title: Medicago truncatula roots' nuclei 24h after exposure to Ensifer meliloti, experimental replicate 1

city: Gainesville

first: Matias

last: Kirst

address: 367 Newins-Ziegler Hall, PO Box 110410

institute: University of Florida

data_processing:
Feature-Barcode Matrices generation: The fastq files were processed using Cell Ranger (10x genomics), version 4.0.0, generating the feature-barcode matrices that can be used as input for downstream analysis.
Genome_build: Medicago truncatula genome, version 5.0, was used as reference. The mentioned genome is available at https://medicago.toulouse.inra.fr/MtrunA17r5.0-ANR/
Supplementary_files_format_and_content: All processed files are feature-barcode matrices, as produced by Cell Ranger (10X genomics). https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices.

organism: Medicago truncatula

source_name: M. truncatula roots' nuclei 24h after exposure to E.meliloti

growth_protocol: Medicago truncatula Jemalong A17 seeds were scarified for 8 min in sulfuric acid and sterilized for 4 min in bleach. After washing with sterilized water, seeds were sown on 1% agar plates with 1 uM of GA3 and stored for 3 days at 4°C before incubating overnight at 24°C in the dark. Germinated seedlings were transferred to square plates containing filter paper-lined modified Fahraeus medium (https://doi.org/10.1105/tpc.12.9.1647) or buffer nodulation medium (BNM) (DOI: 10.1126/science.10744524) supplemented with 0.1 uM aminoethoxyvinylglycine (AVG; Sigma-Aldrich Company Ltd, Darmstadt, Germany) and grown vertically in chambers at 24°C under long-day conditions (16 h light at 150 μmol m-2 s-1 light intensity/8 h dark).

extract_protocol:
After 24 hours of E. meliloti treatment, a 0.5-0.7-cm long root portions around the drop-inoculated spot were cut from 150 2-day-old M. truncatula seedlings. To perform nuclei isolation, root portions were placed on precooled glass plate on the top of an aluminum heating/cooling block kept on ice with 200 uL of NIB1 1× supplemented with 0.5 U/μL Protector RNase Inhibitor. Once all root segments were collected, they were chopped with a razor blade for 2 min. This step was repeated twice with a 30 sec interval in between. Then, chopped mixture was transferred to a 50 mL Falcon tube and nuclei were isolated. After the last wash step, the pellet was gently resuspended in a final volume of 750 μL of NIB2 1× + 0.2 U/μL Protector RNase Inhibitor using a Rainin 1 mL wide-bore tip and transferred to a 5 mL sterile tube compatible with the cell sorter. Nuclei were stained with 5 μg/ml DAPI for 5 min at room temperature and sorted using a BD FACSAria™ IIU/III upgraded cell sorter.
20k nuclei were used to generate each snRNA-seq library following the 10X Genomics Chromium Single Cell v3.1 protocol. The cDNA reaction was prepared as described previously. Two snRNA-seq libraries from two independent replicated experiments were generated.

treatment_protocol: E. meliloti strain 2011 was grown in nodulation medium supplemented with 3 uM luteolin (Sigma-Aldrich Company Ltd, Darmstadt, Germany) and diluted to a final concentration of 0.02 OD 600 nm using modified Fahraeus medium. After 1 day of growth in BNM, the roots susceptibility zone of 150 seedlings was identified and their location marked by puncturing the filter paper . We used a Leica GZ6 stereo microscope to determine the susceptibility zone accurately, which consists of the region where root hairs are emerging but are not fully elongated. A 1 uL drop of E. meliloti suspension was placed onto the marked spot of the susceptibility zone. This experiment was performed twice to generate two experimental replicates.

value: Jemalong A17

tag: treatment/time point

value: 24h after exposure to Ensifer meliloti

value: roots


title: Human Subject SEN_322 CHS DX - Control

status: Public on Aug 01 2025

type: SRA

city: Washington, DC

first: Timothy

last: McCaffrey

state: District of Columbia

address: 2300 I Street, NW, Ross Hall #203

country: USA

institute: The George Washington University Medical Center

description: Library name: SEN 322

library_source: transcriptomic

data_processing:
Low quality reads were removed with Trimmomatic
Sequence quality was measured using FastQC
Alignment was performed using HISAT2
Transcript counts were obtained with FeatureCount
Differential expression analysis was performed with DESeq2.
Assembly: HG38
Supplementary files format and content: csv File Containing Differential Expression Data
Supplementary files format and content: Tabular files with individual counts

molecule: total RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
Whole blood (3 ml) was collected into Tempus Blood RNA Tubes according to the manufacturer’s instructions and then frozen at –80°C.  High-quality mRNA was isolated from whole blood using the Invitrogen Tempus Spin RNA Isolation kit with an on-column DNase treatment to remove any contaminating genomic DNA. Final elution of RNA was performed using DEPC-treated water at 70°C, yielding RNA that was stored at –80°C until further use.
Purified RNA was quantified using Agilent TapeStation analysis. A standardized amount of RNA from each sample was submitted to the GW Genomics Core Facility for sequencing, employing the Illumina Stranded Total RNA Preparation and Ligation with Ribo-Zero Plus, followed by a NextSeq 2000 P1 XLEAP-SBS 300 Cycle sequencing run.

tag: tissue

value: Blood


title: Human Subject SEN_323 CHS DX - Control

description: Library name: SEN 323


title: Human Subject SEN_324 CHS DX - Control

description: Library name: SEN 324


title: Human Subject SEN_321 CHS DX - Control

description: Library name: SEN 321


title: Medicago truncatula roots' nuclei 24h after exposure to Ensifer meliloti, experimental replicate 2

molecule: polyA RNA

tag: genotype


title: Cyp2b-null female gastrocnemius, 1 mg/kg/day PFOS treatment for 21 days via oral gavage rep 4

city: Clemson

first: William

last: Baldwin

state: SC

address: 132 Long Hall

institute: Clemson University

description: Library name: fnul_130_1

data_processing:
PE150 strategy by Novogene. HISAT2 was used to map clean reads.
Assembly: GRCm39
Supplementary files format and content: Excel file containing raw counts performed by Novogene named "gene_count_all.xls"

organism: Mus musculus

source_name: gastrocnemius muscle

extract_protocol:
RNA extractions were performed on approximately 15 mg of liver tissue previously stored at -80C. RNA was extracted with TRIzol (Life Technology, Carlsbad, CA USA) and chloroform. Quality was checked via Nanodrop
Library construction was performed by Novogene (Sacramento, CA USA) using messenger RNA purified from total RNA. Quality was checked with Qubit (Thermo Fisher Scientific, Walkham, MA USA).

value: gastrocnemius muscle


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 105, 32778

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

description: Library name: G185_O06_ABL2_A1_32778_D105

data_processing:
Trimgalorev0.6.4 used to remove low quality reads and bases
Filtered out globin and rRNA reads using bowtie2v2.1.0
Aligned reads with STARv2.7.3
quantified read counts with  htseqv0.11.2
Assembly: Rhesus macaques version 10 Ensembl annoation v98
Supplementary files format and content: ount matrix

organism: Macaca mulatta

source_name: Whole blood

extract_protocol:
Isolation of RNA from Whole Blood Using the RNAdvance Blood Kit – for NHP samples
mRNA Library Prep for RNA from Whole Blood using KAPA HyperPrep Reagents

treatment_protocol: A prime and boost of one of the 4 modified RhCMV/SIV vectors were given to Rhesus macaques

value: Whole blood

tag: treatment

tag: time

value: day 105

tag: animal id

tag: Sex

value: male

tag: dose

tag: treatment outcome

value: notprotected


title: Human Subject CHS_585 CHS DX +

description: Library name: CHS 585


title: Cyp2b-null female gastrocnemius, 1 mg/kg/day PFOS treatment for 21 days via oral gavage rep 3

description: Library name: fnul_123_1


title: Human Subject SEN_320 CHS DX - Control

description: Library name: SEN 320


title: Human Subject CHS_583 CHS DX +

description: Library name: CHS 583


title: Human Subject CHS_584 CHS DX +

description: Library name: CHS 584


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 105, 32321

description: Library name: G183_O06_ABL2_A1_32321_D105


title: Cyp2b-null female gastrocnemius, 1 mg/kg/day PFOS treatment for 21 days via oral gavage rep 1

description: Library name: fnul_116_1


title: Human Subject CHS_564 CHS DX +

description: Library name: CHS 564


title: Human Subject CHS_549 CHS DX +

description: Library name: CHS 549


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 105, 32019

description: Library name: G181_O06_ABL2_A1_32019_D105


title: Cyp2b-null female gastrocnemius, 0 mg/kg/day PFOS treatment for 21 days via oral gavage rep 3

description: Library name: fnul_113_0


title: 10x Multiome with D0, D2, D4 and D7 of iPSC to HPC differentiation in one lane. GEX

city: Stanford

first: Jesse

last: Engreitz

state: CA

address: 450 Serra Mall

department: Genetics

institute: Stanford University

description:
Library name: WTC11_HPC_multiome_GEX
10x Genomics Multiome
Unique processed file id: 2

library_source: transcriptomic single cell

data_processing:
FASTQs were analyzed with 10x cloud analysis web browser version using cellranger-arc-2.0.2
Assembly: human hg38
Supplementary files format and content: filtered feature bc matrix file (.tar.gz format) that is output directly from cellranger. Contains matrix, barcodes and features files for ATAC and GEX

growth_protocol: We seeded human iPS cells (WTC11) harboring dCas9-KRAB (Metzl-Raz et al., Stem Cell Res., 2022) in 6-well plates coated with 1:100 LDEV-Free Reduced Growth Factor Basement Membrane Matrix (Thermo Fisher Scientific). The culture medium used was StemFlex Medium supplemented with 10% StemFlex supplement (SF complete media, Thermo Fisher Scientific), 2   l of Normocin per ml of media (1:500 final, Invivogen), and 0.4   l of 10 mM Rock Inhibitor (Y-27632 Dihydrochloride, STEMCELL Technologies). After 24 hours of seeding, we continued to maintain the cells with SF complete media without Rock Inhibitor and passaged them with 1 ml of accutase (STEMCELL Technologies) as necessary, aiming to maintain below 80-90% confluence and prevent stacked cell growth.

extract_protocol:
hiPSC (WTC11) with the dCas9-KRAB was differentiated into hepatic progenitor cells over 7 days of differentiation. We seeded 550,000 cells per well in 6-well plates in StemFlex media, Normocin with Rock Inhibitor and 1   g/ml Doxycycline. Next day, we changed the media with fresh StemFlex, Normocin and Doxycycline. The following day, we collected the cells from some wells and froze them in CryoStor media (STEMCELL Technologies); these were denoted as Day 0 (D0) cells. For the remaining wells, we changed the media with fresh RPMI (Thermo), B27 supplement (Thermo), 4 uM CHIR99021 (Reprocell), Normocin and Doxycycline. Next day, we changed the media with fresh RPMI, B27, Normocin and Doxycycline. The following day, we collected the cells from some wells and froze them in CryoStor media; these were denoted as Day 2 (D2) cells. For the remaining wells, we changed the media with fresh Hepatic Differentiation Media consisting of Knockout DMEM (Thermo), 20% knockout serum replacement (Thermo), 2 mM GlutaMax (Thermo), 100 uM 2-Mercaptoethanol (Sigma), 1x MEM Non-essential amino acids (Thermo), 1% DMSO (Sigma), along with Normocin and Doxycycline. The cells were incubated for 2 days after which we collected the cells from some of the wells and froze them in CryoStor media; these were denoted as Day 4 (D4) cells. For the remaining wells, we changed the media with fresh Hepatic Differentiation Media with Normocin and Doxycycline. The cells were incubated for 2 days after which the media was again changed with fresh Hepatic Differentiation Media with Normocin and Doxycycline. The following day, we collected the cells from all the wells and froze them in CryoStor media; these were denoted as Day 7 (D7) cells.
For the multiome experiment, we thawed one vial each of D0, D2, D4 and D7 cells and centrifuged at 300 x g for 5 min, then resuspended in 1 ml of chilled PBS with 0.04% BSA. We washed the cells again in PBS with 0.04% BSA and proceeded with nuclei isolation from 0.5-1 million cells. We centrifuged the cells at 500 x g for 5 min at 4  C, removed the supernatant and resuspended in 100 ul of chilled 1x lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP40, 0.01% Digitonin, 1% BSA, 1 mM DTT, 1U/ul Sigma Protector RNase Inhibitor). We incubated the cells for 4 mins on ice and then added 1 ml of chilled wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA, 1 mM DTT, 0.2U/ul Thermo RNaseOUT, 0.2U/ul Takara Recombinant RNase Inhibitor). We centrifuged the nuclei at 500 x g for 5 min at 4  C, removed the supernatant and resuspended in 1 ml of chilled wash buffer. After counting we combined nuclei for the D0-D7 samples, centrifuged at 500 x g for 5 min at 4  C, resuspended in diluted nuclei buffer (1x Nuclei buffer, 1U/ul Sigma Protector RNase Inhibitor, 1 mM DTT), and adjusted the concentration to ~7300 nuclei/ul. We proceeded with transposition and library preparation using the 10x Genomics Multiome kit (PN-1000284), loading the sample onto one well of the multiome chip for GEM generation. ATAC and gene expression (GEX) libraries were prepared according to the 10x Genomics protocol.

tag: cell line


title: Cyp2b-null female gastrocnemius, 1 mg/kg/day PFOS treatment for 21 days via oral gavage rep 2

description: Library name: fnul_117_1


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 105, 32485

description: Library name: G184_O06_ABL2_A1_32485_D105


title: Human Subject CHS_185 CHS DX +

description: Library name: CHS 185


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 101, 35914

description: Library name: G180_O06_ABL2_A3_35914_D101

value: day 101


title: Cyp2b-null female gastrocnemius, 0 mg/kg/day PFOS treatment for 21 days via oral gavage rep 2

description: Library name: fnul_108_0


title: Cyp2b-null female gastrocnemius, 0 mg/kg/day PFOS treatment for 21 days via oral gavage rep 1

description: Library name: fnul_100_0


title: Translatome, ALDH5A1 domainI-MDH2, rep2

city: Pasadena

first: Zikun

last: Zhu

address: 1200 E California Blvd

institute: California Institute of Technology

description:
Library name: Sample 7
Adaptor trimmed (3' adaptor sequence: CGTAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)

data_processing:
3’ adaptor sequences were trimmed from sequencing reads with Cutadapt v4.1 using the following command: cutadapt --cores=0 -q20 -m24 -M42 --discard-untrimmed -O6 --no-indels -a adaptor_sequence -o outfile.fastq.gz infile.fastq.gz 1> Cutadapt_report.txt
Unique molecular identifiers (UMIs, two random 5' nucleotides and five random 3' nucleotides) were trimmed from each read using a Julia script (Script1) from (M. Bertolini, et. al., Science, 2021). This generates an output fastq file containing the 7-nucelotide UMI information in the read name.
The UMI-trimmed reads were mapped to the human ribosomal RNA sequences with Bowtie2 v2.4.5 using the following command: bowtie2 -p 32 -t -x rRNA_index -q infile.fastq.gz -p 16 --un outfile.fastq.gz -S /dev/null > Bowtie2.report.txt
Reads that did not align to ribosomal RNA sequences were mapped to human reference genome (GRCh38p13 downloaded from NCBI) with STAR 2.7.10a using the following command: STAR --runThreadN 32 --genomeDir indexed_genome --readFilesIn infile.fastq.gz --outFilterMultimapNmax 1 --outFilterType BySJout --alignIntronMin 5 --outFileNamePrefix Prefix --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All XS --quantMode GeneCounts --twopassMode Basic
For each gene, the transcript with the longest coding sequence was selected, and ribosome density was assigned to the p-site of each read using a Julia script (Script2) from (M. Bertolini, et. al., Science, 2021).
Assembly: GRCh38p13
Supplementary files format and content: The files are in HDF5 format containing one data set per gene. Each data set consists of a 2-row matrix, with the 1-based nucleotide position within the CDS and the detected p-site reads at this position. The data set attributes contain additional information including gene and protein names, transcript isoform used for position assignment, CDS length, chromosome and strand location of the gene.
Library strategy: Ribo-seq

growth_protocol: HEK293-T cells were cultured in high glucose DMEM media supplemented with GlutaMAX™ and pyruvate (Gibco) + 10% fetal bovine serum (Gibco). Cells were grown at 37 °C and passaged regularly using Trypsin-EDTA for dissociation.

extract_protocol:
RNA was extracted using the Direct-zol kit (Zymo) according to manufacturer’s instructions.
Ribosome profiling libraries were prepared as described in (Z. Zhu, S. Wang, S. Shan, Nat. Commun., 2022) with an additional rRNA depletion step. rRNA depletion was performed on the linker-ligated RNA footprints using the riboPOOL Ribo-Seq (human) kit (Galen) according to the manufacturer’s instructions.

tag: cell type

value: Human embroynic kidney

value: TOM22-Twinstrep, ALDH5A1 domainI-MDH2 knockin


title: TOM interactome, ALDH5A1 domainI-MDH2, rep2

description:
Library name: Sample 8
Adaptor trimmed (3' adaptor sequence: CTAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)


title: TOM interactome, ALDH5A1 domainI-MDH2, rep1

description:
Library name: Sample 6
3' adaptor sequence: CTAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 101, 35910

description: Library name: G178_O06_ABL2_A3_35910_D101

value: protected


title: hCYP2B6-Tg female gastrocnemius, 10 mg/kg/day PFOS treatment for 21 days via oral gavage rep 4

description: Library name: f2B6_152_10


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 101, 35913

description: Library name: G179_O06_ABL2_A3_35913_D101


title: Human Subject SEN_185 CHS DX - Control

description: Library name: SEN 319


title: Human Subject SEN_314 CHS DX - Control

description: Library name: SEN 314


title: TOM interactome, DLAT-dmain reordered, rep1

description:
Library name: Sample 2
Adaptor trimmed (3' adaptor sequence: CGTAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)

value: TOM22-Twinstrep, DLAT-domain reordered knockin


title: hCYP2B6-Tg female gastrocnemius, 10 mg/kg/day PFOS treatment for 21 days via oral gavage rep 3

description: Library name: f2B6_150_10


title: Translatome, ALDH5A1 domainI-MDH2, rep1

description:
Library name: Sample 5
3' adaptor sequence: CGTAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 101, 35886

description: Library name: G176_O06_ABL2_A3_35886_D101


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 101, 35889

description: Library name: G177_O06_ABL2_A3_35889_D101


title: hCYP2B6-Tg female gastrocnemius, 10 mg/kg/day PFOS treatment for 21 days via oral gavage rep 2

description: Library name: f2B6_144_10


title: TOM interactome, DLAT-dmain reordered, rep2

description:
Library name: Sample 4
Adaptor trimmed (3' adaptor sequence: CTAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)


title: Translatome, DLAT-dmain reordered, rep1

description:
Library name: Sample 1
Adaptor trimmed (3' adaptor sequence: CGTAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)


title: Human Subject CHS_569 CHS DX +

description: Library name: CHS 569


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 105, 32215

description: Library name: G182_O06_ABL2_A1_32215_D105


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 101, 35885

description: Library name: G175_O06_ABL2_A3_35885_D101


title: MCF7_MED1KR_MED17_Rep_input

city: New York

first: Douglas

last: Barrows

state: NY

address: 1230 York Ave

institute: Rockefeller University

description: Library name: RL_ChIP_0515_4

library_source: genomic

data_processing:
ChIP-seq reads were aligned using Rsubread’s align method and predicted fragment lengths were calculated by the ChIPQC R Bioconductor package. Normalized, fragment extended signal bigWigs were created using the rtracklayer R Bioconductor package. Peak calls were made using the SEACR software. The 'stringent' setting of SEACR was used and the top 1%  of peaks based on total signal within peaks were kept for further analysis.
Assembly: hg38
Supplementary files format and content: bigwig files
Supplementary files format and content: narrowPeak files from MACS2

molecule: genomic DNA

source_name: MCF7 MED1 6KR

extract_protocol:
Post-confluent cells were fixed with 1% formaldehyde for 10 min, followed by quenching with 125mM glycine and washed with cold TBS (20mM Tris-HCl, 150mM NaCl, pH 7.4) twice. Cells were lysed in cell lysis buffer (10mM Tris-HCl, 10mM NaCl, 0.5% NP-40, pH7.5) and then incubated on ice for 10 mins. Lysates spinned down and resuspended in 500 μl MNase digestion buffer (20mM Tris-HCl, 15mM NaCl, 60mM KCl, 1mM CaCl2, pH 7.5) with MNase (New England, M0247S, 0.25U/1000 cells). After 20 minutes of incubation at 37°C with continuous mixing, digestion was stopped by addition of 500 μl of 2X STOP/ChIP buffer (100mM Tris-HCl, 20mM EDTA, 200mM NaCl, 2% Triton X-100, 0.2% sodium deoxycholate, pH8.1). Samples were sonicated for 7 cycles (30 secs on/30 secs off) with 40% amplitude (Branson Digital Sonifier) and then centrifuged at 12,000rpm for 15min at 4°C to remove insoluble debris. Apart from input samples (1% volume for each ChIP reaction) kept for reverse-crosslinking, lysates were incubated with antibodies (antibody information: see table attached) at 4°C overnight. Antibody-bound complexes were then captured by incubation with Protein A sepharose CL-4B beads (Amersham) for rabbit antibodies or Protein G sepharose 4B beads (Invitrogen) for mouse antibodies (both 20μl per 1mL lysate) for 4 hr at 4 °C. The beads were washed sequentially with STOP/ChIP buffer (50mM Tris-HCl, 10mM EDTA, 100mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, pH8.1), high salt buffer (50mM Tris-HCl, 10mM EDTA, 500mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, pH8.1), LiCl2 buffer (10mM Tris-HCl, 0.25M LiCl2, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA, pH8.0), and TE buffer (50mM Tris-HCl, 10mM EDTA, pH 8.0) (twice). Bound DNA was eluted and reverse-crosslinked at 65°C overnight in ChIP elution buffer (10mM Tris-HCl, 150mM NaCl, 10mM EDTA, 5mM DTT, 1% SDS, pH 8.0). After treatment with RNase A (0.2mg/ml, 37°C, 1h) and proteinase K (2mg/ml, 37°C, 2h), DNA used for sequencing was purified using a MiniElute PCR purification kit (Qiagen), and DNA used for qPCR was purified using a QIAquick PCR purification kit (Qiagen). DNA quality was assessed using an Agilent Bioanalyzer, and quantified using a Qubit Fluorometer (Invitrogen).
ChIP-seq libraries were generated using DNA SMART ChIP-seq kits (Takara Bio) according to the manufacturer's instructions. After size selection (for 250-600bp) by AMPure XP beads (Beckman Coulter), the library was quality was evaluated using the Bioanalyzer and sequenced on Illumina NovaSeq SP (100bp two ends) and Illumina NextSeq High (75 bp single end).

value: MCF7 MED1 6KR

value: breast cancer cell line

value: ectopic 6KR MED1

tag: chip antibody


title: hCYP2B6-Tg female gastrocnemius, 10 mg/kg/day PFOS treatment for 21 days via oral gavage rep 1

description: Library name: f2B6_142_10


title: MCF7_MED1KR_MED17_Rep

description: Library name: RL_ChIP_0515_3

value: anti MED17 (Aviva OAGA04959)


title: MCF7_MED1WT_MED17_Rep

description: Library name: RL_ChIP_0515_1

source_name: MCF7 MED1 WT

value: MCF7 MED1 WT

value: ectopic WT MED1


title: Cyp2b-null female gastrocnemius, 0 mg/kg/day PFOS treatment for 21 days via oral gavage rep 4

description: Library name: fnul_114_0


title: MCF7_MED1WT_MED17_Rep_input

description: Library name: RL_ChIP_0515_2


title: 6KR-H2O2-3

description:
Library name: RNA_KR_12
rep 3

data_processing:
Combined Drosophila biarmipes and hg38 fasta and GTF files were derived from the BSgenome.Hsapiens.UCSC.hg38 and TxDb.Hsapiens.UCSC.hg38.knownGene R Bioconductor packages paired with the files from the RU_DBia_V1.1 genome assembly (RefSeq assembly number GCF_025231255.1). Fastq files were aligned to the combined reference with STAR (v2.5.2b) using default settings except the ‘outSAMmultNmax’ argument was set to 1. The reads that preferentially aligned to the hg38 chromosomes were extracted from the BAM file using the ‘view’ function from Samtools (v1.10), and gene level counts were obtained using the ‘summarizeOverlaps’ function from the GenomicAlignments R Bioconductor package (v1.28.0). The Drosophila biarmipes genes were used to estimate size factors during differential expression with the DESeq2 R Bioconductor package (v1.32.0).
Assembly: hg38 with Drosophila biarmipes spike in
Supplementary files format and content: raw counts from DESeq2

source_name: MCF7 6KR MED1

extract_protocol:
Cells were harvested, washed with PBS, and flash frozen in liquid nitrogen. RNA was isolated using QIAGEN RNeasy kit.
Libraries were generated using mRNA TruSeq stranded 350bp

value: MCF7 6KR MED1

value: ectopic 6KR MED1 (with Drosophila melanogaster spike-in)

value: H2O2 (0.5mM) 6 hours


title: hCYP2B6-Tg female gastrocnemius, 1 mg/kg/day PFOS treatment for 21 days via oral gavage rep 4

description: Library name: f2B6_140_1

value: gastrocnemius muscle


title: 6KR-H2O2-2

description:
Library name: RNA_KR_11
rep 2


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 101, 35822

description: Library name: G174_O06_ABL2_A3_35822_D101

value: Whole blood

value: male


title: Translatome, DLAT-dmain reordered, rep2

description:
Library name: Sample 3
Adaptor trimmed (3' adaptor sequence: CTAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)


title: hCYP2B6-Tg female gastrocnemius, 1 mg/kg/day PFOS treatment for 21 days via oral gavage rep 3

description: Library name: f2B6_131_1


title: 6KR-H2O2-1

description:
Library name: RNA_KR_10
rep 1


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 101, 33878

description: Library name: G173_O06_ABL2_A3_33878_D101

value: day 101


title: WT (KR ctrl)-H2O2-3

description:
Library name: RNA_KR_9
rep 3

source_name: MCF7 WT MED1

value: MCF7 WT MED1

value: ectopic WT MED1 (with Drosophila melanogaster spike-in)


title: hCYP2B6-Tg female gastrocnemius, 1 mg/kg/day PFOS treatment for 21 days via oral gavage rep 2

description: Library name: f2B6_128_1


title: 6KR-ctrl-3

description:
Library name: RNA_KR_6
rep 3

value: control


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 101, 33877

description: Library name: G172_O06_ABL2_A3_33877_D101

value: protected


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 101, 33700

description: Library name: G171_O06_ABL2_A3_33700_D101


title: WT (KR ctrl)-H2O2-2

description:
Library name: RNA_KR_8
rep 2


title: hCYP2B6-Tg female gastrocnemius, 1 mg/kg/day PFOS treatment for 21 days via oral gavage rep 1

description: Library name: f2B6_125_1


title: WT (KR ctrl)-H2O2-1

description:
Library name: RNA_KR_7
rep 1


title: 6KR-ctrl-2

description:
Library name: RNA_KR_5
rep 2


title: hCYP2B6-Tg female gastrocnemius, 0 mg/kg/day PFOS treatment for 21 days via oral gavage rep 4

description: Library name: f2B6_119_0


title: 6KR-ctrl-1

description:
Library name: RNA_KR_4
rep 1


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 101, 32707

description: Library name: G170_O06_ABL2_A3_32707_D101


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 101, 32689

description: Library name: G169_O06_ABL2_A3_32689_D101

value: notprotected


title: WT (KR ctrl)-ctrl-3

description:
Library name: RNA_KR_3
rep 3

value: breast cancer cell line


title: hCYP2B6-Tg female gastrocnemius, 0 mg/kg/day PFOS treatment for 21 days via oral gavage rep 3

description: Library name: f2B6_111_0


title: WT (KR ctrl)-ctrl-2

description:
Library name: RNA_KR_2
rep 2


title: MCF7_MED1_CnR_B

description: Library name: RL_CnR_10

data_processing:
ChIP-seq reads were aligned using Rsubread’s align method and predicted fragment lengths were calculated by the ChIPQC R Bioconductor package. Normalized, fragment extended signal bigWigs were created using the rtracklayer R Bioconductor package. Peak calls were made using the SEACR software. The 'stringent' setting of SEACR was used and the top 1%  of peaks based on total signal within peaks were kept for further analysis.
Assembly: hg38
Supplementary files format and content: bigwig files
Supplementary files format and content: bed files from SEACR
Library strategy: CUT&Run

extract_protocol:
Trypsin-digested cells (5×10^5 cells) were harvested and fixed with freshly prepared 0.5% PFA for 2 min. After stopping the cross-linking using 500 μl 2.5 M Glycine, cells were washed three times with digitonin wash buffer (20 mM HEPES, pH 7.4, 150 mM NaCl, 0.5 mM spermidine, protein inhibitor cocktail, 0.005% digitonin, 0.05% SDS and 1% Triton X100) and bound to Concanavalin A coated beads (Polysciences, Cat# 86057-10) pre-washed by binding buffer (20 mM HEPES, pH 7.4, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). Cells on beads were then incubated with antibodies on a nutator overnight at 4 °C. After overnight incubation, cells were washed three times with 0.005% digitonin wash buffer, resuspended in 100 μl digitonin buffer containing Protein A/G-Micrococcal Nuclease fusion protein (pAG-MNase) and nutated in 4 °C for 1.5 hour. After pAG-MNase binding, cells were washed three times with digitonin wash buffer for 5 min. Finally, cells were resuspended in 100 μl ice cold digitonin buffer in a heating block pre-cooled in ice water bath. Digestion of the chromatin was initiated by addition of 2 mM CaCl2 in the tube, and lasted for 4 hours at 0 °C. The digestion was stopped by addition of 100 μl 2x STOP buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.02% digitonin, 100 μg/ml RNase A, Glycogen 50 μg/ml). Digested DNA was released by incubation at 37 °C for 30 min, and supernatant was collected. Then 5 μl proteinase K (20 mg/ml) and 200 μl 2x elution buffer (20 mM Tris-HCl (pH=8.0), 300 mM NaCl, 20 mM EDTA, 2% SDS, 10 mM DTT) was added to each sample for reverse crosslinking at 65 °C overnight. DNA was extracted by phenol-chloroform and dissolved in low EDTA TE buffer.
Libraries were generated using DNA SMART kit or ThruPLEX kit (both from Takara Bio) according to the manufacturer's instructions. After size selection (for 250-600bp) by AMPure XP beads (Beckman Coulter), the library was quality was evaluated using the Bioanalyzer and sequenced on Illumina NovaSeq SP (100bp two ends) and Illumina NextSeq High (75 bp single end).

value: original

value: anti MED1 (bethyl A300-793A)


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 101, 35915

description: Library name: G168_O06_ABL2_A2_35915_D101


title: hCYP2B6-Tg female gastrocnemius, 0 mg/kg/day PFOS treatment for 21 days via oral gavage rep 2

description: Library name: f2B6_105_0


title: MCF7_MED1_CnR_C

description: Library name: RL_CnR_11


title: MCF7_MED1_CnR_A

description: Library name: RL_CnR_9


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 101, 35912

description: Library name: G167_O06_ABL2_A2_35912_D101


title: hCYP2B6-Tg female gastrocnemius, 0 mg/kg/day PFOS treatment for 21 days via oral gavage rep 1

description: Library name: f2B6_101_0


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 101, 35911

description: Library name: G166_O06_ABL2_A2_35911_D101


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 101, 33543

description: Library name: G165_O06_ABL2_A2_33543_D101


title: MCF7_MED1KR_PolII_CnR

description: Library name: RL_CnR_6

value: MCF7 MED1 6KR

value: ectopic 6KR MED1

value: anti Pol II RPB1 (CTD4H8) (Santa Cruz SC-47701)


title: MCF7_MED1WT_PolII_CnR

description: Library name: RL_CnR_5

value: MCF7 MED1 WT

value: ectopic WT MED1


title: MCF7_MED1KR_HA_CnR_Rep

description: Library name: RL_CnR_4

value: anti HA (C29F4) (Cell Signaling #3724)


title: MCF7_MED1KR_HA_CnR

description: Library name: RL_CnR_3


title: CH310T1/2 cells_FOXS1_KO_clone2_TGFb_DMII_1

city: Boston

first: Matthew

last: Layne

state: Massachusetts

address: 72 East Concord Street

institute: Boston University

description: Library name: C2_TD1

data_processing:
Raw reads were filtered by removing 1) reads with adapter sequences 2) reads with >10% undeterminable bases and 3) low quality reads containing  > 50% of  bases with a quality score ≤ 5
Filtered clean reads were mapped using HISAT2 software
Assembly: mm10
Supplementary files format and content: xls file includes raw counts for each sample

growth_protocol: CH310T1/2 WT and FOXS1 KO clones were maintained in DMEM with 10% Fetal Bovine Serum (FBS) and antibiotics in 5% CO2 at 37°C

extract_protocol:
Total RNA was collected using the GeneJET RNA purification kit (Thermo)
RNA-seq libraries were prepared by Novogene (Sacramento, CA) and included PolyA enrichment, cDNA synthesis, and Illumina adapter ligation

treatment_protocol: CH310T1/2 WT and FOXS1 KO clones were grown to 2 days post-confluence. Cells were then treated with 1 nM TGF-β1 (R&D) for 12 hours, followed by adipogenic induction with DMII for 48 hours. DMII was composed of dexamethasone (Sigma), 3-Isobutyl-1-methylxanthine (Sigma), insulin (Sigma), and indomethacin (Sigma)

value: mesenchymal stem cells

value: FOXS1 KO

value: TGF-β1 + DMII


title: MCF7_MED1WT_HA_CnR_Rep

description: Library name: RL_CnR_2


title: CH310T1/2 cells_FOXS1_KO_clone2_control_3

description: Library name: C2_C3

value: Control


title: MCF7_MED1WT_S2P_CnR

description: Library name: RL_CnR_7

value: anti Pol II RPB1 S2P (Active Motif 61083)


title: F12_HC_subject4_PDC-E2_Treg

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

data_processing:
Reads were trimmed by 1 base at the 3′ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0). FastqMcf (v1.1.2) was used to remove any remaining adapter sequence. To align the trimmed reads, we used the STAR aligner (v2.4.2a) with the GRCh38 reference genome and gene annotations from ensembl release 91. Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134), FASTQC (v0.11.3), Samtools (v1.2), and HTSeq-count (v0.4.1). To identify TCR chains, the Trinity assembler was used to generate contigs. TCR sequences were identified and annotated using MiXCR (v2.1.3).
Assembly: GRCh38
Supplementary files format and content: P461_genecounts.txt: Library by Gene Count Matrix
Supplementary files format and content: P461_tcrs.txt: tab-delimited text file with sequences and metadata

source_name: PBMC

growth_protocol: PBMCs were isolated from fresh whole blood by Ficoll-Hypaque centrifugation and then immediately used in AIM assay.

extract_protocol:
To optimize recovery, PDC-E2-reactive T cells were sorted at single-cell purity directly into individual wells of a 96-well PCR plate with 5μl reaction buffer from the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio) as previously described
Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit (Illumina) to generate Illumina-compatible barcoded libraries.
Libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies). Dual-index, single-read sequencing of pooled libraries was carried out on a NextSeq 2000 sequencer (Illumina) with 58-base reads, using HiSeq v4 Cluster and SBS kits (Illumina) with a target depth of 1 million reads per sample.

treatment_protocol: . For each sample, the gate in antigen-stimulated cultures was set based on the DMSO-treated culture. CEFX stimulation was used as positive control, but not sorted. FOXP3 and Helios were not used to identify Tregs for sorting since permeabilization and fixation are incompatible with scRNA-seq.

value: PBMC

value: Treg

tag: group

value: HC

tag: stimulation

value: PDC-E2 peptides

tag: subject


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 101, 35883

description: Library name: G163_O06_ABL2_A2_35883_D101

value: Whole blood

value: day 101

value: male

value: notprotected


title: F11_HC_subject4_PDC-E2_Treg


title: F10_HC_subject4_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 101, 35827

description: Library name: G162_O06_ABL2_A2_35827_D101


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 101, 35820

description: Library name: G161_O06_ABL2_A2_35820_D101

value: protected


title: WT (KR ctrl)-ctrl-1

description:
Library name: RNA_KR_1
rep 1

value: MCF7 WT MED1

value: breast cancer cell line

value: ectopic WT MED1 (with Drosophila melanogaster spike-in)

value: control


title: CH310T1/2 cells_FOXS1_KO_clone2_control_2

description: Library name: C2_C2

value: mesenchymal stem cells

value: FOXS1 KO


title: MCF7_MED1WT_HA_CnR

description: Library name: RL_CnR_1

value: MCF7 MED1 WT

value: ectopic WT MED1

value: anti HA (C29F4) (Cell Signaling #3724)


title: F9_HC_subject4_PDC-E2_Treg

value: PBMC

value: Treg


title: CH310T1/2 cells_FOXS1_KO_clone2_TGFb_DMII_3

description: Library name: C2_TD3

value: TGF-β1 + DMII


title: CH310T1/2 cells_FOXS1_KO_clone2_control_1

description: Library name: C2_C1

value: Control


title: F8_HC_subject4_PDC-E2_Treg

value: HC

value: PDC-E2 peptides


title: F6_HC_subject4_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 101, 33864

description: Library name: G160_O06_ABL2_A2_33864_D101

value: Whole blood

value: day 101

value: male


title: MCF7_MED1KR_S2P_CnR

description: Library name: RL_CnR_8

value: MCF7 MED1 6KR

value: breast cancer cell line

value: ectopic 6KR MED1

value: anti Pol II RPB1 S2P (Active Motif 61083)


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 101, 32509

description: Library name: G159_O06_ABL2_A2_32509_D101

value: protected


title: CH310T1/2 cells_FOXS1_KO_clone1_TGFb_DMII_3

description: Library name: C1_TD3

value: mesenchymal stem cells

value: FOXS1 KO


title: F7_HC_subject4_PDC-E2_Treg


title: CH310T1/2 cells_FOXS1_KO_clone2_TGFb_DMII_2

description: Library name: C2_TD2


title: CH310T1/2 cells_FOXS1_KO_clone1_TGFb_DMII_2

description: Library name: C1_TD2


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 101, 35884

description: Library name: G164_O06_ABL2_A2_35884_D101


title: E11_HC_subject4_PDC-E2_Treg


title: E12_HC_subject4_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 101, 32119

description: Library name: G158_O06_ABL2_A2_32119_D101


title: E10_HC_subject4_PDC-E2_Treg


title: CH310T1/2 cells_FOXS1_KO_clone1_TGFb_DMII_1

description: Library name: C1_TD1


title: E8_HC_subject4_PDC-E2_Treg


title: E7_HC_subject4_PDC-E2_Treg


title: E6_HC_subject4_PDC-E2_Treg


title: CH310T1/2 cells_FOXS1_KO_clone1_control_3

description: Library name: C1_C3


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 101, 35916

description: Library name: G156_O06_ABL2_A1_35916_D101


title: E5_HC_subject4_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 101, 35890

description: Library name: G155_O06_ABL2_A1_35890_D101

value: notprotected


title: E3_HC_subject4_PDC-E2_Treg

value: PBMC


title: CH310T1/2 cells_FOXS1_KO_clone1_control_1

description: Library name: C1_C1


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 101, 35815

description: Library name: G154_O06_ABL2_A1_35815_D101


title: E2_HC_subject4_PDC-E2_Treg

value: Treg


title: CH310T1/2 cells_WT_TGFb_DMII_3

description: Library name: WT_TD3

value: WT

value: TGF-β1 + DMII


title: E1_HC_subject4_PDC-E2_Treg

value: HC


title: D12_HC_subject4_PDC-E2_Treg

value: PDC-E2 peptides


title: CH310T1/2 cells_WT_TGFb_DMII_2

description: Library name: WT_TD2


title: D11_HC_subject4_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 101, 35808

description: Library name: G153_O06_ABL2_A1_35808_D101

value: Whole blood


title: D9_HC_subject4_PDC-E2_Treg


title: CH310T1/2 cells_WT_TGFb_DMII_1

description: Library name: WT_TD1


title: D10_HC_subject4_PDC-E2_Treg


title: E9_HC_subject4_PDC-E2_Treg


title: CH310T1/2 cells_WT_control_3

description: Library name: WT_C3

value: Control


title: D8_HC_subject4_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 101, 33879

description: Library name: G151_O06_ABL2_A1_33879_D101

value: day 101

value: male


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 101, 32017

description: Library name: G157_O06_ABL2_A2_32017_D101


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 101, 32814

description: Library name: G150_O06_ABL2_A1_32814_D101


title: E4_HC_subject4_PDC-E2_Treg


title: D6_HC_subject4_PDC-E2_Treg


title: D5_HC_subject4_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 101, 32778

description: Library name: G149_O06_ABL2_A1_32778_D101


title: CH310T1/2 cells_FOXS1_KO_clone1_control_2

description: Library name: C1_C2


title: D4_HC_subject4_PDC-E2_Treg


title: CH310T1/2 cells_WT_control_2

description: Library name: WT_C2


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 101, 32485

description: Library name: G148_O06_ABL2_A1_32485_D101


title: D2_HC_subject4_PDC-E2_Treg


title: D7_HC_subject4_PDC-E2_Treg


title: C12_HC_subject4_PDC-E2_Treg


title: D1_HC_subject4_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 101, 33900

description: Library name: G152_O06_ABL2_A1_33900_D101


title: CH310T1/2 cells_WT_control_1

description: Library name: WT_C1


title: cDC1s_cDC2s_pre-cDCs, MCA205 LA OVA tumour, sGSN-/- mice

city: London

first: Cecile

last: Piot

address: 1 Midland road

country: United Kingdom

institute: Francis Crick

description: Library name: A5

data_processing:
Raw FASTQ reads were initially processed by the Cell Ranger pipeline, aligning to the mm10 (GRCm38) transcriptome
All subsequent analyses were performed in R (version 3)  using the Seurat (version 4.0.0) package
Assembly: mm10 [GRCm38]
Supplementary files format and content: Tab-separated barcodes ID's, features files and count files
Supplementary files format and content: csv meta.data from Seurat object extracted from the cDC1s analysis, with annotation, sample and UMAP embeddings per cell.

source_name: Tumour

extract_protocol:
Single cell preparation of tumours were prepared by digesting tumours and performing Percoll. cDC1s, cDC2s and pre-cDCs were FACS-sorted tumours and pooled for sequencing.
scRNA-seq

value: Tumour

value: sGSN-/-


title: C11_HC_subject4_PDC-E2_Treg


title: cDC1s_cDC2s_pre-cDCs, MCA205 LA OVA tumour, sGSN-/-Clec9a-/- mice

description: Library name: A6


title: D3_HC_subject4_PDC-E2_Treg


title: C8_HC_subject4_PDC-E2_Treg


title: cDC1s_cDC2s_pre-cDCs, MCA205 LA OVA tumour, WT mice

description: Library name: A4


title: C9_HC_subject4_PDC-E2_Treg


title: KO_ORX_R6

city: Parkville

last: See

state: VIC

address: Royal Children's Hospital, 50 Flemington Rd

country: Australia

institute: MCRI

description: Library name: KO_ORX_R6

data_processing:
Processing is automated using the RNAsik pipeline. The workflow is as follows:
Reads are aligned using the STAR aligner (version 2.7.1b)
Aligned reads are sorted with Samtools (version 1.9) and marked duplicate with Picard (2.20.2)
Finally, reads assigned to features using featureCounts from SubRead (version 2.0.0)
Assembly: GRCm39
Supplementary files format and content: Tab delimited file including raw feature counts.

source_name: Skeletal Muscle - gastrocnemius

growth_protocol: Mice were aged to 4-5 weeks prior to castration/sham surgery, and/or implantation with silastic tubing (1 cm in length) that are empty or containing 10 mg of dihydrotestosterone. Muscles were harvested after cull and snap frozen using liquid nitrogen for RNA extraction.

extract_protocol:
Total RNA was extracted from ~ 50 mg of mouse gastrocnemius (androgen deprivation experiment) or spinalis (DHT treatment experiment) by phenol chloroform extraction (1 mL TRIsure solution; Bioline), purified using the RNeasy Mini Kit (Qiagen) and RNA integrity was determined using TapeStation (Agilent Technologies 2200).
Libraries were prepared using the Illumina TruSeq Stranded Total RNA GOLD.

treatment_protocol: ORCHIDECTOMY: Male mice aged between 8-10 weeks were given pre-surgical analgesia (buprenorphine 0.1mg/kg) and anaesthetised using isoflurane/oxygen. Incision was made via the abdomen to remove the fat pad, testes and vas deferens; the vas deferens was sutured and wound site was resealed with surgical clips for 10 days.  Control animals received a sham orchiectomy, whereby the testes were surgically exposed but not cut and the wound site sealed with surgical clips. Animals were monitored and sacrificed 12- weeks post-surgery. IMPLANTATION WITH DHT: Silastic tube implant prepacked with 10 mg of solid DHT or empty tubing were subcutaneously implanted between the scapulae in male and female mice aged 4-5 weeks. Mice were given pre-surgical analgesia (buprenorphine 0.1mg/kg) and fully anaesthetised using isoflurane/oxygen during implantation. Male mice were also orchiectomised at the same time to eliminate contributions from endogenous androgens. Mice were euthanised after 6 weeks of treatment.

value: Skeletal Muscle - gastrocnemius

value: Male

tag: age at_treatment

value: 8-10 weeks

tag: strain

value: KO

value: ORX

tag: length of_treatment

value: 12 weeks


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 101, 32321

description: Library name: G147_O06_ABL2_A1_32321_D101

tag: tissue

value: notprotected


title: C7_HC_subject4_PDC-E2_Treg

value: PBMC

value: Treg


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 98, 35914

description: Library name: G144_O06_ABL2_A3_35914_D98

value: day 98


title: C6_HC_subject4_PDC-E2_Treg

value: HC

value: PDC-E2 peptides


title: WT_ORX_R6

description: Library name: WT_ORX_R6

tag: genotype

value: WT


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 101, 32019

description: Library name: G145_O06_ABL2_A1_32019_D101

value: Whole blood

tag: treatment

value: day 101


title: C4_HC_subject4_PDC-E2_Treg


title: WT_ORX_R5

description: Library name: WT_ORX_R5


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 101, 32215

description: Library name: G146_O06_ABL2_A1_32215_D101

tag: time

value: male


title: C10_HC_subject4_PDC-E2_Treg


title: B12_HC_subject4_PDC-E2_Treg


title: WT_ORX_R3

description: Library name: WT_ORX_R3


title: B10_HC_subject4_PDC-E2_Treg


title: C5_HC_subject4_PDC-E2_Treg


title: WT_ORX_R2

description: Library name: WT_ORX_R2


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 98, 35913

description: Library name: G143_O06_ABL2_A3_35913_D98

tag: animal id


title: B9_HC_subject4_PDC-E2_Treg


title: B11_HC_subject4_PDC-E2_Treg


title: WT_ORX_R4

description: Library name: WT_ORX_R4

tag: Sex


title: C2_HC_subject4_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 98, 35910

description: Library name: G142_O06_ABL2_A3_35910_D98

tag: dose

value: protected


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 98, 35885

description: Library name: G139_O06_ABL2_A3_35885_D98

tag: treatment outcome


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 98, 35886

description: Library name: G140_O06_ABL2_A3_35886_D98


title: C3_HC_subject4_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 98, 35889

description: Library name: G141_O06_ABL2_A3_35889_D98


title: B8_HC_subject4_PDC-E2_Treg


title: WT_ORX_R1

description: Library name: WT_ORX_R1

value: Skeletal Muscle - gastrocnemius


title: B6_HC_subject4_PDC-E2_Treg


title: B7_HC_subject4_PDC-E2_Treg


title: B5_HC_subject4_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 98, 35822

description: Library name: G138_O06_ABL2_A3_35822_D98


title: C1_HC_subject4_PDC-E2_Treg


title: WT_SHAM_R5

description: Library name: WT_SHAM_R5

value: Male

value: SHAM


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 98, 33878

description: Library name: G137_O06_ABL2_A3_33878_D98


title: B4_HC_subject4_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 98, 33877

description: Library name: G136_O06_ABL2_A3_33877_D98


title: B2_HC_subject4_PDC-E2_Treg


title: B3_HC_subject4_PDC-E2_Treg


title: B1_HC_subject4_PDC-E2_Treg


title: A10_HC_subject4_PDC-E2_Treg


title: A12_HC_subject4_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 98, 32707

description: Library name: G134_O06_ABL2_A3_32707_D98


title: WT_SHAM_R3

description: Library name: WT_SHAM_R3

value: 8-10 weeks


title: WT_SHAM_R4

description: Library name: WT_SHAM_R4


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 98, 33700

description: Library name: G135_O06_ABL2_A3_33700_D98


title: A11_HC_subject4_PDC-E2_Treg


title: A9_HC_subject4_PDC-E2_Treg


title: A8_HC_subject4_PDC-E2_Treg


title: WT_SHAM_R2

description: Library name: WT_SHAM_R2


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 98, 32689

description: Library name: G133_O06_ABL2_A3_32689_D98


title: WT_SHAM_R1

description: Library name: WT_SHAM_R1


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 98, 35915

description: Library name: G132_O06_ABL2_A2_35915_D98


title: WT_SHAM_R6

description: Library name: WT_SHAM_R6


title: A6_HC_subject4_PDC-E2_Treg


title: KO_ORX_R5

description: Library name: KO_ORX_R5

value: KO

value: ORX


title: A5_HC_subject4_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 98, 35912

description: Library name: G131_O06_ABL2_A2_35912_D98

value: notprotected


title: A4_HC_subject4_PDC-E2_Treg

value: PBMC


title: A3_HC_subject4_PDC-E2_Treg

value: Treg


title: KO_ORX_R4

description: Library name: KO_ORX_R4

value: 12 weeks


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 98, 35911

description: Library name: G130_O06_ABL2_A2_35911_D98

value: day 98


title: A2_HC_subject4_PDC-E2_Treg

value: HC

value: PDC-E2 peptides


title: KO_ORX_R3

description: Library name: KO_ORX_R3


title: F12_HC_subject4_PDC-E2_Tconv

value: Tconv


title: A1_HC_subject4_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 98, 33543

description: Library name: G129_O06_ABL2_A2_33543_D98

value: Whole blood


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 98, 35827

description: Library name: G126_O06_ABL2_A2_35827_D98

value: male


title: G4_HC_subject4_PDC-E2_Tconv


title: F11_HC_subject4_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 98, 35820

description: Library name: G125_O06_ABL2_A2_35820_D98

value: protected


title: KO_SHAM_R6

description: Library name: KO_SHAM_R6

value: Skeletal Muscle - gastrocnemius


title: G6_HC_subject4_PDC-E2_Tconv


title: KO_SHAM_R4

description: Library name: KO_SHAM_R4

value: Male


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 98, 33864

description: Library name: G124_O06_ABL2_A2_33864_D98


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 98, 35884

description: Library name: G128_O06_ABL2_A2_35884_D98


title: A7_HC_subject4_PDC-E2_Treg


title: F8_HC_subject4_PDC-E2_Tconv


title: KO_SHAM_R3

description: Library name: KO_SHAM_R3

value: SHAM


title: G3_HC_subject4_PDC-E2_Tconv


title: KO_ORX_R1

description: Library name: KO_ORX_R1

value: 8-10 weeks


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 98, 35883

description: Library name: G127_O06_ABL2_A2_35883_D98


title: F6_HC_subject4_PDC-E2_Tconv


title: F5_HC_subject4_PDC-E2_Tconv


title: G2_HC_subject4_PDC-E2_Tconv


title: G1_HC_subject4_PDC-E2_Tconv


title: KO_SHAM_R1

description: Library name: KO_SHAM_R1

value: KO


title: F4_HC_subject4_PDC-E2_Tconv


title: KO_SHAM_R5

description: Library name: KO_SHAM_R5


title: G5_HC_subject4_PDC-E2_Tconv


title: KO_SHAM_R2

description: Library name: KO_SHAM_R2


title: F10_HC_subject4_PDC-E2_Tconv


title: F9_HC_subject4_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 98, 32509

description: Library name: G123_O06_ABL2_A2_32509_D98


title: F7_HC_subject4_PDC-E2_Tconv


title: F2_HC_subject4_PDC-E2_Tconv


title: KO_ORX_R2

description: Library name: KO_ORX_R2

value: ORX


title: F3_HC_subject4_PDC-E2_Tconv


title: E10_HC_subject4_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 98, 32119

description: Library name: G122_O06_ABL2_A2_32119_D98


title: E9_HC_subject4_PDC-E2_Tconv


title: KO_DHT_R3

description: Library name: KO_DHT_R3

source_name: Skeletal Muscle - spinalis

value: Skeletal Muscle - spinalis

value: Female

value: 4-5 weeks

value: DHT

value: 6 weeks


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 98, 35815

description: Library name: G118_O06_ABL2_A1_35815_D98

value: day 98

value: notprotected


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 98, 32017

description: Library name: G121_O06_ABL2_A2_32017_D98


title: KO_DHT_R6

description: Library name: KO_DHT_R6


title: E7_HC_subject4_PDC-E2_Tconv

value: PBMC

value: Tconv

value: HC

value: PDC-E2 peptides


title: F1_HC_subject4_PDC-E2_Tconv


title: E12_HC_subject4_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 98, 35916

description: Library name: G120_O06_ABL2_A1_35916_D98

value: Whole blood

value: male

value: protected


title: KO_DHT_R5

description: Library name: KO_DHT_R5


title: E5_HC_subject4_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 98, 35890

description: Library name: G119_O06_ABL2_A1_35890_D98


title: E11_HC_subject4_PDC-E2_Tconv


title: E6_HC_subject4_PDC-E2_Tconv


title: E8_HC_subject4_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 98, 35808

description: Library name: G117_O06_ABL2_A1_35808_D98


title: E4_HC_subject4_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 98, 33900

description: Library name: G116_O06_ABL2_A1_33900_D98


title: KO_DHT_R4

description: Library name: KO_DHT_R4


title: E3_HC_subject4_PDC-E2_Tconv


title: KO_Empty_R4

description: Library name: KO_Empty_R4

value: Empty


title: KO_Empty_R5

description: Library name: KO_Empty_R5

value: KO


title: E1_HC_subject4_PDC-E2_Tconv


title: KO_DHT_R1

description: Library name: KO_DHT_R1


title: D9_HC_subject4_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 98, 32778

description: Library name: G113_O06_ABL2_A1_32778_D98


title: KO_Empty_R3

description: Library name: KO_Empty_R3


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 98, 32485

description: Library name: G112_O06_ABL2_A1_32485_D98


title: D8_HC_subject4_PDC-E2_Tconv


title: KO_DHT_R2

description: Library name: KO_DHT_R2


title: KO_Empty_R2

description: Library name: KO_Empty_R2


title: D7_HC_subject4_PDC-E2_Tconv


title: D6_HC_subject4_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 98, 32321

description: Library name: G111_O06_ABL2_A1_32321_D98


title: KO_Empty_R1

description: Library name: KO_Empty_R1


title: D5_HC_subject4_PDC-E2_Tconv


title: E2_HC_subject4_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 98, 32814

description: Library name: G114_O06_ABL2_A1_32814_D98


title: WT_DHT_R6

description: Library name: WT_DHT_R6

value: WT


title: D4_HC_subject4_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 98, 32215

description: Library name: G110_O06_ABL2_A1_32215_D98


title: D2_HC_subject4_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 98, 32019

description: Library name: G109_O06_ABL2_A1_32019_D98


title: D3_HC_subject4_PDC-E2_Tconv


title: D1_HC_subject4_PDC-E2_Tconv


title: D12_HC_subject4_PDC-E2_Tconv


title: WT_DHT_R5

description: Library name: WT_DHT_R5

value: Skeletal Muscle - spinalis


title: D10_HC_subject4_PDC-E2_Tconv


title: C12_HC_subject4_PDC-E2_Tconv


title: WT_DHT_R4

description: Library name: WT_DHT_R4

value: Female


title: C11_HC_subject4_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 7, 35913

description: Library name: G107_O06_ABL2_A3_35913_D7

value: day 7


title: C10_HC_subject4_PDC-E2_Tconv


title: D11_HC_subject4_PDC-E2_Tconv


title: WT_DHT_R3

description: Library name: WT_DHT_R3

value: 4-5 weeks

value: DHT


title: C9_HC_subject4_PDC-E2_Tconv


title: C8_HC_subject4_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 7, 35910

description: Library name: G106_O06_ABL2_A3_35910_D7


title: C7_HC_subject4_PDC-E2_Tconv


title: C6_HC_subject4_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 7, 35889

description: Library name: G105_O06_ABL2_A3_35889_D7


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 98, 33879

description: Library name: G115_O06_ABL2_A1_33879_D98

value: day 98


title: C5_HC_subject4_PDC-E2_Tconv


title: C4_HC_subject4_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 7, 35886

description: Library name: G104_O06_ABL2_A3_35886_D7

value: notprotected


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 7, 35914

description: Library name: G108_O06_ABL2_A3_35914_D7


title: WT_Empty_R5

description: Library name: WT_Empty_R5

value: 6 weeks


title: C2_HC_subject4_PDC-E2_Tconv

value: PBMC

value: Tconv


title: WT_Empty_R4

description: Library name: WT_Empty_R4


title: B11_HC_subject4_PDC-E2_Tconv

value: HC

value: PDC-E2 peptides


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 7, 33878

description: Library name: G101_O06_ABL2_A3_33878_D7

value: Whole blood

value: male


title: WT_DHT_R2

description: Library name: WT_DHT_R2


title: B8_HC_subject4_PDC-E2_Tconv


title: WT_DHT_R1

description: Library name: WT_DHT_R1


title: B6_HC_subject4_PDC-E2_Tconv


title: Cx43-ko mice Retina, elevated IOP 3w-4

city: Shanghai

first: Guoli

last: Zhao

address: 131 Dongan Road

country: China

institute: Fudan University

description:
Library name: Cx43-G3w-4
Column name in processed FPKM matrix: Cx43-G3w-4

data_processing:
Raw reads were quality filtered using Cutadapt (v1.9.1) with parameters: phred cutoff 20, error rate 0.1, min length 75, max N 0.1.
Reads were aligned to the mouse reference genome (GRCm38/mm10) using HISAT2 (v2.2.1).
Gene-level expression was quantified using HTSeq (v0.6.1).
Differential expression analysis was performed using DESeq2 (Bioconductor) with adjusted p-value threshold of 0.05.
GO enrichment was performed using GOSeq (v1.34.1); KEGG enrichment was performed using in-house scripts.
Assembly: GRCm38/mm10
Supplementary files format and content: matrix of FPKM values. Rows represent Ensembl gene IDs and columns represent individual samples.

source_name: retina

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 1 μg of total RNA was used for the construction of sequencing libraries.
1 μg total RNA was used for library construction. Poly(A) mRNA was isolated with Oligo(dT) beads. Libraries were prepared using standard methods including fragmentation, cDNA synthesis, adapter ligation, and PCR.

value: retina

value: Cx43 knockdown

value: Cx43-ko mice elevated IOP 6w

tag: batch


title: B5_HC_subject4_PDC-E2_Tconv


title: C3_HC_subject4_PDC-E2_Tconv


title: Cx43-ko mice Retina, elevated IOP 3w-3

description:
Library name: Cx43-G3w-3
Column name in processed FPKM matrix: Cx43-G3w-3

value: Cx43-ko mice elevated IOP 5w


title: B4_HC_subject4_PDC-E2_Tconv


title: B3_HC_subject4_PDC-E2_Tconv


title: Cx43-ko mice Retina, elevated IOP 3w-2

description:
Library name: Cx43-G3w-2
Column name in processed FPKM matrix: Cx43-G3w-2

value: Cx43-ko mice elevated IOP 4w


title: B1_HC_subject4_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 7, 35915

description: Library name: G096_O06_ABL2_A2_35915_D7

value: day 7


title: A12_HC_subject4_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 7, 35912

description: Library name: G095_O06_ABL2_A2_35912_D7


title: Wild type mice Retina, elevated IOP 3w-4

description:
Library name: WT-G3w-4
Column name in processed FPKM matrix: WT-G3w-4

value: WT

value: wild type elevated IOP 3w


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 7, 35911

description: Library name: G094_O06_ABL2_A2_35911_D7

value: protected


title: Wild type mice Retina, elevated IOP 3w-3

description:
Library name: WT-G3w-3
Column name in processed FPKM matrix: WT-G3w-3


title: A7_HC_subject4_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 7, 33543

description: Library name: G093_O06_ABL2_A2_33543_D7


title: A6_HC_subject4_PDC-E2_Tconv


title: Wild type mice Retina, elevated IOP 3w-2

description:
Library name: WT-G3w-2
Column name in processed FPKM matrix: WT-G3w-2


title: A3_HC_subject4_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 7, 35885

description: Library name: G103_O06_ABL2_A3_35885_D7


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 7, 35822

description: Library name: G102_O06_ABL2_A3_35822_D7

value: notprotected


title: A1_HC_subject4_PDC-E2_Tconv


title: B12_HC_subject4_PDC-E2_Tconv


title: WT_Empty_R3

description: Library name: WT_Empty_R3

value: Skeletal Muscle - spinalis

value: Female

value: 4-5 weeks

value: Empty

value: 6 weeks


title: B10_HC_subject4_PDC-E2_Tconv

value: PBMC

value: Tconv

value: HC

value: PDC-E2 peptides


title: WT_Empty_R2

description: Library name: WT_Empty_R2


title: B9_HC_subject4_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 7, 33877

description: Library name: G100_O06_ABL2_A3_33877_D7

value: Whole blood

value: male


title: WT_Empty_R1

description: Library name: WT_Empty_R1


title: B7_HC_subject4_PDC-E2_Tconv


title: Wild type mice Retina, no treatment-3

description:
Library name: Ctr-3
Column name in processed FPKM matrix: Ctr-3

value: retina

value: wild type control


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 7, 32707

description: Library name: G098_O06_ABL2_A3_32707_D7

value: day 7


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 7, 33700

description: Library name: G099_O06_ABL2_A3_33700_D7


title: E9_HC_subject5_PDC-E2_Treg

value: Treg


title: Cx43-ko mice Retina, elevated IOP 3w-1

description:
Library name: Cx43-G3w-1
Column name in processed FPKM matrix: Cx43-G3w-1

value: Cx43 knockdown

value: Cx43-ko mice elevated IOP 3w


title: C1_HC_subject4_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 7, 32689

description: Library name: G097_O06_ABL2_A3_32689_D7

value: notprotected


title: A8_HC_subject4_PDC-E2_Tconv


title: Wild type mice Retina, no treatment-2

description:
Library name: Ctr-2
Column name in processed FPKM matrix: Ctr-2

value: WT


title: A9_HC_subject4_PDC-E2_Tconv


title: A10_HC_subject4_PDC-E2_Tconv


title: E8_HC_subject5_PDC-E2_Treg


title: A11_HC_subject4_PDC-E2_Tconv


title: B2_HC_subject4_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 7, 33864

description: Library name: G088_O06_ABL2_A2_33864_D7

value: protected


title: A5_HC_subject4_PDC-E2_Tconv


title: Wild type mice Retina, elevated IOP 3w-1

description:
Library name: WT-G3w-1
Column name in processed FPKM matrix: WT-G3w-1

value: wild type elevated IOP 3w


title: A4_HC_subject4_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 7, 35884

description: Library name: G092_O06_ABL2_A2_35884_D7


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 7, 35883

description: Library name: G091_O06_ABL2_A2_35883_D7


title: A2_HC_subject4_PDC-E2_Tconv


title: Wild type mice Retina, no treatment-4

description:
Library name: Ctr-4
Column name in processed FPKM matrix: Ctr-4


title: E10_HC_subject5_PDC-E2_Treg


title: iBMDM cells, CCDC134KO-2-LPS repeat-2

first: Yang

last: Bai

address: Yueyang Road No.320

institute: Chinese Academy of Sciences

description: Library name: 16

data_processing:
Libaries were sequenced on an Illumina Novaseq 6000 platform (Illumina).
Image analysis and base calling were conducted using the Illumina RTA software.
Sequencing reads were aligned to the Mus musculus reference genome (GRCm39) obtained from GENCODE.
R package DESeq2 was used to analyze differential expression and fold change.
Assembly: GRCm39
Supplementary files format and content: Excel file includes raw counts and for each sample

source_name: iBMDM

growth_protocol: Cells were grown in DMEM (Gibco) supplemented with 10% fetal bovine serum (Gibco), 2 mM L-glutamine (Gibco), 50 U/ml penicillin and 50 mg/ ml streptomycin (Gibco), and 50 μM 2-ME at 37°C in humidified air with 5% CO2.

extract_protocol:
Total RNA was extracted with TRIzol Reagent (Thermo Fisher Scientific, 15596026) according the manufacturer’s instructions as described. 20 to 30 μg of total RNA each group was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using the VAHTS mRNA-seq V3 library prep kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: iBMDMs were challenged with 1 μg/ml LPS or equal volume of vehicle (ddwater) for 4 hr.

tag: cell line

value: iBMDM

tag: cell type

value: immortalized macrophage

value: CCDC134 gene knockout

value: LPS stimulated


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 7, 35827

description: Library name: G090_O06_ABL2_A2_35827_D7


title: H11_PBC_subject5_PDC-E2_Treg

value: PBMC

tag: group

value: PBC

value: PDC-E2 peptides


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 7, 35820

description: Library name: G089_O06_ABL2_A2_35820_D7

value: Whole blood

value: male


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 7, 32017

description: Library name: G085_O06_ABL2_A2_32017_D7

value: day 7


title: E7_HC_subject5_PDC-E2_Treg

value: Treg

value: HC

tag: stimulation


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 7, 35916

description: Library name: G084_O06_ABL2_A1_35916_D7


title: H5_PBC_subject5_PDC-E2_Treg

tag: subject


title: E6_HC_subject5_PDC-E2_Treg


title: Wild type mice Retina, no treatment-1

description:
Library name: Ctr-1
Column name in processed FPKM matrix: Ctr-1

value: retina

value: wild type control


title: iBMDM cells, CCDC134KO-1-LPS repeat-1

description: Library name: 13


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 7, 32509

description: Library name: G087_O06_ABL2_A2_32509_D7


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 7, 32119

description: Library name: G086_O06_ABL2_A2_32119_D7


title: H10_PBC_subject5_PDC-E2_Treg


title: H9_PBC_subject5_PDC-E2_Treg


title: iBMDM cells, CCDC134KO-2-LPS repeat-1

description: Library name: 15


title: H8_PBC_subject5_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 7, 35815

description: Library name: G082_O06_ABL2_A1_35815_D7

value: notprotected


title: iBMDM cells, WT-2-LPS repeat-2

description: Library name: 12

value: WT


title: H1_PBC_subject5_PDC-E2_Treg


title: H7_PBC_subject5_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 7, 35890

description: Library name: G083_O06_ABL2_A1_35890_D7


title: iBMDM cells, CCDC134KO-1-LPS repeat-2

description: Library name: 14


title: H6_PBC_subject5_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 7, 33900

description: Library name: G080_O06_ABL2_A1_33900_D7


title: H12_PBC_subject5_PDC-E2_Treg


title: H4_PBC_subject5_PDC-E2_Treg


title: iBMDM cells, WT-2-LPS repeat-1

description: Library name: 11


title: G11_PBC_subject5_PDC-E2_Treg


title: H2_PBC_subject5_PDC-E2_Treg


title: G12_PBC_subject5_PDC-E2_Treg


title: G10_PBC_subject5_PDC-E2_Treg


title: G6_PBC_subject5_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 7, 35808

description: Library name: G081_O06_ABL2_A1_35808_D7

value: protected


title: G8_PBC_subject5_PDC-E2_Treg


title: G7_PBC_subject5_PDC-E2_Treg


title: iBMDM cells, WT-1-LPS repeat-1

description: Library name: 9

value: iBMDM


title: iBMDM cells, CCDC134KO-1 repeat-2

description: Library name: 6

value: immortalized macrophage


title: G4_PBC_subject5_PDC-E2_Treg


title: G9_PBC_subject5_PDC-E2_Treg


title: F12_PBC_subject5_PDC-E2_Treg


title: H3_PBC_subject5_PDC-E2_Treg


title: iBMDM cells, CCDC134KO-2 repeat-2

description: Library name: 8

value: CCDC134 gene knockout


title: G5_PBC_subject5_PDC-E2_Treg


title: iBMDM cells, WT-1-LPS repeat-2

description: Library name: 10

value: LPS stimulated


title: G3_PBC_subject5_PDC-E2_Treg

value: PBMC


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 7, 32814

description: Library name: G078_O06_ABL2_A1_32814_D7


title: iBMDM cells, CCDC134KO-2 repeat-1

description: Library name: 7


title: F11_PBC_subject5_PDC-E2_Treg

value: PBC


title: G2_PBC_subject5_PDC-E2_Treg

value: PDC-E2 peptides


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 7, 32778

description: Library name: G077_O06_ABL2_A1_32778_D7

value: Whole blood


title: G1_PBC_subject5_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 7, 32485

description: Library name: G076_O06_ABL2_A1_32485_D7

value: male


title: F9_PBC_subject5_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 7, 32321

description: Library name: G075_O06_ABL2_A1_32321_D7

value: day 7


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 7, 33879

description: Library name: G079_O06_ABL2_A1_33879_D7


title: F10_PBC_subject5_PDC-E2_Treg

value: Treg


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 7, 32215

description: Library name: G074_O06_ABL2_A1_32215_D7


title: iBMDM cells, CCDC134KO-1 repeat-1

description: Library name: 5


title: iBMDM cells, WT-1 repeat-2

description: Library name: 2


title: F7_PBC_subject5_PDC-E2_Treg


title: F6_PBC_subject5_PDC-E2_Treg


title: iBMDM cells, WT-1 repeat-1

description: Library name: 1


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 7, 32019

description: Library name: G073_O06_ABL2_A1_32019_D7


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 3, 35914

description: Library name: G072_O06_ABL2_A3_35914_D3

value: day 3


title: F4_PBC_subject5_PDC-E2_Treg


title: iBMDM cells, WT-2 repeat-2

description: Library name: 4


title: F3_PBC_subject5_PDC-E2_Treg


title: iBMDM cells, WT-2 repeat-1

description: Library name: 3


title: F2_PBC_subject5_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 3, 35913

description: Library name: G071_O06_ABL2_A3_35913_D3


title: Mouse lung immune cells, RTX-treated, IAV PR8 7 DPI

first: Adam

middle: L

last: Haber

state: MA

address: 665 Huntington Ave

department: Environmental Health

institute: Harvard T.H. Chan School of Public Health

description:
Library name: RTX_7DPI
10X Genomics

data_processing:
log transformation and TPM normalization (Seurat R)
PCA (Seurat R)
UMAP and clustering (Seurat R)
Assembly: mm10
Supplementary files format and content: Log2(Counts per million (CPM) + 1) expression values for each gene (rows) in each single-cell (columns)

source_name: Lung

growth_protocol: Mice were bred and housed in a full-barrier, specific pathogen free animal facility.

extract_protocol:
Mice were sacrificed by carbon dioxide followed by cervical dislocation and were immediately perfused transcardially with 10ml PBS solution. Collected lung lobes were rinsed in 10% FBS/RPMI and minced into small pieces. Samples were digested (100µg/ml DNase and 0.4 mg/ml collagenase in 10% FBS/RPMI) using GentleMacs Dissociator (Miltenyi biotec), followed by filtering with 70μm strainer using 10% FBS/RPMI. Samples were then labeled with CD45 MicroBeads (Miltenyi Biotec) at 4°C for 15 minutes, washed with MACS buffer (Miltenyi biotec), and filtered with 40μm strainer. The resulting cell suspensions were then used for magnetic-activated cell sorting (MACS)-based purification using MS MACS columns (Miltenyi Biotec) following the manufacturer’s directions. Cells were resuspended in 0.04% BSA/PBS and pooled from two mice for each of the naïve samples (vehicle and RTX), and from three mice for each of the 7 DPI samples (vehicle and RTX) to generate a total of four cDNA libraries.
Library samples were sequenced on an Illumina NovaSeq with Nextera XT assay.
10X Chromium V3 Chemistry Single-cell RNA Seq

treatment_protocol:
Systemic nociceptor neuron ablation by resiniferatoxin (RTX) treatment was performed as previously described. Briefly, 4-week-old C57BL/6 mice were anesthetized with isoflurane and injected subcutaneously in the flank with escalating doses (30, 70, 100 mg/kg on consecutive days) of resiniferatoxin (RTX, Alomone Lab) or vehicle (2% DMSO/0.15% Tween-80/PBS). Mice were allowed to rest for 4 weeks before experiments.
Influenza A virus Puerto Rico strain 8 (PR8) was purchased from Charles River Laboratories. Vehicle and RTX-treated mice were intranasally inoculated with a total dose of 50 TCID50 IAV PR8.

value: Lung

value: RTX

tag: infection

value: PR8 7 DPI


title: F1_PBC_subject5_PDC-E2_Treg


title: F8_PBC_subject5_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 3, 35910

description: Library name: G070_O06_ABL2_A3_35910_D3


title: E12_PBC_subject5_PDC-E2_Treg


title: Mouse lung immune cells, Vehicle-treated, IAV PR8 7 DPI

description:
Library name: Vehicle_7DPI
10X Genomics

tag: strain

value: Vehicle


title: E9_PBC_subject5_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 3, 35889

description: Library name: G069_O06_ABL2_A3_35889_D3

value: notprotected


title: Mouse lung immune cells, RTX-treated, Naïve uninfected

description:
Library name: RTX_Naive
10X Genomics

value: Naïve


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 3, 35885

description: Library name: G067_O06_ABL2_A3_35885_D3

value: protected


title: E10_PBC_subject5_PDC-E2_Treg


title: E8_PBC_subject5_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 3, 35886

description: Library name: G068_O06_ABL2_A3_35886_D3


title: Mouse lung immune cells, Vehicle-treated, Naïve uninfected

description:
Library name: Vehicle_Naive
10X Genomics


title: F5_PBC_subject5_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 3, 35822

description: Library name: G066_O06_ABL2_A3_35822_D3


title: KD-3

city: Tokyo

first: Seien

last: Ko

address: 35 Shinanomachi, Shinjuku-ku

department: Cardiology

country: Japan

institute: Keio University School of Medicine

description: Library name: KD-3

data_processing:
Reads are mapped to reference genome with HISAT2. After the read mapping, Stringtie was used for transcript assembly Gene-level and transcript-level quantifications were performed as raw read counts, fragments per kilobase of transcript per million mapped reads (FPKM), and transcripts per million (TPM).
Assembly: mm10
Supplementary files format and content: xlsx files contain FPKM, TPM, and read counts of  each sample

source_name: Heart

growth_protocol: Culture medium was consisted of DMEM with 20% FBS, 100 U/mL penicillin, 100 µg/mL streptomycin sulfate, and 0.25 µg/mL amphotericin B. Isolated cardiac fibroblasts were cultured at 37°C in 5% CO2. The medium was changed every 2–3 days. Cells that had not been passaged were used for the following treatment.

extract_protocol:
Cultured cardiac fibroblasts were washed by PBS twice and added with 1 ml of TRIzol reagent on ice, followed by addition of 200 µl of chloroform and vigorous shaking. Each sample was centrifuged at 25,000×g in 4°C for 15 minutes, and the top layer was transferred to a new RNase free tube. Then, 500 µl of isopropanol was added to the tube and  incubate at room temperature for 10 minutes,followed by  centrifugation at 25,000×g in 4°C for 15 minutes.  Supernatant was removed and the RNA pellet was washed by 75% ethanol, and finally dissolved in Rnase-free water.
RNA library construction was performed after confirming that the sample RNA integrity numbers were greater than seven using a TapeStation RNA screentape. A library was independently prepared with 1 µg of total RNA from each sample using an Illumina TruSeq Stranded mRNA Sample Prep Kit. As for library kit, TruSeq Stranded mRNA Library Prep Kit was used. As for library protocol, TruSeq Stranded mRNA Reference Guide #1000000040498 v00 was used. The first step in the workflow involved purifying the poly-A containing mRNA molecules using poly-T-attached magnetic beads. Following purification, mRNA was fragmented into small pieces using divalent cations at elevated temperatures. The cleaved RNA fragments were copied into first-strand cDNA using SuperScript II reverse transcriptase and random primers, followed by second-strand cDNA synthesis using DNA Polymerase I, RNase H, and dUTP. These cDNA fragments went through an end repair process, the addition of a single ‘A’ base, and ligation of the adapters. The products were purified and enriched using PCR to create a final cDNA library. The libraries were quantified using KAPA Library Quantification kits for Illumina Sequencing platforms according to the qPCR Quantification Protocol Guide, and qualified using the TapeStation D1000 ScreenTape system. Indexed libraries were then submitted to an Illumina NovaSeq6000 (Illumina) and paired-end (2×100 bp) sequencing reads were generated on the Illumina sequencing NovaSeq platform.

treatment_protocol: Lentivirus containing  vector coding short hairpin RNA targeting Sipa1 with an EGFP reporter or scramble were transfected to cultured cardiac fibroblasts using polybrene at 8 µg/mL and incubated at 37°C in 5% CO2. After 72 hours, 1 µg/mL of lipopolysaccharide (LPS) was added for stimulation of cardiac fibroblasts and incubated for 24 hours.

value: Heart

value: fibroblast

value: Sipa1 knockdown

value: LPS stimulation


title: E3_PBC_subject5_PDC-E2_Treg

value: PBMC

value: PBC

value: PDC-E2 peptides


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 3, 33878

description: Library name: G065_O06_ABL2_A3_33878_D3

value: Whole blood

value: male


title: E6_PBC_subject5_PDC-E2_Treg

value: Treg


title: KD-2

description: Library name: KD-2


title: KD-1

description: Library name: KD-1


title: E11_PBC_subject5_PDC-E2_Treg


title: E2_PBC_subject5_PDC-E2_Treg


title: E1_PBC_subject5_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 3, 33877

description: Library name: G064_O06_ABL2_A3_33877_D3

value: day 3


title: D12_PBC_subject5_PDC-E2_Treg


title: Ctrl-3

description: Library name: Ctrl-3

value: WT


title: E7_PBC_subject5_PDC-E2_Treg


title: D11_PBC_subject5_PDC-E2_Treg


title: Ctrl-2

description: Library name: Ctrl-2


title: D10_PBC_subject5_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 3, 33700

description: Library name: G063_O06_ABL2_A3_33700_D3


title: E5_PBC_subject5_PDC-E2_Treg


title: E4_PBC_subject5_PDC-E2_Treg


title: D8_PBC_subject5_PDC-E2_Treg


title: D9_PBC_subject5_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 3, 32707

description: Library name: G062_O06_ABL2_A3_32707_D3


title: Ctrl-1

description: Library name: Ctrl-1


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 3, 35915

description: Library name: G060_O06_ABL2_A2_35915_D3


title: D5_PBC_subject5_PDC-E2_Treg


title: D6_PBC_subject5_PDC-E2_Treg


title: FR-HF/HS Diet-6

city: Omaha

first: Sankarasubramanian

last: Jagadesan

state: NE

address: 42end and Emile st

department: Department of Genetics, Cell Biology & Anatomy

institute: University of Nebraska Medical Center

description: Library name: SG93

data_processing:
The original fastq format reads were trimmed by fqtirm tool to remove adapters, terminal unknown bases (Ns) and low quality 3’ regions (Phred score < 30).
The trimmed fastq files were processed by our newly developed standard pipelines utilizing STAR as the aligner and RSEM as the tool for annotation and quantification at both gene and isoform levels.
The trimmed fastq files were mapped to Mouse reference genome
TPM values for individual samples were used for the comparisons and other statistical analyses
Assembly: mm10
Supplementary files format and content: Processed data file contains the TPM, FPKM and cell counts, which are provided in .xlsx files

source_name: Ovary

extract_protocol:
Extraction was by Qiagen’s RNeasy mini kit
Generation of the RNA-Seq libraries derived from poly(A) selected RNA was completed using the Nugen Universal mRNA library prep kit (#0508)

value: Ovary

value: Fshb-/- HFSHBWT

value: High Fat /High Sucrose Diet


title: FR-HF/HS Diet-5

description: Library name: SG92


title: D7_PBC_subject5_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 3, 32689

description: Library name: G061_O06_ABL2_A3_32689_D3

value: notprotected


title: D2_PBC_subject5_PDC-E2_Treg


title: D3_PBC_subject5_PDC-E2_Treg


title: FR-HF/HS Diet-4

description: Library name: SG91


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 3, 35912

description: Library name: G059_O06_ABL2_A2_35912_D3


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 3, 35911

description: Library name: G058_O06_ABL2_A2_35911_D3

value: protected


title: D1_PBC_subject5_PDC-E2_Treg


title: FR-HF/HS Diet-3

description: Library name: SG90


title: C12_PBC_subject5_PDC-E2_Treg


title: C11_PBC_subject5_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 3, 33543

description: Library name: G057_O06_ABL2_A2_33543_D3


title: FRP-HF/HS Diet-6

description: Library name: SG89

value: Fshb-/- HFSHBMut


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 3, 35884

description: Library name: G056_O06_ABL2_A2_35884_D3


title: D4_PBC_subject5_PDC-E2_Treg


title: FRP-HF/HS Diet-5

description: Library name: SG88


title: C7_PBC_subject5_PDC-E2_Treg


title: C10_PBC_subject5_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 3, 35883

description: Library name: G055_O06_ABL2_A2_35883_D3


title: FRP-HF/HS Diet-4

description: Library name: SG87


title: C6_PBC_subject5_PDC-E2_Treg


title: C5_PBC_subject5_PDC-E2_Treg


title: C4_PBC_subject5_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 3, 35820

description: Library name: G053_O06_ABL2_A2_35820_D3


title: FR-HF/HS Diet-2

description: Library name: SG83


title: C9_PBC_subject5_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 3, 35827

description: Library name: G054_O06_ABL2_A2_35827_D3


title: FRP-HF/HS Diet-3

description: Library name: SG86


title: C2_PBC_subject5_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 3, 33864

description: Library name: G052_O06_ABL2_A2_33864_D3


title: B11_PBC_subject5_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 3, 32509

description: Library name: G051_O06_ABL2_A2_32509_D3


title: C1_PBC_subject5_PDC-E2_Treg


title: C3_PBC_subject5_PDC-E2_Treg


title: FRP-HF/HS Diet-2

description: Library name: SG82


title: B12_PBC_subject5_PDC-E2_Treg


title: B10_PBC_subject5_PDC-E2_Treg


title: FR-HF/HS Diet-1

description: Library name: SG81


title: B9_PBC_subject5_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 3, 32119

description: Library name: G050_O06_ABL2_A2_32119_D3


title: C8_PBC_subject5_PDC-E2_Treg


title: FRP-HF/HS Diet-1

description: Library name: SG80


title: B8_PBC_subject5_PDC-E2_Treg


title: B7_PBC_subject5_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 3, 32017

description: Library name: G049_O06_ABL2_A2_32017_D3


title: FR-Regular Diet-6

description: Library name: SG79

value: Regular Diet


title: B6_PBC_subject5_PDC-E2_Treg


title: FRP-Regular Diet-6

description: Library name: SG78


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 3, 35916

description: Library name: G048_O06_ABL2_A1_35916_D3


title: B5_PBC_subject5_PDC-E2_Treg


title: B4_PBC_subject5_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 3, 35890

description: Library name: G047_O06_ABL2_A1_35890_D3


title: B2_PBC_subject5_PDC-E2_Treg


title: B3_PBC_subject5_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 3, 35815

description: Library name: G046_O06_ABL2_A1_35815_D3


title: FR-Regular Diet-5

description: Library name: SG77


title: FR-Regular Diet-4

description: Library name: SG76


title: A11_PBC_subject5_PDC-E2_Treg


title: A9_PBC_subject5_PDC-E2_Treg


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 3, 33900

description: Library name: G044_O06_ABL2_A1_33900_D3


title: FRP-Regular Diet-4

description: Library name: SG74


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 3, 35808

description: Library name: G045_O06_ABL2_A1_35808_D3


title: FRP-Regular Diet-5

description: Library name: SG75


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 3, 33879

description: Library name: G043_O06_ABL2_A1_33879_D3


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 3, 32814

description: Library name: G042_O06_ABL2_A1_32814_D3


title: A5_PBC_subject5_PDC-E2_Treg


title: A8_PBC_subject5_PDC-E2_Treg


title: A10_PBC_subject5_PDC-E2_Treg


title: A7_PBC_subject5_PDC-E2_Treg


title: FR-Regular Diet-3

description: Library name: SG73


title: A4_PBC_subject5_PDC-E2_Treg


title: FR-Regular Diet-2

description: Library name: SG72


title: A6_PBC_subject5_PDC-E2_Treg


title: B1_PBC_subject5_PDC-E2_Treg


title: A12_PBC_subject5_PDC-E2_Treg


title: A3_PBC_subject5_PDC-E2_Treg


title: FR-Regular Diet-1

description: Library name: SG71


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 3, 32485

description: Library name: G040_O06_ABL2_A1_32485_D3


title: A2_PBC_subject5_PDC-E2_Treg


title: A1_PBC_subject5_PDC-E2_Treg


title: FRP-Regular Diet-3

description: Library name: SG70


title: H12_PBC_subject5_PDC-E2_Tconv

value: Tconv


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 3, 32321

description: Library name: G039_O06_ABL2_A1_32321_D3


title: H11_PBC_subject5_PDC-E2_Tconv


title: FRP-Regular Diet-2

description: Library name: SG69


title: H10_PBC_subject5_PDC-E2_Tconv


title: H9_PBC_subject5_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 3, 32215

description: Library name: G038_O06_ABL2_A1_32215_D3


title: H8_PBC_subject5_PDC-E2_Tconv


title: FRP-Regular Diet-1

description: Library name: SG68


title: H6_PBC_subject5_PDC-E2_Tconv


title: Tumor NK cells, sorted, ITDT + anti-CD4, rep 3

city: Oakland

first: Chenyu

last: Zhang

address: 521 33rd St, Unit #2

department: MCB

institute: UC Berkeley

description: Library name: DRCZ37

data_processing:
Differential Gene Expression: Gene expression was modeled using the formula Y_i~0+T, where Y_i is the log-CPM value for gene i, T is the treatment (i.e. PBS, ITDT, or ITDT+aCD4). We then performed three pairwise comparisons (PBS vs ITDT, PBS vs ITDT+aCD4 and ITDT vs ITDT+aCD4) between the three treatment groups to identify genes with significant log2 foldchange >1 and adjusted p-value <0.05). This superset of significantly changing genes was used in downstream analyses. We used enrichR and GSEA for pathway enrichment analysis of the significant genes. For plotting gene quantifications, we transformed the count data using rlog (regularized logarithm) function ><0.05. Plots were generated using ggplot2 package.
Assembly: mm10
Supplementary files format and content: transposed_kallisto_NK_only.csv

source_name: sorted tumor NK cells

extract_protocol:
To prepare RNA, cells were lysed in RLT buffer (Qiagen) containing 1% 2-mercaptoethanol (Thermo Fisher Scientific) before being purified with RNeasy Miniprep kits (Qiagen) and validated with Qubit, bioanalyzer and fragment analyzer (QB3 Genomics, UC Berkeley, Berkeley, CA, RRID:SCR_022170).
Sequencing libraries were prepared using KAPA Hyper Prep Kit (KAPA Biosystems)

value: sorted tumor NK cells

value: NK cells (NK1.1+CD3-)

tag: cell sorting

value: FACS sorting


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 0, 35914

description: Library name: G036_O06_ABL2_A3_35914_D0

tag: tissue

value: day 0


title: H7_PBC_subject5_PDC-E2_Tconv

value: PBMC

value: PBC

value: PDC-E2 peptides


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 0, 35913

description: Library name: G035_O06_ABL2_A3_35913_D0

value: Whole blood

value: male


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 3, 32778

description: Library name: G041_O06_ABL2_A1_32778_D3

value: day 3


title: H5_PBC_subject5_PDC-E2_Tconv


title: Tumor NK cells, sorted, ITDT, rep 3

description: Library name: DRCZ35

value: ITDT

tag: genotype


title: Tumor NK cells, sorted, ITDT + anti-CD4, rep 2

description: Library name: DRCZ32

tag: treatment


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 0, 35910

description: Library name: G034_O06_ABL2_A3_35910_D0

tag: time


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 0, 35889

description: Library name: G033_O06_ABL2_A3_35889_D0

tag: animal id


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 0, 35886

description: Library name: G032_O06_ABL2_A3_35886_D0

tag: Sex


title: G10_PBC_subject5_PDC-E2_Tconv


title: Tumor NK cells, sorted, PBS, rep 2

description: Library name: DRCZ28

value: PBS


title: G6_PBC_subject5_PDC-E2_Tconv


title: G5_PBC_subject5_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 0, 35822

description: Library name: G030_O06_ABL2_A3_35822_D0

tag: dose

value: notprotected


title: Tumor NK cells, sorted, PBS, rep 1

description: Library name: DRCZ23


title: G2_PBC_subject5_PDC-E2_Tconv


title: Tumor NK cells, sorted, ITDT, rep 2

description: Library name: DRCZ30


title: G1_PBC_subject5_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 0, 33877

description: Library name: G028_O06_ABL2_A3_33877_D0

tag: treatment outcome

value: protected


title: G8_PBC_subject5_PDC-E2_Tconv


title: Plaque macrophages, Lipa overexpression, replicate 2

first: Fang

last: Li

department: Medicine

institute: Columbia University Irving Medical Center

description:
Library name: HF25
M-LipaKI2
batch 2

data_processing:
Raw sequencing reads were mapped to the mouse genome version GRCm39 (M33) using Salmon (version 1.10.2) to obtain transcript abundance counts. MultiQC was used to generate quality control reports based on Salmon read mapping results.
The transcript-level count information was summarized to the gene level using tximport (version 1.28.0).
Differential expression was assessed using DESeq2 (version 1.40.0) with batch correction. Genes with an absolute fold change > 1.5 and false discovery rate (FDR) < 0.05 were considered as differentially expressed (DE).
Assembly: mm10
Supplementary files format and content: csv format, Rld normalized counts
Supplementary files format and content: csv format, Salmon Counts

source_name: plaque macrophage

extract_protocol:
Total RNAs were extracted from plaque macrophages using the Quick-RNA miniprep plus kit (Zymo). n = 4 biological replicates per genotype, with each replicate comprising pooled samples from 2-3 male mice, resulting a total of 10 male mice per genotype.
The SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara) was used to reverse transcribe and amplify small amounts of RNA (10 ng per sample). After generating cDNA, the library was prepared using Nextera XT (Illumina).

value: plaque macrophage

value: LysMCre+/-, LipaKI/WT, Ldlr-/-

value: Male


title: H3_PBC_subject5_PDC-E2_Tconv

value: Tconv


title: H4_PBC_subject5_PDC-E2_Tconv


title: H2_PBC_subject5_PDC-E2_Tconv


title: Tumor NK cells, sorted, PBS, rep 3

description: Library name: DRCZ33

value: sorted tumor NK cells

value: NK cells (NK1.1+CD3-)


title: F5_PBC_subject5_PDC-E2_Tconv


title: H1_PBC_subject5_PDC-E2_Tconv


title: G12_PBC_subject5_PDC-E2_Tconv


title: G11_PBC_subject5_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-FLpol/∆pp71-FLgag/nef #6.27, day 3, 32019

description: Library name: G037_O06_ABL2_A1_32019_D3

data_processing:
Trimgalorev0.6.4 used to remove low quality reads and bases
Filtered out globin and rRNA reads using bowtie2v2.1.0
Aligned reads with STARv2.7.3
quantified read counts with  htseqv0.11.2
Assembly: Rhesus macaques version 10 Ensembl annoation v98
Supplementary files format and content: ount matrix

extract_protocol:
Isolation of RNA from Whole Blood Using the RNAdvance Blood Kit – for NHP samples
mRNA Library Prep for RNA from Whole Blood using KAPA HyperPrep Reagents


title: Tumor NK cells, sorted, ITDT + anti-CD4, rep 1

description: Library name: DRCZ27

value: FACS sorting


title: G9_PBC_subject5_PDC-E2_Tconv

value: PBMC


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 0, 35885

description: Library name: G031_O06_ABL2_A3_35885_D0

value: day 0


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 0, 35912

description: Library name: G023_O06_ABL2_A2_35912_D0


title: Tumor NK cells, sorted, ITDT, rep 1

description: Library name: DRCZ25


title: Plaque macrophages, Control, replicate 3

description:
Library name: HF22
Ctrl3
batch 3

value: LysMCre-/-, LipaKI/WT, Ldlr-/-


title: F3_PBC_subject5_PDC-E2_Tconv

value: PBC

value: PDC-E2 peptides


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 0, 33878

description: Library name: G029_O06_ABL2_A3_33878_D0

value: Whole blood

value: male


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 0, 33700

description: Library name: G027_O06_ABL2_A3_33700_D0


title: G7_PBC_subject5_PDC-E2_Tconv


title: F11_PBC_subject5_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 0, 32707

description: Library name: G026_O06_ABL2_A3_32707_D0


title: G3_PBC_subject5_PDC-E2_Tconv


title: F1_PBC_subject5_PDC-E2_Tconv


title: Plaque macrophages, Lipa overexpression, replicate 3

description:
Library name: HF26
M-LipaKI3
batch 3


title: G4_PBC_subject5_PDC-E2_Tconv


title: F9_PBC_subject5_PDC-E2_Tconv


title: Plaque macrophages, Lipa overexpression, replicate 4

description:
Library name: HF27
M-LipaKI4
batch 4


title: F8_PBC_subject5_PDC-E2_Tconv


title: F7_PBC_subject5_PDC-E2_Tconv


title: F6_PBC_subject5_PDC-E2_Tconv


title: Plaque macrophages, Lipa overexpression, replicate 1

description:
Library name: HF24
M-LipaKI1
batch 1


title: Plaque macrophages, Control, replicate 2

description:
Library name: HF21
Ctrl2
batch 2


title: F10_PBC_subject5_PDC-E2_Tconv


title: Whole blood, 68-1miR124 ∆Rh107-pol con/∆pp71-gag/nef con #10.3, day 0, 32689

description: Library name: G025_O06_ABL2_A3_32689_D0


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 0, 35915

description: Library name: G024_O06_ABL2_A2_35915_D0


title: Plaque macrophages, Control, replicate 1

description:
Library name: HF20
Ctrl1
batch 1


title: Plaque macrophages, Control, replicate 4

description:
Library name: HF23
Ctrl4
batch 4


title: Whole blood, 68-1miR124 ∆Rh107-pol hyb/∆pp71-gag/nef hyb #1.6.25, day 0, 35884

description: Library name: G020_O06_ABL2_A2_35884_D0


title: F4_PBC_subject5_PDC-E2_Tconv