Ingelheim, Beijing, China) were incubated at 37°C for nine days before isolating CEF. Cells were maintained in Dulbecco’s modified essential medium (DMEM) (Solarbio, Beijing, China) containing 5% fetal bovine serum (FBS) (Gibco, CA, USA).

extract_protocol:
RNA was harvested using Trizol reagent. Purified RNA was used for RNA-seq library generation with NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, USA) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The experimental group was inoculated the Md5 strain for 7 days

value: embryo fibroblast cells

tag: treatment

value: inoculated with Md5 strain for 7 days

tag: antibody


title: 203-37D

city: Columbia

first: Sathesh

middle: K

last: Sivasankaran

state: MO

address: Bond Life Sciences Center Suite 106, 1201 Rollins Street

institute: University of Missouri

description: Bacteria grown to mid-log phase in HAN medium at 37 °C

data_processing:
Raw sequence reads were mapped against the Leptospira borgpetersenii serovar Hardjo (JB197 RefSeq ID: chromosome 1: NC_008510.1, chromosome 2: NC_008511.1 and HB203 : chromosome 1: NZ_CP021412.1, chromosome 2: NZ_CP021413.1) using Segemehl with mapping with default mapping parameters.
Number of reads mapped to each genes was calculated using custom Perl script.
Reads were normalized using VST transformation (Log2 normalized read counts) from DESeq2 package
Differential gene expression was calculated using DESeq2 package
Genome_build: JB197 - NC_008510.1 & NC_008511.1 and HB203 - NZ_CP021412.1 & NZ_CP021413.1
Supplementary_files_format_and_content: Tab-delimited text file includes VST transformaed log2 normalized read counts for each samples.

source_name: Bacterial cell

growth_protocol: Both strains were grown in HAN medium until mid-log phase at either 29 or 37 °C.

extract_protocol:
RNeasy Mini Kit (Cat. No. 74104, Qiagen, MD, USA)
Ribo-Zero rRNA removal kit (Cat. No. MRZB12424, Illumina, Inc., San Diego, CA, USA)
Illumina TruSeq stranded total RNA kit (Cat. No. RS-122-2203, Illumina, Inc., San Diego, CA, USA

treatment_protocol: Transcriptomic differences between temperature and strains was observed

value: Bacterial cell

tag: growth stage

value: Test


title: SMG_g1_3

tag: genotype


title: Md5-2 input

description: Md5-2 input

tag: cell type


title: 01_Mabs_B2_PE

description: Planktonic Early_t1

tag: tissue

value: bacterial culture

tag: age

value: 24 hour


title: 10_S26: Infected 24h replicate 1


title: 8_S24: Infected 4h replicate 2


title: PB-Ctrl-lmm

source_name: Peripheral Blood, Control,lmm

value: male

value: 36 years


title: 02_Mabs_B2_PL

description: Planktonie Late_t2

value: 48 hour


title: 03_Mabs_B2_BE

description: Biofilm Early_T1

value: 5 day


title: 04_Mabs_B2_BL

description: Biofilm Late_T2

value: 7 day


title: SMG_g3_2

value: 4 months old


title: Torpor [PN0186_0015]

city: Belfast

first: Gary

last: Hardiman

state: Antrim

address: 19 Chlorine Gardens

department: Institute for Global Food Security

institute: Queen's University Belfast

description:
PN0186_0015
DEG_torpor_group_zebrafish_human_Ids.txt
Htseq_counts_torpor_group.xlsx

data_processing:
Sequence quality was assessed with FastQC to identify over-represented sequences and low quality reads
Low quality reads and over-represented sequences were removed with Cutadapt
The STAR aligner was utilised to align the RNA-Seq reads to the zebrafish genome (GRCz11)
HTSeq was used to determine the number of reads per transcript
DESeq2 was used for determination of differentially expressed genes
Genome_build: zebrafish genome (GRCz11)
Supplementary_files_format_and_content: HTSeq counts, DESeq output

organism: Danio rerio

source_name: Gastrointestinal tract

extract_protocol:
Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit (Qiagen, Hilden, Germany).
To prepare mRNA-Seq libraries the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA, USA) was utilized; 100–200 ng of total input GIT RNA was used in accordance with the manufacturer’s protocol.
High through-put sequencing was performed at the University of North Carolina-Chapel Hill High Throughput Sequencing Facility, Chapel Hill, NC and the Queens University Belfast, Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of ~25 million reads.

treatment_protocol: A melatonin group (28.5- melatonin) received melatonin daily for 10 days at a concentration of 24 µM for 10 days to reduce locomotion and arousal. A reduced temperature group (18.5-Ctrl) received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group (18.5-mel) was established with a 10°C reduction in ambient temperature and the addition of 24 µM melatonin.A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.

tag: radiation (cgy)

tag: temperature (°c)

tag: melatonin (µm)


title: SMG_g2_1

value: 2 years old


title: 203-37B

organism: Leptospira borgpetersenii serovar Hardjo


title: S17_Y_B_AT2_Saline_R5

city: Chicago

first: Alexander

middle: V

last: Misharin

state: Illinois

address: 303 E Superior

institute: Northwestern University

data_processing:
Reads were demultiplexed using bcl2fastq version 2.19.1
Quality of reads was assessed with FastQC and trimmed with Trimmomatic version 0.36
Trimmed reads were aligned to Mus musculus genome (mm10, version 78) with STAR version 2.6.0
Aligned reads were associated with genes and counted with HTSeq count version 0.11.2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited table of gene counts

source_name: Sorted alveolar type 2 cells

extract_protocol:
RNA was harvested following manufactures directions for Arcturus PicoPure RNA isolation kit (Applied Biosystems)
RNA-seq libraries were prepared from 3 ng total RNA using NEBNext RNA Ultra I kit (New England Biolabs, catalog number E7530L) with polyA mRNA isolation module (New England Biolabs, catalog number E7490S) (Samples 1–8). RNA-seq libraries were prepared from 0.35 ng total RNA using SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Samples 9–17).

value: 2 months

value: AT2 cells

value: Vehicle

tag: condition

value: Bleomycin


title: PB-Ctrl-ltx

source_name: Peripheral Blood, Control,ltx

value: left ventricle tissue

value: female

value: 29 years


title: 203-37C

value: Bacterial cell

value: Test


title: PB-PAP-zyh

source_name: Peripheral Blood, PAP, zyh

value: 39 years


title: Torpor [PN0186_0016]

description:
PN0186_0016
Htseq_counts_torpor_group.xlsx


title: PB-PAP-wy

source_name: Peripheral Blood, PAP, wy

value: male

value: 25 years


title: 203-37A


title: PB-Ctrl-wxl

source_name: Peripheral Blood, Control,wxl

value: 49 years


title: Md5-3 IP

description: Md5-3 IP

data_processing:
Library strategy: MeRIP-SEQ
Basecalls performed using CASAVA version 1.8
clean reads of input libraries were aligned to reference genome (Gallus_gallus-5.0,GaHV-2) by STAR software.
circRNAs were identified by DCC software using the STAR alignment results.
clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of LncRNA and circRNA were figured out and chosen by home-made scripts.
GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes, the associated genes of differentially methylated LncRNAs and the source genes of differentially methylated circRNAs separately.
Genome_build: Gallus_gallus-5.0,GaHV-2
Supplementary_files_format_and_content: Number of raw junction read

value: embryo fibroblast cells

value: inoculated with Md5 strain for 7 days


title: SMG_g1_2

value: 3 years old


title: SMG_g1_1


title: PB-Ctrl-ldl

source_name: Peripheral Blood, Control, ldl

value: 21 years


title: PB-PAP-myf

source_name: Peripheral Blood, PAP, myf

value: 27 years


title: S16_Y_B_AT2_Saline_R4

value: 2 months

value: AT2 cells


title: PB-PAP-ljt

source_name: Peripheral Blood, PAP, ljt

value: 34 years


title: SB825_g3_3

value: 4 months old


title: 203-29D

description: Bacteria grown to mid-log phase in HAN medium at 29 °C

value: Control


title: S12_Y_N_AT2_Saline_R4

value: Vehicle

value: Naive


title: SB825_g3_2


title: 203-29C

value: Bacterial cell


title: SB825_g2_2

value: 2 years old


title: 197-37D

value: Test


title: Md5-2 IP

description: Md5-2 IP


title: S10_Y_N_AT2_Saline_R2


title: S15_Y_B_AT2_Saline_R3

value: Bleomycin


title: CEF-3 input

description: CEF-3 input

value: untreated


title: CEF-3 IP

description: CEF-3 IP

value: embryo fibroblast cells


title: CEF-2 IP

description: CEF-2 IP


title: Md5-1 IP

description: Md5-1 IP

value: inoculated with Md5 strain for 7 days


title: S14_Y_B_AT2_Saline_R2


title: SB825_g3_1


title: SB825_g1_2

value: 3 years old


title: 203-29B


title: 2_S18: Infected 4h replicate 1

source_name: Chicken macrophage cell culture

tag: infection status

value: Infected

value: Macrophage HD-11

value: Houghton


title: SB825_g1_1


title: 197-37A


title: PB-PAP-mt

source_name: Peripheral Blood, PAP, mt

value: left ventricle tissue

value: male

value: 45 years


title: S13_Y_B_AT2_Saline_R1

value: 2 months

value: AT2 cells


title: Acs2 Input

city: Wuhan

first: Zhou

last: Jian

address: Wuhan China

institute: AJBK

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using trimmomatic, then mapped to yeast whole genome using bwa v0.12.20.7.15-r1140 with parameters mem -M -k 48 -t 7
picard software was used to remove duplicated reads
macs2 was used to call peak with parameters -f BAMPE -q 0.05 -g 1.3e7 -m 5 50 --keep-dup 1
Genome_build: yeast(GCF_000146045.2_R64)
Supplementary_files_format_and_content: peak file were generated using macs2 callpeak software

organism: Saccharomyces cerevisiae

source_name: budding yeast

growth_protocol: Yeast cells were grown in 200 ml YPD mediacontaining 2% glucose  at 28℃ until OD600 of 0.7–1.0

extract_protocol: Crosslinking was performed by adding 5.6 ml 37% formaldehyde to a final concentration of 1% and quenched by adding 10 ml of 2.5 M glycine.

value: Yeast cells

tag: genotype/variation


title: SB825_g2_3

source_name: Whole colony


title: Mtb_uninfected_cells_1

first: Davide

address: 930 Campus Road

institute: Cornell University

description:
Cite-seq with ADT and HTO - Bystander and Uninfected cells
scRNA-seq
mtb_integrated.csv
mtb_integrated.RDS

data_processing:
scRNA-seq: Raw sequencing reads from each run were processed using the software CellRanger (v.3.0) from 10X for the mRNA libraries and CITE-Seq-Count (v. 1.4.3) (https://hoohm.github.io/CITE-seq-Count/ ) for the ADT and HTO libraries, to generate raw count matrices for both mRNA and proteins.  Downstream analysis of the datasets was performed in Seurat (v. 3.1.4) as previously described.(Stuart et al., 2019)  Briefly, we first filtered out cells with  < 200 unique genes/cell and with very-high mitochondrial content (> 30% mitochondrial reads), then multiplexed samples were demultiplexed using the MULTIseqDemux function in Seurat ((McGinnis et al., 2019)), doublets and empty droplets were identified and removed, and the correct identity assigned to each sample. scRNA-seq datasets for each sample were pre-processed using the regularized negative binomial regression in Seurat (regressing out both the number of counts and percentage of mitochondrial reads) (Hafemeister and Satija, 2019) and analyzed to identify myeloid cell subsets. Myeloid cell subsets from the different samples were then merged to generate an annotated object containing information from all the different datasets. Subsequently, the RNA slot (containing the raw counts) of the merged object was used as an input for Harmony, as previously described (Korsunsky et al., 2019). Briefly, raw counts were log-normalized and the first 3000 highly variable genes identified. The expression of these genes was scaled and centered, PCA was computed on the scaled expression values and data integration with Harmony was performed using both “Batch” and “Infection Status” as covariates for the murine datasets and “Batch” for the human datasets. The aligned Harmony embeddings were then used to perform graph-based cluster detection using PCs (principal components) that were identified as statistically significant by the jackstraw method. (Chung and Storey, 2015) The Louvain algorithm was used for community detection. (Blondel, 2008) We annotated clusters of cell types by reference-based and canonical marker genes analysis, as described in the text. Trajectory and pseudotime analysis was performed in Monocle (v3.0), using the SeuratWrappers package in R (v. 0.2.0) to convert the integrated Seurat object. For unbiased trajectory and pseudotime analysis of the macrophage populations in both murine and human datasets, all cells previously classified as macrophages were assigned to the same partition and trajectory/pseudotime analysis was conducted as previously described.(Qiu et al., 2017)  Pathway enrichment analysis was performed in g:Profiler, using an ordered by fold change list of genes as a query, using the g:SCS method for multiple testing correction and the Reactome database as a data source. Only pathways enriched with FDR <0.05 were considered statistically significative.
Dual RNA-seq: Data analysis for the Dual RNA-seq datasets was performed as previously described. (Pisu et al., 2020a; Pisu et al., 2020b) Briefly, low quality reads and Illumina adapters were removed using FlexBar (v. 3.4) (Roehr et al., 2017) while remaining rRNA reads were removed using Bowtie2 (-sensitive mode) (Langmead and Salzberg, 2012) and a custom GTF file. The filtered fastq files were split using Bowtie2 (–very-sensitive mode) into species-specific files using the two reference genomes, GRCm38.94 for Mus musculus and NCBI assembly GCA_00668235.1 for Mtb Erdman. Hisat2 (v. 2.1.0) (Kim et al., 2015) was then used to align Mtb reads to the M.tuberculosis transcriptome and raw read counts for each sample were obtained using HTSeq. (v. 0.11.0)(Anders et al., 2015) The raw read count matrices obtained in this study (hspx-high and hspx-low) were then combined with the matrices obtained from samples of a previous study (Mtb in AM and Mtb in IM) (Pisu et al., 2020a) to compare bacterial responses belonging to ontogeny vs activation of the host immune cell. Exploratory, visualization and differential gene expression analysis was then carried out in R using DESeq2 and APEGLM for LFC estimation, as previously described (Pisu et al., 2020a). Genes with less than 10 raw counts across all samples were excluded from downstream analysis. The protein-protein interaction network for the Mtb genes was created in Cytoscape using the String app. (v. 1.4.1) . Only high-confidence interactions (co-expression, experiments, neighborhood, co-occurrence with a score > 0.7) relative to query proteins were considered.
ATAC-seq: Paired-end sequencing reads of length 2 x 42 bp were trimmed to remove adapter sequences using cutadapt (ver. 2.5) (Martin, 2011) and quality checked using FASTQC. The reads were aligned to the mm10 (GRCm38) mouse reference genome using bwa (ver. 0.7.17) (Li and Durbin, 2009). Low quality alignments (MAPQ < 30), secondary alignments, unmapped reads and reads with unmapped mate were discarded using samtools. For reads with multiple alignments only five best alignments were retained. PCR duplicates were removed using Picard MarkDuplicates. The remaining clean alignments were analysed for fragment length distribution using the ATACseqQC R/Bioconductor library (Ou et al., 2018). Read alignments to the positive strand were shifted 4 bp downstream and alignments to the negative strand were shifted 5bp upstream to centre the reads on the transposon binding events. Subsequently, peaks were called using macs2 (ver. 2.1.1.20160309) callpeak command with the parameters “-p 0.01 --shift -75 --extsize 150 --nomodel -B --SPMR --keep-dup all --call-summits”. Fold enrichment and p-value tracks normalized to input were produced using macs2 bdgcmp command (options -m FE and -m ppois respectively). Peaks with a q-value < 0.01 were shortlisted. Peaks in the blacklisted regions specified by ENCODE project were removed. For each of the four sample groups, viz. Uninfected AM, Infected AM, Uninfected IM and Infected IM, pooled samples were generated by pooling together reads from all individual replicates of the same group. These pooled samples were also analysed in the same manner as above. Peaks called in the pooled samples were compared against peaks called in the individual samples of the same condition using irreproducible discovery rate (IDR) framework. High quality reproducible peaks were shortlisted based on IDR < 0.05. Subsequently, the IDR peaks from the four groups were merged using “bedtools merge” to generate a final set of peaks (n = 127,513). Counts of reads aligned at each peak interval in each sample was determined using summarizeOverlaps function of the GenomicAlignments R/Bioconductor package (Lawrence et al., 2013) and TMM normalized using edgeR (Robinson et al., 2010).
Genome_build: Mus Musculus: GRCm38.94 / Homo Sapiens: GRCh38.98 / M.tuberculosis: GCA_00668235.1
Supplementary_files_format_and_content: TSV files: contains raw count matrices to import in R for downstream analysis
Supplementary_files_format_and_content: CSV files: contains raw or normalized count data, they were generated from the integrated Seurat objects and contain count data from all datasets
Supplementary_files_format_and_content: RDS file: Integrated Seurat objects that contain all datasets, metadata, dimensional reductions and cluster informations described in the manuscript

source_name: Lung uninfected cells

extract_protocol:
Three weeks post-infection mice were sacrificed, the lungs aseptically removed and placed in PBS containing 5% FBS. To minimize unwanted changes in the gene expression profile of both host and bacteria, samples were kept on ice and immediately processed using a GentleMACS tissue dissociator (Miltenyi Biotec)(Pisu et al., 2020b). The dissociated lung material was then passed through a 70mM cell strainer and red blood cells were lysed with ACK lysis buffer (Lonza). Bystander populations: Single cell suspensions from mice infected with smyc’::mCherry (n=3, 2 batches, total 6 mice) were incubated for 20 minutes in the dark with fluorophore-conjugated antibodies against CD45 (104, BD). Stained samples were washed twice in PBS, resuspended in sorting buffer, passed through a 40M strainer and sorted according to the gating strategy depicted in Figure S1B. Samples were maintained at 4C during sorting and collected directly into Cell Staining Buffer (Biolegend).  Uninfected populations: Single cell suspensions from uninfected healthy mice (n=3, 2 batches, total 6 mice) were incubated for 20 minutes in the dark with fluorophore-conjugated antibodies against CD45 (104, BD). Stained samples were washed twice in PBS, resuspended in sorting buffer, passed through a 40M strainer and sorted according to the gating strategy depicted in Figure S1C. Samples were maintained at 4C during sorting and collected directly into Cell Staining Buffer (Biolegend). Unstained uninfected mice were used to define the sorting gate for the CD45 signal.
Sorted murine populations were stained with HTO and ADT antibodies (Biolegend) following published protocols (Stoeckius et al., 2017), with slight modifications. Briefly, sorted cells were spun down at 500g for 5’, resuspended in 50mL of Cell Staining buffer containing 0.25mg of TruStain FcX PLUS (anti-mouse CD16/32 blocking reagent) (Biolegend) and incubated for 10’ at 4oC. 50mL of an ADT + HTO antibody cocktail mix was then added to the samples and incubated for another 30’ at 4C. After incubation, samples were washed 2X in cell staining buffer and differentially tagged samples (Hspx-high/Hspx-low and Bystander/Uninfected) mixed together and resuspended in DPBS 1X. Ice-cold methanol was then added drop-by-drop to a final concentration of 90% (V/V). Fixed samples were stored at -20oC O/N. After fixation, samples were taken out of the BSL3 facility, equilibrated on ice for 15’, washed twice with Rehydration Buffer (1X DPBS containing 1.0 % BSA (Thermo-Fisher) and 0.5U/μl RNAse Inhibitor (Sigma)) and the amount of recovered cells quantified before loading into the 10X chip. For the mRNA library preparation, we followed the commercially available 10X protocol (CG000206 Rev D), with a slight modification in Step 2.2 and the addition of 1uL of ADT and HTO additive primers (0.2uM stock) as previously described. (Stoeckius et al., 2017) For both murine and human samples, HTO and ADT libraries were generated following Biolegend commercially available protocols.

value: lung

tag: timepoint

value: 3 weeks

tag: disease state

value: Uninfected

tag: pathogen


title: CEF-1 input

description: CEF-1 input

source_name: chicken embryo fibroblast cells


title: S11_Y_N_AT2_Saline_R3

tag: strain

value: Vehicle

value: Naive


title: Md5-1 input

description: Md5-1 input

value: embryo fibroblast cells

tag: treatment


title: SB825_g2_1

value: 2 years old


title: CEF-2 input

description: CEF-2 input

value: untreated

tag: antibody


title: Mtb infected cells_1

description:
Cite-seq with ADT and HTO - Mtb infected cells
scRNA-seq
mtb_integrated.csv
mtb_integrated.RDS

source_name: Lung infected cells

extract_protocol:
Three weeks post-infection mice were sacrificed, the lungs aseptically removed and placed in PBS containing 5% FBS. To minimize unwanted changes in the gene expression profile of both host and bacteria, samples were kept on ice and immediately processed using a GentleMACS tissue dissociator (Miltenyi Biotec)(Pisu et al., 2020b). The dissociated lung material was then passed through a 70mM cell strainer and red blood cells were lysed with ACK lysis buffer (Lonza). Single-cell suspensions from infected mice (n=5, 3 batches, total 15 mice) were washed in PBS+5%FBS, resuspended in sorting buffer (PBS, 5% FBS, 5mM EDTA, 25mM HEPES), passed through a 40M cell strainer and sorted according to the gating strategy depicted in Figure S1A. Samples were maintained at 4C during sorting and collected directly into Cell Staining Buffer (Biolegend). Mice infected with either smyc’::mCherry or hsp60’::GFP were used as a control to define the sorting gates for the hspx’::GFP/smyc’::mCherry infected cells.
Sorted murine populations were stained with HTO and ADT antibodies (Biolegend) following published protocols (Stoeckius et al., 2017), with slight modifications. Briefly, sorted cells were spun down at 500g for 5’, resuspended in 50mL of Cell Staining buffer containing 0.25mg of TruStain FcX PLUS (anti-mouse CD16/32 blocking reagent) (Biolegend) and incubated for 10’ at 4oC. 50mL of an ADT + HTO antibody cocktail mix was then added to the samples and incubated for another 30’ at 4C. After incubation, samples were washed 2X in cell staining buffer and differentially tagged samples (Hspx-high/Hspx-low and Bystander/Uninfected) mixed together and resuspended in DPBS 1X. Ice-cold methanol was then added drop-by-drop to a final concentration of 90% (V/V). Fixed samples were stored at -20oC O/N. After fixation, samples were taken out of the BSL3 facility, equilibrated on ice for 15’, washed twice with Rehydration Buffer (1X DPBS containing 1.0 % BSA (Thermo-Fisher) and 0.5U/μl RNAse Inhibitor (Sigma)) and the amount of recovered cells quantified before loading into the 10X chip. For the mRNA library preparation, we followed the commercially available 10X protocol (CG000206 Rev D), with a slight modification in Step 2.2 and the addition of 1uL of ADT and HTO additive primers (0.2uM stock) as previously described. (Stoeckius et al., 2017) For both murine and human samples, HTO and ADT libraries were generated following Biolegend commercially available protocols.

value: Infected


title: SB825_g1_3

value: 3 years old


title: 197-37C

source_name: Bacterial cell

value: Bacterial cell

tag: growth stage

value: Test


title: NK_rep2

status: Public on Apr 27 2021

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

data_processing:
BCL2FASTQ Conversion Software 1.8.4 in the CASAVA 1.8.2 pipeline used for basecalling.
The sequence reads were mapped to hg19 reference genome, downloaded on December 10, 2012, using TopHat v2.0.8b, and quantified using RPKMforGenes.
RUV were conducted for normalization. expression matrix was described as TPM counts.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values.

source_name: NK

growth_protocol: iPSCs were cocultured with 10T1/2 to generate HPCs for 7 days in low O2 condition (5%) then for 7 days in normal condition in Basal Eagle's medium supplemented with 10% FBS, 1% PSG, 20ng/ml SCF and 20ng/ml Flt3L. Then HSCs were cocultured with OP9-DL1 to generate DP cells for 21 days in aMEM supplemented with 15% FBS, 1% PSG, 50 mg/ml ascorbic acid 2-phosphate, 1 ng/ml IL-7 and 10 ng/ml Flt3L. Lastly to differentiate from DP to CD8SP, DP cells were cultured for 2 days on OP9-DL1 in the presence of 1 g/ml anti-CD3 antibody, 10 ng/ml IL-7, 10 ng/ml Flt3L, 15% FBS, 1% PSG, ITS and ascorbic acid 2-phosphate, then the antibody was washed away, and the cells were transferred to a Retronectin-coated culture dish and cultured for 5 days in the presence of 10 ng/ml IL-7, 10 ng/ml Flt3L, 20 ng/ml IL-21, 15% FBS, 1% PSG, ITS and ascorbic acid 2-phosphate.

extract_protocol:
Cells were directly lyzed with lysis buffer of SMARTer Ultra Low kit.
cDNA was synthesized using a SMARTer Ultra Low Input RNA and sequenced with an Illumina Sequencing-HV kit (Clontech, Mountain View, CA, USA), after which the Illumina library was prepared using a Low Input Library Prep kit (Clontech).

treatment_protocol: CD8ab+CD5+NKp44- sorting was conducted by FACSAria II after generation of CD8ab iPSC-CTLs

value: Natural killer cells


title: Mtb infected cells_2

last: Pisu


title: TEMRA_rep3

source_name: TEMRA

value: CCR7-CD45RA+ effector memory RA T cells


title: 203-29A

value: Control


title: S09_Y_N_AT2_Saline_R1

source_name: Sorted alveolar type 2 cells

value: 2 months

value: AT2 cells


title: Mtb_uninfected_cells_2

value: lung


title: CEF-1 IP

description: CEF-1 IP


title: 197-29D


title: 197-37B


title: TEM_rep2

source_name: TEM

value: CCR7-CD45RA- effector memory T cells


title: TEM_rep1


title: Mtb infected cells_3

value: 3 weeks


title: 197-29C


title: TCM_rep1

source_name: TCM

value: CCR7+CD45RA- central memory T cells


title: 197-29B


title: TSCM_rep2

source_name: TSCM

value: CCR7+CD45RA+CD95+ memory stem T cells


title: Untagged Input

value: Yeast cells

value: Untagged


title: 197-29A


title: NK_rep3


title: Acs2 ChIP-seq

value: FLAG M2(F1804-1MG, Sigma)


title: Untagged ChIP-seq


title: TN_rep1

source_name: TN

value: CCR7+CD45RA+ naive T cells


title: TN_rep3


title: TEMRA_rep2


title: TEMRA_rep1


title: TEM_rep3


title: TCM_rep3


title: TCM_rep2


title: NK_rep1


title: TSCM_rep3


title: TSCM_rep1


title: TN_rep2


title: iPSC-CTL_rep1

source_name: iPSC-CTL

value: iPSC-derived cytotoxic T lymphocyte


title: iPSC-CTL_rep2