title: 72-123-17-I-3

data_processing:
QC on raw reads was processed using fastqc package (version=0.11.8).
Raw reads were aligned to the human GRCh38 genome using HISAT2 (version=2.1.0).
Raw counts were extracted from bam files by featureCounts function (from package subread version=1.6.4).
FPKM values were calculated based on the raw counts.
Genome_build: GRCh38
Supplementary_files_format_and_content: csv files storing the FPKM values per gene per sample

source_name: iPSCs

growth_protocol: hiPSCs were grown on matrigel-coated plates with mTeSR1 or stemflex medium. Cells were maintained at 37 °C with 5% CO2.

extract_protocol: Followed by the instruction of TruSeq Stranded mRNA LP

treatment_protocol: iPSCs or iPSC-derived cells were plated one day before infection and then infected with ZIKV. Cells were incubated with medium containing ZIKV (MOI=0.15) at 37 ºC for 2 hours. At 72hpi, cells were collected for RNA seq.

tag: zika infected

value: infected

tag: iPS cell line


title: THP1_sgMEF2D_2_2

status: Public on Sep 07 2022

type: SRA

city: PHILADELPHIA

first: Zhendong

last: Cao

state: PA

address: BRB Rm620, 421 Curie Blvd

department: Cancer biology

country: USA

institute: university of pennsylvania

library_source: transcriptomic

data_processing:
Sequencing reads were aligned to human genome hg38 using STAR Aligner. Raw read counts were generated via HTSeq-count.
Genome_build: hg38
Supplementary_files_format_and_content: txt, raw read counts

molecule: total RNA

organism: Homo sapiens

source_name: human AML THP1 cell line

growth_protocol: MOLM-13, MV4-11, THP1 and K562 were cultured in RPMI 1640-Media with 25mM HEPES supplemented with 10% Bovine Calf Serum (FCS) and 1% Penicillin/ Streptomycin.

extract_protocol:
Total RNA was isolated from 1~5 million cells using Direct-zol RNA Miniprep Plus kit (ZYMO) with DNase I treatment in column.
RNA-seq libraries were prepared using QuantSeq 3’ mRNA-seq Library Prep Kit (Lexogen) with 0.5-2 µg of total RNA according to the manufacturer's protocol. Library quality was checked by High Sensitivity Bioanalyzer (Agilent) and libraries with different barcodes were pooled and sequenced on the Nextseq 500 platform with 75 or 150 bp single-end reads.

treatment_protocol: MOLM-13 cells were harvested on day 5 post-infection of sgRNA, MV4;11 and K562 cells were harvested on day 4 post-infection, and THP-1 cells were harvested on day 10 post-infection.

tag: post infection

value: day 10 after infection

tag: cell ine


title: p592_H3K27ac

library_source: genomic

data_processing:
reads were aligned to hg19 using Bowtie2 v2.3.5 (Langmead and Salzberg, 2012), following parameters as previously described (Skene et al., 2018): --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 -k1 -N1. Picard tools v1.96 (Broad Institute) was applied to displace presumed PCR duplicates using the MarkDuplicates command. Bam files with uniquely mapped reads retained were generated using Samtools v1.1(Li et al., 2009). Fragments between 40-1000 bp were kept. Blacklist regions defined by ENCODE (ref), random chromosomes, and mitochondria were removed, and filtered bam files were used for further analysis. Reads per kilobase per million mapped reads (RPKM)-normalized bigwig files were created using deeptools bamCoverage (Ramírez et al., 2016) with parameters -bs 10 --smoothLength 50 --normalizedUsing RPKM --skipNAs to visualize binding signals. Tracks were loaded to UCSC genome browser for visualization.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files for binding signals

molecule: genomic DNA

source_name: primary human AML sample #592

growth_protocol: MOLM-13 were cultured in RPMI 1640-Media with 25mM HEPES supplemented with 10% Bovine Calf Serum (FCS) and 1% Penicillin/ Streptomycin.

extract_protocol:
CUT&RUN experiments were slightly modified from a previous protocol (Skene et al., 2018). Concanavalin A-coated beads were washed with Binding buffer (20 mM HEPES-KOH, 10 mM KCl, 1 mM NaCl and 1 mM MnCl2) prior to use. Around 2x106 live cells were collected, washed twice in Wash buffer (150 mM NaCl, 20 mM HEPES-KOH pH 7.9, 0.5 mM Spermidine and protease inhibitor cocktail), and incubated in 1ml of Wash buffer containing 20 μl of Concanavalin A-coated beads for 5-10 min with rotation at room temperature. Cell-attached beads were then resuspended with 300 μl Antibody buffer (Wash buffer with 0.05% Digitonin and 2mM EDTA) in combination with 20 μl MEF2D antibody (Abcam, #ab32845) or 2 μl IgG overnight at 4°C with rotation. Based were washed once with Dig-wash buffer (Wash buffer with 0.05% Digitonin) and resuspended in 300 μl Dig-wash buffer with 700 ng/ml pA-MN purified protein at 4°C for 1 hr with rotation. Beads were then washed twice with Dig-wash buffer, resuspended in Dig-wash buffer and chilled on a heat block on ice. Chromatin digestion was conducted in the presence of CaCl2 for 30 min, and sequestered with an equal volume of 2x STOP solution (340 mM NaCl, 20 mM EDTA, 50 μg/mL RNase A, 4 mM EGTA, 0.02% Digitonin, 50 μg/mL Glycogen and 2 pg/mL heterogenous spike-in DNA) at 37°C for 10 min. The supernatant was collected and DNA was subject to Phenol-Chloroform extraction.
Sequencing libraries were constructed with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina following a previously described method for TF. Adapters were diluted 50x and 10-12 cycles of PCR amplification were applied. Library quality was assessed using the high sensitivity Bioanalyzer kit (Agilent) and libraries were pooled and paired-end sequenced for 2x42bp on the Nextseq 500 platform.
CUT&RUN

tag: cell line

value: primary human AML sample #592

tag: antibody


title: 121-6

type: RNA

city: Copenhagen

first: Lasse

last: Folkersen

address: Artellerivej

department: Bioinformatics

country: Denmark

institute: National Genome Center

hyb_protocol: RNA was hybridized to Affymetrix GeneChip HT HG-U219 arrays, and processed in a Gene Titan Platform (Affymetrix, Santa Clara, USA).

data_processing: The resulting CEL files were pre-processed using the RMA algorithm as implemented in Affymetrix Power Tools, including a log2 transformation step (version 1.16.1) [cite 12925520]. The probes were summarized using custom CDF files remapped to Ensembl genes (Brain array) [PMID 16284200].

label: biotin

molecule: polyA RNA

source_name: sigmoideum

growth_protocol: Human samples, no growth protocol

extract_protocol: All intestinal biopsies were placed immediately in RNAlater (Qiagen) stored in a refrigerator and later transferred to a -80ºC freezer for long time storage until RNA extraction. The biopsy tissue was transferred into a tube and homogenized with Ultra Turrax (IKA, Staufen, Germany), together with 700µl Qiazol reagent (company ref). The quality and concentration of the purified total RNA was investigated on a Bioanalyzer 2100  (Agilent) using the RNA 6000 Nano Labchip kit (Agilent technologies, Santa Clara, CA), and all RNA sample concentrations were measured on a ND-8000 NanoDrop (Thermo Fisher Scientific, Waltham, MA).  RNA quality was evaluated based on the 28S/18S ratio RIN (RNA integrity number. The RIN value from the human biopsy materials varied but all values above 7 were used for Array. RNA was stored at -80°C until use.

treatment_protocol: Mucosal biopsies were obtained from patients with chronic inflammatory bowel disease (IBD), ulcerative colitis (UC) or Crohn’s disease (CD) diagnosed according to generally accepted standard (Lennard-Jones PMID 2617184). Consecutively included were IBD patients followed at the IBD clinic Northsealand Hospital and referred to colonoscopy or sigmoidoscopy due to clinical activity of at least 14 days duration. As control patients were included persons referred to endoscopy for reasons other than IBD revealing normal endoscopy. Exclusion criteria were for IBD patients and controls: age below 18 years, any gastrointestinal disease other than IBD, malignant disease, or known autoimmune disease not associated to IBD. Totally 109 biopsy donors were included, 53 UC, 25 CD, and 28 controls.

tag: patient

tag: biopsy

tag: age

tag: diagnosis

value: Control

tag: gastroscopy

value: FALSE

tag: inflammation

value: non

tag: tissue

value: sigmoideum


title: Gallus gallus utricle, cell-001

city: South San Francisco

first: Daniel

middle: C

last: Ellwanger

state: CA

address: 1120 Veterans Blvd

department: Genome Analysis Unit

institute: Amgen Inc

library_source: transcriptomic single cell

data_processing:
Reads were aligned to the NCBI Gallus gallus v6.0 (GCF_000002315.6) reference genome and gene expression values were quantified with a customized STAR-RSEM pipeline for single-cell data.
FastQC and Scater were used for quality control.
Low-quality cells, ERCC spike-in transcripts, and low-level expressed genes were removed.
Assembly: NCBI Gallus gallus v6.0 (GCF_000002315.6) reference genome
Supplementary files format and content: Tab-separated values file reporting counts

organism: Gallus gallus

source_name: Utricle sensory epithelia

extract_protocol:
Utricles were dissected in ice-cold Medium 199, otolithic membranes were mechanically removed, and tissue was incubated in thermolysin (0.5 mg/mL M199 medium) for 20 minutes at 37°C. Thermolysin activity was attenuated with 10% FBS in M199. The sensory epithelia were carefully peeled off from the underlying stromal cells using a 30- gauge 1⁄2-inch hypodermic needle attached to a 1 mL syringe. For each experiment, we pooled 4-8 sensory epithelia. The epithelia were dissociated using 1X Accutase for 20 minutes at 37°C, followed by mild mechanical trituration, and washed twice with PBS using a centrifugation step (300 x g, 5 min, room temperature (RT)). Viable single cells were isolated with a Becton Dickinson FACSAria Fusion flow cytometer (Ellwanger et al., 2018). Two independent batches of 270 cells were deposited into individual wells of 96-well plates, prefilled with 4 μl of a premade lysis solution with 1 U/μl of recombinant RNase inhibitor, 0.1% Triton X-100, 2.5 mM dNTP mix, 2.5 μM oligo d(T)30 VN (5’-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’, IDT). Plates containing sorted cells were immediately sealed, frozen on dry ice, and stored at −80°C.
Single-cell RNA-seq was performed via Picelli and colleagues’ method (Picelli et al., 2014) using SMARTscribe for reverse transcription followed by 22 amplification cycles. Amplified cDNAs were purified by AMPure Beads cleanup using a Biomek FX automated platform and assessed with a fragment analyzer (Agilent) for quantitation and quality assurance. Barcoded libraries were synthesized using a scaled-down Nextera XT protocol (Mora-Castilla et al., 2016) in a total volume of 4 μl. A total of 384 libraries were pooled, and paired-end sequenced (2 x 150 bp) on a NextSeq 500/550 High Output flow cell.

value: Utricle sensory epithelia

tag: genotype

value: Wildtype

value: Posthatch day 7 (P7)

tag: well plate

tag: plate position


title: Gallus gallus utricle, cell-002


title: K562_sgMEF2D_2

source_name: human CML K562 cell line

value: day 4 after infection


title: PBRM1 KO3 Untreated - RNA-seq

city: London

first: HUGANG

last: FENG

address: Chester Beatty Laboratories, 237 Fulham Road

department: Cancer Biology

country: United Kingdom

institute: The Institute of Cancer Research

data_processing:
Bcl2fastq software (v2.2.20, Illumina) was used for converting the raw basecalls to fastqs and to further demultiplex the sequencing data
The STAR alignment software (v.2.5.1b) was used to align reads to the reference genome
HTSeq-count (HTSeq v0.6.1) was used to count the number of reads mapping unambiguously to genomic features in each sample
Normalised count data was generated in R using the Bioconductor package DESeq2 (v1.14.1)
The normalised data was filtered further to remove all the rows where the row sum was less than 1
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: Excel spreadsheet with normalised gene counts for every gene and every sample

source_name: Immortalised fibroblast cell line

growth_protocol: 1BR3-hTERT cells were cultured in DMEM medium with 10% FBS and 1% Penicillin-Streptomycin

extract_protocol:
Cell pellets were subjected to Trizol lysis and RNA extraction with ZYMO Direct-zol RNA purification kit
RNA libraries were prepared for sequencing using NEBNext rRNA Depletion Kit (Human/Mouse/Rat) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

treatment_protocol: 6Gy X-ray ionising radiation for Sample 4-6

tag: cell strain

value: PBRM1 Knockout

tag: treatment

value: 48hr post 6Gy X-ray treatment


title: 6_15_CD4

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

data_processing:
Illumina Casava1.7 software used for basecalling.
Transcript counts calculated from Fastq files using Kallisto.
Transcript counts summarized to gene counts using tximport.
Abundance (logTPM) and estimated count measures from tximport normalized using TMM and filtered for expressed genes.
Assembly: hg19

extract_protocol:
Tumor infiltrating immune cells (TIICs) were obtained from a non-necrotic tumor piece at approximately 2 cm in diameter that could be spared for research purpose after the clinical specimens were prioritized and were dissected by pathologist. RPMI-1640 media were used to resuspend all the cells after disruption and homogenization. The cell suspension was filtered with a 70Œºm cell strainer and a layer of mononuclear cells that contained TIICs were then isolated using the Ficoll density gradient centrifugation with Ficoll-Paque‚Ñ¢ PLUS (Cytiva) as described 39. TIICs were washed three times using 40 ml of the complete RPMI media each time. After the final wash with the RPMI media, isolated TIICs were cryopreserved in the liquid nitrogen freezer or subjected to cell sorting. Peripheral blood mononuclear cells were obtained from patient‚Äôs whole blood using the Ficoll-Paque‚Ñ¢ PLUS gradient centrifugation to serve as the FACS staining control. TIICs and peripheral blood mononuclear cells were stained with the Zombie Green viability dye (Biolegend), anti-CD4-PE-CF594 (Biolegend), anti-CD8-APC (Biolegend), anti-CD19-PE (Biolegend), and anti-CD11b-BV421 (Biolegend) antibodies. After sorting with the BD FACSAria IIu Cell Sorter (Biosciences), bulk tumor RNA was extracted by using the All Prep DNA/RNA Micro Kit (Qiagen) according to the manufacturer‚Äôs instruction and sent to a commercial vendor (BGI Genomics) for whole transcriptomic RNA sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell type

tag: arm

tag: os

tag: cd66b gr_status

tag: treg status

tag: cd8 cd137_status

tag: m1 status

tag: m2 status

tag: jtm normcount_inc

value: Y

tag: jtm tpm_inc

value: N

tag: cancercell inc

tag: cd4 th17_status


title: K562_sgNeg_1_2

tag: post infection

tag: cell ine


title: THP1_sgNeg_1


title: 6_15_RLT_CD19


title: 87-1

scan_protocol: RNA was hybridized to Affymetrix GeneChip HT HG-U219 arrays, and processed in a Gene Titan Platform (Affymetrix, Santa Clara, USA).

source_name: transversum

tag: patient

tag: biopsy

tag: age

tag: diagnosis

value: CD

tag: gastroscopy

tag: inflammation

value: yes

tag: tissue

value: transversum


title: 17-1

source_name: descendens

label_protocol: RNA was hybridized to Affymetrix GeneChip HT HG-U219 arrays, and processed in a Gene Titan Platform (Affymetrix, Santa Clara, USA).

value: UC

value: descendens


title: 120-3

value: Control


title: K562_sgNeg_1_1


title: 6_15_CD11b

tag: cell type

tag: arm

tag: os

tag: cd66b gr_status

tag: treg status


title: A40_J15237_P26_CD19

tag: cd8 cd137_status

tag: m1 status

tag: m2 status

tag: jtm normcount_inc

tag: jtm tpm_inc


title: 85-2

source_name: rectum

tag: patient

value: FALSE

value: rectum


title: MV4-11_sgNeg_1

source_name: human AML MV4-11 cell line

tag: post infection

tag: cell ine


title: A38_J15237_P26_CD8

tag: cancercell inc

tag: cd4 th17_status


title: 111-3

source_name: coecum

tag: biopsy

tag: age

tag: diagnosis

tag: gastroscopy

tag: inflammation

value: non

value: coecum


title: 14-1

tag: tissue


title: 72-123-17-I-2

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

tag: zika infected

value: infected

tag: iPS cell line

tag: genotype


title: THP1_sgMEF2D_2_1

value: day 10 after infection


title: WT-1-I-1

value: WT{delta}


title: 42-6


title: 6_15_RLT_CD11b

tag: cell type

tag: arm

tag: os

tag: cd66b gr_status

tag: treg status

tag: cd8 cd137_status

tag: m1 status

tag: m2 status


title: 72-123-17-I-1


title: 6_15_CD8

tag: jtm normcount_inc

tag: jtm tpm_inc

tag: cancercell inc

tag: cd4 th17_status


title: THP1_sgNeg_2

tag: post infection

tag: cell ine


title: 72-123-17-M-3

tag: zika infected

value: mock


title: WT-1-M-3

tag: iPS cell line


title: 35-6

tag: patient

tag: biopsy

tag: age

tag: diagnosis

tag: gastroscopy

tag: inflammation

tag: tissue

value: sigmoideum


title: 14-3


title: 72-123-17-M-2

tag: genotype


title: MOLM13_sgNeg_2

source_name: human AML MOLM-13 cell line

value: day 5 after infection


title: A35_J15237_P19_CD11b

tag: cell type

tag: arm

tag: os

tag: cd66b gr_status

tag: treg status

tag: cd8 cd137_status

tag: m1 status

tag: m2 status

value: Y

value: N


title: MV4-11_sgMEF2D_2

tag: post infection

value: day 4 after infection

tag: cell ine


title: 6_15_CD19

tag: jtm normcount_inc

tag: jtm tpm_inc

tag: cancercell inc

tag: cd4 th17_status


title: WT-1-M-1

tag: zika infected

tag: iPS cell line


title: 72-123-17-M-1

tag: genotype


title: MOLM13_sgNeg_1


title: 85-1

tag: patient

tag: biopsy

tag: age

tag: diagnosis

tag: gastroscopy

tag: inflammation

value: yes

tag: tissue


title: 14-2

source_name: ascendens

value: ascendens


title: A33_J15237_P19_CD4

tag: cell type

tag: arm

tag: os

tag: cd66b gr_status

tag: treg status

tag: cd8 cd137_status

tag: m1 status

tag: m2 status


title: MOLM13_IgG_control

data_processing:
Library strategy: CUT&RUN
reads were aligned to hg19 using Bowtie2 v2.3.5 (Langmead and Salzberg, 2012), following parameters as previously described (Skene et al., 2018): --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 -k1 -N1. Picard tools v1.96 (Broad Institute) was applied to displace presumed PCR duplicates using the MarkDuplicates command. Bam files with uniquely mapped reads retained were generated using Samtools v1.1(Li et al., 2009). Fragments between 40-1000 bp were kept. Blacklist regions defined by ENCODE (ref), random chromosomes, and mitochondria were removed, and filtered bam files were used for further analysis. Reads per kilobase per million mapped reads (RPKM)-normalized bigwig files were created using deeptools bamCoverage (Ramírez et al., 2016) with parameters -bs 10 --smoothLength 50 --normalizedUsing RPKM --skipNAs to visualize binding signals. Tracks were loaded to UCSC genome browser for visualization.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files for binding signals

extract_protocol:
CUT&RUN experiments were slightly modified from a previous protocol (Skene et al., 2018). Concanavalin A-coated beads were washed with Binding buffer (20 mM HEPES-KOH, 10 mM KCl, 1 mM NaCl and 1 mM MnCl2) prior to use. Around 2x106 live cells were collected, washed twice in Wash buffer (150 mM NaCl, 20 mM HEPES-KOH pH 7.9, 0.5 mM Spermidine and protease inhibitor cocktail), and incubated in 1ml of Wash buffer containing 20 μl of Concanavalin A-coated beads for 5-10 min with rotation at room temperature. Cell-attached beads were then resuspended with 300 μl Antibody buffer (Wash buffer with 0.05% Digitonin and 2mM EDTA) in combination with 20 μl MEF2D antibody (Abcam, #ab32845) or 2 μl IgG overnight at 4°C with rotation. Based were washed once with Dig-wash buffer (Wash buffer with 0.05% Digitonin) and resuspended in 300 μl Dig-wash buffer with 700 ng/ml pA-MN purified protein at 4°C for 1 hr with rotation. Beads were then washed twice with Dig-wash buffer, resuspended in Dig-wash buffer and chilled on a heat block on ice. Chromatin digestion was conducted in the presence of CaCl2 for 30 min, and sequestered with an equal volume of 2x STOP solution (340 mM NaCl, 20 mM EDTA, 50 μg/mL RNase A, 4 mM EGTA, 0.02% Digitonin, 50 μg/mL Glycogen and 2 pg/mL heterogenous spike-in DNA) at 37°C for 10 min. The supernatant was collected and DNA was subject to Phenol-Chloroform extraction.
Sequencing libraries were constructed with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina following a previously described method for TF. Adapters were diluted 50x and 10-12 cycles of PCR amplification were applied. Library quality was assessed using the high sensitivity Bioanalyzer kit (Agilent) and libraries were pooled and paired-end sequenced for 2x42bp on the Nextseq 500 platform.

tag: cell line

tag: antibody

value: IgG (Sigma I8140)

tag: infection

value: not infected


title: MV4-11_sgMEF2D_1

tag: post infection

tag: cell ine


title: A32_J15237_P18_CD19

value: Control

tag: jtm normcount_inc

tag: jtm tpm_inc

tag: cancercell inc

tag: cd4 th17_status


title: WT-1-I-3

tag: zika infected

tag: iPS cell line

tag: genotype


title: MOLM13_MEF2D_sgMEF2D_d5

value: MEF2D (abcam #ab32845)

value: Cells were collected on day 5 post-infection of sgRNA


title: 115-3

tag: patient

tag: biopsy

tag: age

tag: diagnosis

value: UC

tag: gastroscopy

value: FALSE

tag: inflammation

tag: tissue

value: rectum


title: MV4-11_sgNeg_2


title: WT-1-I-2

value: infected

value: WT{delta}


title: 35-4

value: transversum


title: KO3-M-3

value: mock


title: MOLM13_MEF2D

tag: cell line

tag: antibody

tag: infection


title: A37_J15237_P26_CD4

tag: cell type

tag: arm

tag: os

tag: cd66b gr_status

tag: treg status

tag: cd8 cd137_status

tag: m1 status

tag: m2 status

tag: jtm normcount_inc

value: Y


title: MOLM13_sgPU.1_1

tag: post infection

value: day 5 after infection

tag: cell ine


title: 83-2

tag: patient

tag: biopsy

tag: age

tag: diagnosis

tag: gastroscopy

value: non

value: descendens


title: A36_J15237_P19_CD19

tag: jtm tpm_inc

value: N

tag: cancercell inc

tag: cd4 th17_status


title: WT-1-M-2

tag: zika infected

tag: iPS cell line

tag: genotype


title: MOLM13_sgPU.1_2


title: 14-5

tag: inflammation

tag: tissue

value: sigmoideum


title: 42-5


title: A34_J15237_P19_CD8

tag: cell type

tag: arm

tag: os

tag: cd66b gr_status

tag: treg status

tag: cd8 cd137_status

tag: m1 status

tag: m2 status


title: 109-1

tag: patient

tag: biopsy

tag: age

tag: diagnosis

tag: gastroscopy


title: KO3-I-3

tag: zika infected

tag: iPS cell line


title: KO3-I-2

tag: genotype


title: MOLM13_dI8_24hr_dTAG_H3K4me1

data_processing:
Reads were aligned to human genome hg19 using Bowtie2 v2.3.5 , following parameters as previously suggested (Skene et al., 2018): --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 -k1 -N1. Picard tools v1.96 was used to remove presumed PCR duplicates using the MarkDuplicates command. Bam files containing uniquely mapped reads were created using Samtools v1.1. Fragments of <40 bp or >1000 bp were filtered out. Blacklist regions defined by ENCODE, random chromosomes, and mitochondria were removed, and filtered bam files were used for downstream analysis. Read count per million (RPM)-normalized bigwig files were created by bedGraphToBigWig (UCSC).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig, gene track

growth_protocol: MOLM-13 cells were cultured in RPMI 1640-Media with 25mM HEPES supplemented with 10% Bovine Calf Serum (FCS) and 1% Penicillin/ Streptomycin.

extract_protocol:
For all the experiments, cells were collected in culture media, and crosslinked in 1% formaldehyde for 20 min at room temperature, and the reaction was sequestered with 0.125M Glycine in PBS for 10 min. The crosslinked cells were spun down, washed with PBS and freezed in -80°C until use. Ten million cells were used for H3K27ac and H3K4me1, and 50 million cells for the SPI1, respectively. Cell pellets were lysed in cell lysis buffer (10mM Tris pH 8.0, 10 mM NaCl, 0.2% NP-40) with protease inhibitor (Roche) and incubated for 15 min on ice. The cells were spun down for 30 seconds at 4,200 RPM and the buffer was removed. The cells were resuspended in 1ml nuclear lysis buffer (50 mM Tris pH 8.0, 10 mM EDTA, 1% SDS) per 10 million cells, followed by a 10 min incubation on ice. The cells were sonicated with a bioruptor for 5 mins at 4°C and spun down at max speed for 15 mins at 4°C. Supernatants containing fragmented chromatins were collected, diluted with 7ml IP dilution buffer (20 mM Tris pH 8.0, 2 mM EDTA, 50 mM NaCl, 1% Triton X-100, 0.01% SDS) per 10 million cells, and applied with respective antibodies (PU.1: 10 μg, CST#2266; H3K27ac: 2 μg, #ab4729, H3K4me1: 2μg, #ab8895). For each antibody, 30 μl of protein A magnetic beads (Invitrogen) were applied after washing with 0.5% BSA in TBS for 3 times and blocked at 4°C on a rotor for 2h. The mixture was incubated overnight at 4°C in rotation. The beads were washed once with IP wash I buffer (20 mM Tris pH 8.0, 2 mM EDTA, 50 mM NaCl, 1% Triton X-100, 0.01% SDS), twice with high salt buffer (20 mM Tris pH 8.0, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.01% SDS), once with IP wash 2 buffer (10 mM Tris pH 8.0, 1 mM EDTA, 0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate), and twice with 1xTE. The beads were incubated with 200 μl elution buffer (50mM Tris 8.0,10mM EDTA, 1%SDS), vortexed 3x for 5s, followed by shaking at 950 RPM at 65°C for 15 mins. Supernatants were collected, and reverse crosslinking was performed in 0.25M NaClat 65°C overnight. non-DNA content was eliminated with 2 μl RNase A for 1 hr at 37 °C, followed by 0.2 mg/ml Proteinase K for 2 hr at 42°C.
ChIP DNA was purified using QIAquick PCR purification kit according to manufacturer’s instructions, and eluted with 40 μl water. ChIP-seq libraries were constructed using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (E7645L), and the optimal cycle numbers were determined by NEBNext® Library Quant Kit for Illumina (E7630L). Library quality was assessed using the high sensitivity Bioanalyzer kit (Agilent) and libraries were pooled and single-end sequenced for 75 bp on the Nextseq 500 platform.

treatment_protocol: For targeted degradation, MOLM13-dIRF8 (cells derived from MOLM13 expressing degradable IRF8 via dTAG system with endogenous IRF8 depletion) cells were treated with either DMSO or 500 nM dTAG-47 compound and collected at 4h and 24h timepoints.

tag: cell line

tag: antibody

tag: treatment

value: dTAG


title: KO3-I-1


title: 14-4

value: Control

tag: inflammation

tag: tissue


title: 83-1

value: yes


title: MOLM13_MEF2D_sgNeg1_d5

value: MEF2D (abcam #ab32845)

tag: infection

value: Cells were collected on day 5 post-infection of sgRNA


title: WT2-I-2

value: WT


title: A26_P_41_CD8

tag: cell type

tag: arm

value: B

tag: os

tag: cd66b gr_status

value: High

tag: treg status

tag: cd8 cd137_status

value: Low

tag: jtm normcount_inc

tag: jtm tpm_inc

tag: cancercell inc

tag: cd4 th17_status


title: 105-1

tag: patient

tag: biopsy

tag: gastroscopy

value: FALSE

value: transversum


title: A31_J15237_P18_CD11b

tag: m1 status

tag: m2 status

value: Y


title: A25_P_41_CD4


title: A30_J15237_P18_CD8


title: WT2-I-3

tag: zika infected

value: infected

tag: iPS cell line

tag: genotype


title: A29_J15237_P18_CD4

tag: cell type

tag: arm


title: KO3-M-2

value: mock


title: MOLM13_input_forH3K27ac

tag: cell line

tag: antibody

tag: treatment


title: 82-3

tag: age

tag: diagnosis

value: UC

tag: tissue

value: rectum


title: MOLM13_H3K27ac_ChIP


title: 97-2

tag: inflammation

value: descendens


title: MOLM13_dI8_24hr_DMSO_H3K4me1

value: DMSO


title: KO3-M-1


title: A23_P_17_CD11b

tag: os

tag: cd66b gr_status

tag: treg status

tag: cd8 cd137_status

tag: jtm normcount_inc

tag: jtm tpm_inc

tag: cancercell inc

tag: cd4 th17_status


title: 28-2

tag: patient

tag: biopsy

tag: gastroscopy

value: non

value: sigmoideum


title: A28_P_41_CD19

tag: cell type

tag: arm

tag: m1 status

tag: m2 status


title: A27_P_41_CD11b


title: MOLM13_dI8_24hr_dTAG_H3K27ac

tag: cell line

tag: antibody

tag: treatment

value: dTAG


title: MOLM13_dI8_24hr_dTAG_input


title: 100-5

tag: age

tag: diagnosis

value: CD

tag: inflammation

tag: tissue


title: WT2-M-3

tag: zika infected

tag: iPS cell line

tag: genotype

value: WT


title: MOLM13_dI8_4hr_dTAG_SPI1

value: PU.1 (Cell Signaling Technology (Cat #:2266)


title: A24_P_17_CD19

value: B

tag: os

tag: cd66b gr_status

value: High

tag: treg status

tag: cd8 cd137_status

tag: jtm normcount_inc

tag: jtm tpm_inc

tag: cancercell inc

tag: cd4 th17_status


title: 82-2

tag: patient

tag: biopsy

tag: gastroscopy

value: FALSE


title: A21_P_17_CD4

tag: cell type

tag: arm

tag: m1 status

tag: m2 status


title: 14-6

tag: age

tag: diagnosis

value: Control

tag: inflammation

tag: tissue


title: MOLM13_dI8_24hr_DMSO_H3K27ac

tag: cell line

tag: antibody

tag: treatment


title: MOLM13_dI8_4hr_dTAG_H3K4me1


title: WT2-M-1

tag: zika infected

tag: iPS cell line

tag: genotype


title: MOLM13_dI8_4hr_dTAG_H3K27ac


title: WT2-M-2


title: MOLM13_dI8_24hr_DMSO_input


title: H8-M-3

description: FPKM-SNP.csv

value: risk (G/G; C/C)


title: WT2-I-1

value: infected


title: A22_P_17_CD8

tag: os

tag: cd66b gr_status

tag: treg status

tag: cd8 cd137_status

tag: jtm normcount_inc

value: Y

tag: jtm tpm_inc

tag: cancercell inc

tag: cd4 th17_status


title: 25-3

tag: patient

tag: biopsy

tag: age

tag: diagnosis

tag: gastroscopy

value: transversum


title: 82-1

value: UC

tag: tissue


title: H8-I-3

description: FPKM-SNP.csv

tag: zika infected


title: H8-I-2

description: FPKM-SNP.csv

tag: iPS cell line


title: MOLM13_dI8_4hr_DMSO_SPI1

tag: cell line

tag: antibody

tag: treatment


title: H8-M-2

description: FPKM-SNP.csv

value: mock

tag: genotype


title: A16_P_2_CD19

tag: cell type

tag: arm

value: A

tag: os

tag: cd66b gr_status

tag: treg status

value: Low

tag: cd8 cd137_status

tag: m1 status

tag: m2 status


title: 16-1

tag: patient

tag: biopsy

tag: age

tag: diagnosis

tag: inflammation

value: non

value: descendens


title: H8-M-1

description: FPKM-SNP.csv

tag: zika infected

tag: iPS cell line


title: A20_P_42_CD19

tag: jtm normcount_inc

tag: jtm tpm_inc

tag: cancercell inc

tag: cd4 th17_status


title: 53-6

tag: gastroscopy

tag: tissue

value: rectum


title: 92-5

value: sigmoideum


title: A19_P_42_CD11b

tag: cell type

tag: arm

tag: os

tag: cd66b gr_status

tag: treg status


title: H8-I-1

description: FPKM-SNP.csv

tag: genotype


title: A17_P_42_CD4

tag: cd8 cd137_status

tag: m1 status

tag: m2 status


title: MOLM13_dI8_4hr_dTAG_input

tag: cell line

tag: antibody

tag: treatment

value: dTAG


title: 9137-I-2

description: FPKM-SNP.csv

tag: zika infected

tag: iPS cell line

value: non-risk (T/T; T/T)


title: 9137-I-3

description: FPKM-SNP.csv


title: MOLM13_dI8_4hr_DMSO_H3K27ac

value: DMSO


title: A14_P_2_CD8

value: High

tag: jtm normcount_inc

tag: jtm tpm_inc

tag: cancercell inc

tag: cd4 th17_status


title: 21-1

tag: patient

tag: biopsy

tag: age

tag: diagnosis

tag: gastroscopy

value: FALSE

tag: inflammation

tag: tissue


title: 9137-I-1

description: FPKM-SNP.csv

tag: genotype


title: A18_P_42_CD8

tag: cell type

tag: arm

tag: os

tag: cd66b gr_status

tag: treg status

tag: cd8 cd137_status

tag: m1 status

tag: m2 status


title: A15_P_2_CD11b

tag: jtm normcount_inc

tag: jtm tpm_inc

tag: cancercell inc

tag: cd4 th17_status


title: 17-2

tag: patient

tag: biopsy

tag: age

tag: diagnosis

value: yes


title: NAcc, EcoliHS, Coc, Proteo6

city: Madison

first: Santiago

last: Cuesta

state: Wisconsin

address: 3205 Microbial Sciences Building - 1550 Linden Drive

department: Department of Medical Microbiology and Immunology

institute: University of Wisconsin School of Medicine and Public Health

data_processing:
Base-calling software: Illumina CASAVA
Reads were trimmed and clipped for quality control using FASTQC software
Read alignment software: TopHat2
Raw and normalized counts were generated using featureCounts and Cufflinks softwares
Differential expression analysis software: iDEP9.1 using the DESeq2 package
Enrichment analysis software: iDEP9.1 based on the hypergeometric distribution using the KEGG database
Assembly: mm9
Supplementary files format and content: tab-delimited text file reports normalized counts for each sample
Supplementary files format and content: colum-delimited excel file reports direction, adj.Pva, nGenes, Pathways and Genes significantly changed when comparing FMT-reconstituted mice vs proteobacteria-reconstituted mice (DescN and EcoliHS combined)

organism: Mus musculus

source_name: Brain, NAcc

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
DNAse-treated RNA were prepared with TruSeq Stranded Total RNA LT Sample Prep kit from Illumina. Poly-A RNA was purified and fragmented before strand specific cDNA synthesis. cDNA were then A-tailed and indexed adapters were ligated. After adapter ligation, samples were PCR amplified and purified with Ampure XP beads, then validated and quantified again using Agilent 2100 Bioanalyzer and Qubit fluorimeter. Then, cDNA libraries were sequenced on an Illumina HiSeq 2500 platform using SBS v3 reagents.

treatment_protocol: Brain punches of the NAcc of mice were collected 24 hs after the last injection of a 5 day repeated cocaine treatment (15mg/kg i.p.) in animals antibiotic-treated reconstituted with a full microbiota (FMT, fecal microbiota transplant) or with a proteobacteria representative (Citrobacter rodentium DescN or Escherichia coli HS)

tag: tissue

value: Brain, NAcc

tag: Sex

value: Male

tag: microbiota

value: E coli HS

tag: genotype

value: WT

tag: treatment

value: Cocaine (15mg/kg, i.p.)


title: MOLM13_dI8_4hr_DMSO_input

tag: cell line

tag: antibody


title: A13_P_2_CD4

tag: cell type

tag: arm

value: A

tag: os

tag: cd66b gr_status

tag: treg status

tag: cd8 cd137_status

tag: m1 status

value: Y


title: 46-2

tag: patient

tag: biopsy

value: UC

tag: gastroscopy

tag: inflammation


title: 127-3

tag: age

tag: diagnosis

value: CD

tag: tissue


title: 16-2


title: MOLM13_dI8_4hr_DMSO_H3K4me1

tag: treatment


title: 9137-M-3

description: FPKM-SNP.csv

tag: zika infected

value: mock

tag: iPS cell line

tag: genotype


title: NAcc, EcoliHS, Coc, Proteo4

tag: Sex

tag: microbiota


title: A12_P_24_CD19

tag: cell type

tag: arm

value: B

tag: os

tag: cd66b gr_status

value: Low

tag: m2 status

tag: jtm normcount_inc

tag: jtm tpm_inc

tag: cancercell inc

tag: cd4 th17_status


title: 9137-M-1

description: FPKM-SNP.csv

value: non-risk (T/T; T/T)


title: NAcc, DescN, Coc, Proteo3

value: C. rodemtium DescN


title: A11_P_24_CD11b

value: High

tag: treg status

tag: cd8 cd137_status

tag: m1 status


title: 81-2

tag: patient

tag: biopsy

tag: age

tag: diagnosis

tag: gastroscopy

value: FALSE

tag: inflammation

value: non

tag: tissue

value: coecum


title: 124-3

value: descendens


title: 9137-M-2

description: FPKM-SNP.csv

tag: zika infected

tag: iPS cell line

tag: genotype


title: NAcc, DescN, Coc, Proteo2

value: Brain, NAcc

tag: Sex

value: Male

tag: microbiota

tag: treatment


title: 1_05_CD8

tag: cell type

tag: arm

value: Control

tag: os

tag: cd66b gr_status

tag: m2 status

tag: jtm normcount_inc

tag: jtm tpm_inc

value: N

tag: cancercell inc

tag: cd4 th17_status


title: 15-1

source_name: ileum

tag: patient

tag: biopsy

tag: age

tag: diagnosis

tag: gastroscopy

tag: inflammation

value: ileum


title: 81-1

value: yes

tag: tissue


title: A10_P_24_CD8

tag: treg status

tag: cd8 cd137_status

tag: m1 status

value: Y


title: IPS19-I-1

description: FPKM-ips.csv

tag: zika infected

value: infected

tag: iPS cell line

tag: genotype

value: WT


title: IPS19-I-3

description: FPKM-ips.csv


title: 1_05_CD4

tag: cell type

tag: arm

tag: os

tag: cd66b gr_status

tag: m2 status

tag: jtm normcount_inc


title: IPS19-I-2

description: FPKM-ips.csv


title: scNanoATAC_mESC

city: Beijing

first: Fuchou

last: Tang

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

country: China

institute: Biomedical Pioneering Innovation Center, Peking University

description: Single-cell long-read ATAC-seq of mouse embryonic stem cell

data_processing:
To call fastq from electric signals of Oxford Nanopore sequencing, we used MinKNOW (v20.06.18), MinKNOW Core (v4.0.5), Bream (v6.0.10), and Guppy (v4.0.11).
Single cells of each library were demultiplexed by nanoplexer (v0.1). According to our double barcode design of library structure, demultiplexing were performed twice on outer and inner barcodes in succession.
Adaptors of single-cell demultiplexed reads were removed by cutadapt (v3.2). The adaptor sequences include 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG' at 5' ends and 'CTGTCTCTTATACACATCTCCGAGCCCACGAGA' at 3' ends. Once at least 12 bases on each read were matched with adaptor sequences, those bases were to be removed. As sequencing error is common for long-read sequencing, the mismatch error tolerance of base matching was set as 0.2. We also filtered reads shorter than 1Kb, which are rare in our long-read libraries.
Trimmed reads were aligned to reference genome in 'map-ont' mode by minimap2 (v2.17-r941). Reads with mapping quality less than 30 were filtered by samtools (v1.10). PCR duplicates were removed by single cell with 'samtools rmdup'.
To generate chromatin accessibility signal, single-cell long ATAC-seq mapped reads were converted from bam to bed by 'bamtobed' command of bedtools (v2.30.0). Then both ends of each read were extracted by 'bedtools flank' command with 1 bp flanking size. Those ends of reads are regarded as chromatin accessibility signal and merged by single cell into fragment files for each library.
Fragment files of libraries were input to ArchR (v1.0.2) to generate arrow files with 'createArrowFiles' function.
In ArchR analysis of single-cell ATAC-seq signal, cells with fragment count > 10k and TSS enrichment > 1 were kept. Pseudo bulk coverage tracks by cell line were generated by 'addGroupCoverages' function. Peak calling sets by cell line were calculated by 'addReproduciblePeakSet' function with 0.01 as adjusted P value cut-off.
We phased long reads from scNanoATAC-seq library of GM12878 by 'haplotag' command of whatshap (v1.2.1) based on the benchmark SNP from GIAB. We test significance of bias on each peak of GM12878 by 'binom.test(c(mat, pat), p=0.5)' in R, where 'mat' and 'pat' are counts of allele-specific ends inside each peak.
After testing all candidate peaks, we made multiple test corrections with methods of Benjamini-Hochberg, and the FDR was set to 0.05. Significantly biased peaks were divided into paternal or maternal peaks according to the strength of accessibility by haplotype.
Genome_build: hg38 for human; mm10 for mouse
Supplementary_files_format_and_content: Bigwig files recorded ATAC-seq signal strength tracks. Bed files recorded coordinates of ATAC-seq peaks called by MACS2 (`-llocal 500000`).

source_name: Mouse embryonic stem cell

growth_protocol: K526 cells were cultured in RPMI-1640 (Gibco; 11875093) supplemented with 10% fetal bovine serum (Gibco; 26140079). HEK293T, HFF1 and MEF cells were cultured in DMEM (Gibco; 11995040) supplemented with 10% fetal bovine serum.  GM12878 cells were cultured in RPMI-1640 supplemented with 15% fetal bovine serum. eHAP1 cells were cultured in IMDM (Gibco; 12440053) supplemented with 10% fetal bovine serum. Mouse embryonic stem cells (mESCs) were cultured without feeders in equal volume of Dulbecco’s modified eagle’s medium (DMEM/F-12, Gibco; 11320033) and Neurobasal Medium (Gibco; 21103049) supplemented with 1,000 U/ml leukemia inhibitory factor (LIF, Millipore, ESG1107), 0.5× N-2 (Gibco, 17502048), 0.5× B-27 (Gibco, 10889038), 50 μg/ml Bovine Serum Albumin (BSA, Sigma-Aldrich, A3311), 2 mM L-Glutamine (Gibco, 2503081), 0.1 mM β-Mercaptoethanol (Sigma-Aldrich, M7522), 1× MEM Non-Essential Amino Acids Solution (NEAA, Gibco, 11140050), 100 U/ml Penicillin and 0.1mg/ml Streptomycin (Gibco, 15140122).

extract_protocol:
Cells (100,000-200,000 cells before freezing) were quickly thawed at 37℃ and centrifuged at 500 g for 5 min at 4℃. Then nuclei were isolated with Omni-ATAC lysis buffer (10 mM Tris-HCl (pH 7. 4), 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA630, 0.1% Tween-20, 0.01% digitonin) and incubated on ice for 3-5 min.
Nuclei were tagmentated with customized Tn5 transposome which was embed with one adaptor sequence. The reaction was incubated on a thermomixer at 800 rpm, 37℃,30 min and stopped by tagmentation stop buffer. Single nucleus stained with DAPI was flow sorted into each plate well containing lysis buffer and then incubated at 65 °C for 30 min. SDS was quenched with 4μL 10% Tween-20, and PCR was performed using PrimeSTAR GXL DNA Polymerase. Then thermal cycled as follows: 68°C for 10 min, 95°C for 1 min, 16 cycles of 94°C for 15 s, 63°C for 30 s, 68°C for 8 min and finally 68 °C for 5 min. 48 wells with different inner barcodes were pooled and purified with 1X AMPure XP beads. Another four cycles of amplification was carried out in a 50 µL GXL DNA Polymerase system with 1 μM Outer Primer. The amplified products were purified with 1X AMPure XP beads twice. 20 products with different outer barcodes (960 cells in total) were pooled together and sequenced on one MinION flow cell (Oxford Nanopore Technologies; R9.4.1).

tag: cell line

value: Mouse embryonic stem cell


title: NAcc, EcoliHS, Coc, Proteo5

tag: Sex

tag: microbiota

value: E coli HS

tag: treatment

value: Cocaine (15mg/kg, i.p.)


title: NAcc, FMT, Coc, Control3

tag: tissue

value: FMT


title: 1_05_CD19

tag: treg status

tag: jtm tpm_inc

tag: cancercell inc

tag: cd4 th17_status


title: 1_05_CD11b

tag: cd8 cd137_status

tag: m1 status


title: NAcc, FMT, Coc, Control2

tag: genotype


title: 123-3

tag: patient

tag: biopsy

tag: age

tag: diagnosis

value: UC

tag: gastroscopy

value: FALSE

tag: inflammation

value: ascendens


title: 45-1

value: non


title: IPS19-M-2

description: FPKM-ips.csv

source_name: iPSCs

tag: zika infected

value: mock

tag: iPS cell line


title: NAcc, FMT, Coc, Control1

value: Brain, NAcc

tag: Sex

value: Male

tag: microbiota

tag: treatment


title: scNanoATAC_K562

description: Single-cell long-read ATAC-seq of K562

tag: cell line


title: IPS19-M-3

description: FPKM-ips.csv


title: A09_P_24_CD4

tag: cell type

tag: arm

value: B

tag: os

tag: cd66b gr_status

value: High

tag: treg status

value: Low

tag: m2 status

tag: jtm normcount_inc

tag: jtm tpm_inc

tag: cancercell inc


title: scNanoATAC_HFF1

description: Single-cell long-read ATAC-seq of HFF1


title: Embryo E9.5 dpc, Trated heterozygous,2

city: Naples

first: Gabriella

last: Lania

address: Via Pietro Castellino

country: Italy

institute: IGB-CNR

data_processing:
The quality control on raw reads was performed using FastQC
The reads were mapped to the mouse genome (mm9) using TopHat2 (version.2.0.7)  with the following options: -G annotation_file.gtf  --transcriptome-index transcriptome.
Gene count matrix was obtained as output using featureCount function from Rsubread R package (version 0.5.4) on ‘exon’ feature type, considering reverse strand for paired end reads with the annotation GTF file
The raw counts were filtered applying Proportion test or a total of 14488 genes RNA-SeqGUI R package .Batch effects were removed using ARSyNseq function from filtered gene count matrix and considering rpkm normalization approach
The differential expression between pair-conditions was evaluated using the non-parametric NOISeqBIO function after applying upper quartile as normalization method. A posterior probability (PP) greater or equal to 0.95 was used to determine DEGs.
Assembly: mm9
Supplementary files format and content: UQUA_normalised_read_count_matrix.txt
Supplementary files format and content: TXT file ; Proportion test filtered and Upper quartile method normalised read counts of expressed genes

source_name: whole embryo

growth_protocol: Male Tbx1 +/- mice were mate with wild type females

extract_protocol:
RNA was harvested usingTrizol extraction. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using ??.

treatment_protocol: Pregnant female  were injected by i.p. with  20mg/Kg/day of vit.B12  at E7.5, E8.5, and 4 hrs ahead of the E9.5 harvest.  .

value: whole embryo

tag: genotype

tag: time

tag: description

value: sequencing run:2


title: IPS19-M-1

description: FPKM-ips.csv

tag: zika infected

tag: iPS cell line

value: WT


title: IPS1-I-3

description: FPKM-ips.csv

value: infected


title: A08_P_16_CD19

value: A

tag: cd8 cd137_status

tag: m1 status

value: Y

tag: cd4 th17_status


title: NAcc, DescN, Coc, Proteo1

tag: tissue

tag: Sex

tag: microbiota

value: C. rodemtium DescN

tag: treatment

value: Cocaine (15mg/kg, i.p.)


title: Embryo E9.5 dpc, Trated heterozygous,1

tag: cell line

value: sequencing run:1


title: IPS1-I-2

description: FPKM-ips.csv


title: Embryo E9.5 dpc, untreated heterozygous,3

value: PBS


title: A06_P_16_CD8

tag: cell type

tag: arm

tag: os

tag: cd66b gr_status

tag: treg status

tag: m2 status


title: scNanoATAC_GM12878

description: Single-cell long-read ATAC-seq of GM12878


title: IPS1-I-1

description: FPKM-ips.csv

tag: genotype


title: Embryo E9.5 dpc, untreated heterozygous,2

tag: time

tag: description


title: A05_P_16_CD4

tag: cd8 cd137_status

tag: jtm normcount_inc

tag: jtm tpm_inc

tag: cancercell inc


title: scNanoATAC_MEF

description: Single-cell long-read ATAC-seq of mouse embryonic fibroblast

source_name: Mouse embryonic fibroblast

value: Mouse embryonic fibroblast


title: Sham1_cells [miRNA_expression_cells]

city: Shenzhen

first: Xinjin

last: Chi

state: Guagndong

address: No. 628, Zhenyuan Road, Guangming New District

institute: he Seventh Affiliated Hospital of Sun Yat-Sen University

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp(version 0.20.0) softeware with default parameters in pair end mode.
The clean data were obtained for downstream analyses by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data.
The clean reads were mapped to reference of mouse mRNAs and lncRNAs using bowtie2(version 2.3.1) with parameters -q -L 16 --phred64 -p 6
TPM value and read counts of each transcript were obtained by eXpress(version 1.5.1) with parameters --no-update-check --rf-stranded.
Assembly: mm10
Supplementary files format and content: abundance measurements

source_name: RAW264.7 cells

extract_protocol:
Total RNA of intestine samples was extracted respectively using the TRIzol (Thermo Scientific, USA) reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). A total amount of 1 µg RNA per sample was used as initial material for the RNA sample preparations. Ribosomal RNA was removed using Ribo-off™ rRNA Depletion Kit (Human/Mouse/Rat) (Vazyme, China).
The sequencing libraries were generated following manufacturer recommendations with varied index label by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, USA). The libraries were sequenced on an BGISEQ-500 platform.

value: Macrophages

value: untreated


title: scNanoATAC_eHAP1

description: Single-cell long-read ATAC-seq of eHAP1


title: A04_P_14_CD19

tag: m1 status

tag: cd4 th17_status


title: IPS1-M-2

description: FPKM-ips.csv

tag: zika infected

value: mock

tag: iPS cell line


title: Embryo E9.5 dpc, untreated heterozygous,1

tag: cell line

tag: treatment


title: Sham2_cells [miRNA_expression_cells]

tag: cell type


title: GL2_cells [miRNA_expression_cells]

value: Treat with high glucose+LPS for 24 hours


title: IPS1-M-1

description: FPKM-ips.csv


title: IPS1-M-3

description: FPKM-ips.csv


title: A02_P_14_CD8

tag: arm

tag: os

tag: cd66b gr_status


title: scNanoATAC_HEK293T

description: Single-cell long-read ATAC-seq of HEK293T


title: Embryo E9.5 dpc, untreated control,3

tag: genotype


title: A03_P_14_CD11b

tag: treg status

tag: m2 status


title: A07_P_16_CD11b

value: High

tag: cd8 cd137_status


title: A01_P_14_CD4

tag: jtm normcount_inc


title: Embryo E9.5 dpc, untreated control,1

tag: time

tag: description


title: Embryo E9.5 dpc, untreated control,2


title: PMC_H3K27me3_rep2

status: Public on Sep 06 2022

city: Xuzhou

first: Cen

middle: Ai

last: Zhang

state: Jiangsu

address: No.2 Kunpeng

institute: Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District

data_processing:
Raw reads of all sequencing data were trimmed using fastp (Chen et al. 2018). Reads with quality value (Q < 25) and read length (< 50 bp) were discarded.
The clean reads were then mapped to the rice MSU7.0 reference genome with Bowtie2 aligner .
Picard MarkDuplicates was used to remove any PCR duplicates. Samtools (Li et al., 2009) was used to select only reads with mapping quality (MapQ) higher than 30 for further analyses.
Deeptools (Ramirez et al. 2016) was used to convert the bam files to the bigwig file with the bam files normalized by RPKM (Reads Per Kilobase per Million mapped reads).
MACS2 software (Zhang et al. 2008) was used for H3K4me3 and H3K27me3 enriched peak calling.
Assembly: MSU 7.0
Supplementary files format and content: bigWig, narrowPeak

organism: Oryza sativa

source_name: male meiocytes(at the early prophase I stage)

extract_protocol:
8-10K cross-linked PMC pellet was suspended in pre-cooled cell lysis buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 0.6% NP-40) for lysis on ice for 10min. After centrifuge at 12,000 rpm at 4℃ for 5min, the cell pellet was resuspended in the cell lysis buffer for additional 5 min incubation on ice. After washing twice using 1xMNase digestion buffer (20 mM Tris-HCl, pH 7.5, 15 mM NaCl, 60 mM KCl, 1 mM CaCl2), the lysates were trimmed using MNase (Cat# M0247S, New England Biolabs) for 10 min at 37 °C. After adding 2x stopping buffer (100 mM Tris-HCl, pH 8.1, 20 mM EDTA, 200 mM NaCl, 2% Triton X-100, 0.2% sodium deoxycholate), MNase trimmed chromatin was sonicated for 10 cycles (20s on, 40s off). After centrifuge twice at 12,000 rpm at 4℃, 5min each, the clean supernatant was incubated with anti-H3K27me3 (Cat# 9733, Cell Signaling Technology) or anti-H3K4me3 (Cat#ab8580, abcam) with constant rotation at 4℃ overnight. The remaining procedures for recovery of ChIPed DNA were conducted following the published procedures (Saleh et al. 2008). Each antibody was biologically replicated.
Biologically replicated ChIP-seq and input libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB, E7645S). All prepared libraries were sequenced on the Illumina NovaSeq platform.

tag: chip antibody


title: PMC_H3K27me3_rep1

value: H3K27me3 (Cat# 9733, Cell Signaling Technology)

value: male meiocytes(at the early prophase I stage)


title: Lin-4A8+ cells sorted from a rhCMV+ rhesus macaque

city: Göttingen

first: Lutz

last: Walter

address: Kellnerweg 4

department: Primate Genetics

country: Germany

institute: German Primate Center

data_processing:
Lin-4A8+ cells were sorted from a rhCMV+ rhesus macaque for single cell RNA sequence analysis using the single cell RNA-seq platform iCELL8 (Takara) combined with the single cell dispenser and imaging system CellenONE X1 (Cellenion) essentially as recently described by one of our co-authors.
High-throughput sequencing of the single cell libraries was performed using an Illumina HiSeq4000.
For preprocessing of single cell data, the Macaca mulatta reference genome Mmul 10 (Ensembl release 105) was manually reviewed and curated to include in-house annotations of NKG2C-1, NKG2C-2 and NKG2C-3 and KIR genes.
Alignment and count matrix generation was done in STAR 2.7.10a using “--quantMode GeneCounts”.
Analysis of single cell data was performed using Seurat version 4.1.0 (satijalab.org/seurat)
Assembly: custom ENSEMBL Mmul10 annotation (Macaca_mulatta.Mmul_10.105_custom.gtf.gz)
Supplementary files format and content: RDS file and FASTQ

organism: Macaca mulatta

source_name: blood

extract_protocol: From stained rhPBMCs, the populations of CD3-CD14-CD20- (lineage negative, lin- NK) and lin-4A8+ cells were sorted using a SH800 cell sorter (Sony) and collected into mediumPBMC.

treatment_protocol: Peripheral blood and spleen samples from rhesus macaques (Macaca mulatta) kept at the German Primate Center were obtained from the Animal Husbandry Unit and from the Pathology Unit, respectively.

tag: tissue

value: blood

value: NK cell

tag: cmv status

value: CMV+


title: PMC_H3K4me3_rep1

value: H3K4me3 (Cat#ab8580, abcam)


title: PMC_input

value: none (input)


title: CD11cCreIRF8FL TAM Tumor Rep 2

first: Fengshen

last: Kuo

state: New York

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

description: bulk RNAseq related to Fig 3

data_processing:
Illumina bcl2fastq2 version 2.18.0 and 2.20.0.422 were used for generating FASTQ files.
Raw bulk RNA sequencing FASTQ files were aligned against the mm10 assembly by STAR (v020201). Gene level count values were then computed by the summarizeOverlaps function from the R package "GenomicAlignments" with UCSC mm10 KnownGene as the base gene model. The Union counting mode was used and only mapped paired reads were considered. The sample size factor normalized read counts and FPKM (Fragments Per Kilobase Million) values were then computed from gene level counts by using the counts function and the fpkm function, respectively, from the R package DESeq2.
The scRNAseq gene counting data in HDF5 format were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) run with input FASTQ files and aligned against mouse transcriptome, mm10-3.0.0, along the expect-cells option to be 1000.
Assembly: mm10
Supplementary files format and content: Bulk RNAseq gene raw count marix is generated individually per sample and is in Comma-separated values (CSV) format with Entrez ID as the row name.
Supplementary files format and content: scRNAseq gene count marix is generated individually per sample through Cell Ranger count option and is in HDF5 format.

source_name: PyMT Tumor

growth_protocol: Mice were aged and tumor growth was monitored, cells were harvested from mice with large tumor burden, approaching 3000 mm3 among all mammary tumors.

extract_protocol:
RNA from sorted cells suspended in Trizol was extracted with chloroform. Isopropanol and linear acrylamide were added, and the RNA was precipitated with 75% ethanol. Sample were resuspended in RNase-free water.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 0.387-1ng total RNA with RNA integrity numbers ranging from 3.6 to 10 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech catalog # 63488), with 12 cycles of amplification. Subsequently, 0.4-10ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR

value: PyMT Tumor

value: Tumor-associated macrophage

tag: Sex

value: female


title: IRF8FL TAM Tumor Rep 2

description: bulk RNAseq related to Fig 3


title: DC2 Tumor Rep 2

description: bulk RNAseq related to Fig 1

value: PyMT

value: Type 2 Dendritic cell


title: IRF8FL TAM Tumor Rep 1

description: bulk RNAseq related to Fig 3


title: CD11cCreIRF8FL TAM Tumor Rep 1

description: bulk RNAseq related to Fig 3


title: DC1 Tumor Rep 2

description: bulk RNAseq related to Fig 1

value: Type 1 Dendritic cell


title: Monocyte Tumor Rep 2

description: bulk RNAseq related to Fig 1

extract_protocol:
RNA from sorted cells suspended in Trizol was extracted with chloroform. Isopropanol and linear acrylamide were added, and the RNA was precipitated with 75% ethanol. Sample were resuspended in RNase-free water.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 0.649-1ng total RNA with RNA integrity numbers ranging from 1 to 9.5 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech catalog # 63488), with 12 cycles of amplification. Subsequently, 4ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR

value: Monocyte


title: Monocyte Tumor Rep 3

description: bulk RNAseq related to Fig 1


title: Monocyte Tumor Rep 1

description: bulk RNAseq related to Fig 1


title: TAM Tumor Rep 3

description: bulk RNAseq related to Fig 1


title: GL1_cells [miRNA_expression_cells]

value: Macrophages

tag: cell line


title: MTM Tumor Rep 2

description: bulk RNAseq related to Fig 1

value: Mammary tissue macrophage


title: MTM Tumor Rep 1

description: bulk RNAseq related to Fig 1


title: TAM Tumor Rep 1

description: bulk RNAseq related to Fig 1


title: MTM Tumor Rep 3

description: bulk RNAseq related to Fig 1


title: Dss day6, replicate 2, RNA-seq

city: JiNan

first: Shiyang

last: Li

address: Wenhua West Road

institute: Shandong University

data_processing:
Filtered reads were mapped against the mouse mm10 reference genome using hisat2 (Version 2.2.1).
Then, normalized count per gene was counted using featureCounts program (Version 2.0.1)
Assembly: mm10
Supplementary files format and content: normalized count matrix with rows as genes and columns as samples

source_name: colon

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: colon

tag: time point

value: day 6


title: Dss day6, replicate 3, RNA-seq


title: Dss day4, replicate 3, RNA-seq

value: day 4


title: TAM Tumor Rep 2

description: bulk RNAseq related to Fig 1

tag: cell type


title: Dss day6, replicate 1, RNA-seq


title: Dss day4, replicate 2, RNA-seq


title: Dss day4, replicate 1, RNA-seq


title: Dss day2, replicate 2, RNA-seq

value: day 2


title: Dss day2, replicate 1, RNA-seq


title: Dss day0, replicate 3, RNA-seq

value: day 0


title: Dss day0, replicate 1, RNA-seq


title: Dss day0, replicate 2, RNA-seq


title: PMC_H3K4me3_rep2

value: male meiocytes(at the early prophase I stage)


title: VDJLibrary_S2_L003

city: Madrid

first: Carmen

middle: Gómez-Escolar

last: Arias

state: Madrid

address: Calle Melchor Fernández Almagro 3

country: Spain

institute: CNIC

description: Multiplexed spleen tomato+ cells isolated from 2 Aicda-Cre+/ki;Rosa26tdTomato+/ki and 2 Aicda-Cre-/ki;Rosa26tdTomato+/ki mice

data_processing:
Sequencing data were processed with RTA v1.18.66.3.
FastQ files for each sample were obtained using bcl2fastq v2.20.0.422 software (Illumina).
GEX + prot surface aligned by cellranger-3.1.0/cellranger-cs/3.1.0/bin/count --libraries=library_featured_ab_comma.csv –feature-ref=feature_file_ab_comma.csv --expect-cells=10000 –chemistry=SC5P-R2
VDJ alignment by cellranger-cs/3.1.0/bin/vdj
Genome_build: Refdata-cellranger-mm10-3.0.0; refdata-cellranger-vdj-GRCm38-alts-ensembl-3.1.0
Supplementary_files_format_and_content: comma separated table

source_name: Spleen

extract_protocol:
Singe Cell RNA was isolated from pooled sorted Tomato+ spleen cells (2 Aicda-Cre+/ki;Rosa26tdTomato+/ki and 2 Aicda-Cre-/ki;Rosa26tdTomato+/ki mice) with the Feature Barcoding technology for Cell Surface Protein (10x Genomics).
cDNA libraries were prepared with the Feature Barcoding technology for Cell Surface Protein (10x Genomics).
Libraries were sequenced on a HiSeq 4000 system (Illumina) to generate paired-end reads of 50 and 91 nt.

treatment_protocol: OVA immunization

tag: developmental stage


title: GEX5Library_S1_L004


title: GEX5Library_S1_L003


title: Dss day2, replicate 3, RNA-seq


title: Sample_509_RORg_MHCII

first: Chrysothemis

last: Brown

department: Immunology Program, Sloan Kettering Institute

description:
RORgt+ MHCII+ from 3-week old mice
smart-seq2 protocol

data_processing:
base-calling was performed using HiSeq Control Software HD v3.4.0.38
samples were demultiplexed using bcl2FASTQ v2.20.0.422
FASTQ files from demultiplexed samples were aligned to GRCm38 (mm10) using STAR v2.7.7a with ‘--twopassMode Basic --outFilterMultimapNmax 1 --quantMode TranscriptomeSAM’
The alignments of each sample were name-sorted using Samtools v1.11
The count matrix for all cells was created by counting alignments using featureCounts (subread v2.0.1)
Low-quality cells/genes were filtered and downstream analyses (normalization, PCA, etc.) was performed using Seurat v3.2.3.
Cells were clustered using PhenoGraph and UMAP embedding was computed using Seurat v3.2.3.
Genome_build: mm10
Supplementary_files_format_and_content: the count matrix (tab-delimited table) includes raw counts for all cells (smart-seq2 samples).
Supplementary_files_format_and_content: the cell metadata (csv table) includes clusters, annotations, etc. for all cells (corresponding to rows in the count matrix).

source_name: Mouse MLN RORgt+ MHCII+

extract_protocol:
RORgt+MHCII+ cells were enriched from a pool of MLN from 3-week-old RorcVenus-CreERT2 mice. Cells were depleted of Lineage (TCRb, TCRgd, CD19, B220, NK1.1)+ cells via staining with biotinylated antibodies followed by magnetic bead negative selection. Live, Lin(CD3, TCRb, TCRgd CD19, B220, NK1.1)–CD64–Ly6C–MHCII+RORgt(Venus)+ cells were then sorted into single wells. Cells were also stained for CD90, CD11c and CD11b for acquiring index sorting information on cell surface expression. Aire+ mTECs were enriched from a pool of thymi from 3-week old mice via staining with biotinylated antibodies against CD45 followed by magnetic bead negative selection. CD45–Epcam+MHCII+Aire(GFP)+ cells were sorted into single wells. Aire+ DCs were enriched from a pool of MLN from the same 3-week old mice. Cells were depleted of Lin+ cells as described above and live, Lin(CD3, TCRb, TCRgd CD19, B220, NK1.1)–CD90–CD64–Ly6C–CD11c+MHCII+Aire(GFP)+ cells were then sorted into single wells.
Single cells were sorted into Buffer RLT (Qiagen). Cell lysates were immediately sealed and spun down before transferring to dry ice and storing at -80 ºC. RNA was purified using the Agencourt RNAClean XP beads (Beckman Coulter) at a 2.2X ratio. First-strand cDNA synthesis was achieved using Maxima H Minus Reverse Transcriptase (ThermoFisher) according to the manufacturer’s protocol using oligo dT primers, with the addition of a custom template-switch oligo in a 1mM final concentration. cDNA was amplified for 24 cycles using KAPA HiFi HotStart ReadyMix (Kapa Biosystems KK2601). After PicoGreen quantification, 0.1-0.2ng of cDNA was used to prepare libraries with the Nextera XT DNA Library Preparation Kit (Illumina) in a total volume of 6.25µL with 12 cycles of PCR. Indexed libraries were pooled by volume and cleaned by aMPure XP beads (Beckman Coulter) at a 1X ratio. Pools were sequenced on a HiSeq 4000 in a PE50 or PE100 run using the HiSeq 3000/4000 SBS Kit (Illumina).

value: mesenteric lymph nodes (MLN)

tag: age

value: three weeks

value: RORgt+ MHCII+


title: Sample_508_RORg_MHCII


title: Sample_504_RORg_MHCII


title: Sample_505_RORg_MHCII


title: Sample_506_RORg_MHCII


title: Sample_507_RORg_MHCII


title: Sample_512_RORg_MHCII


title: Sample_513_RORg_MHCII


title: Sample_511_RORg_MHCII


title: Sample_499_RORg_MHCII


title: Sample_500_RORg_MHCII


title: Sample_501_RORg_MHCII


title: Sample_498_RORg_MHCII


title: Sample_497_RORg_MHCII


title: Sample_494_RORg_MHCII


title: Sample_502_RORg_MHCII


title: Sample_496_RORg_MHCII


title: Sample_492_RORg_MHCII


title: Sample_495_RORg_MHCII


title: SurfaceProteinLibrary_S3_L003


title: Sample_493_RORg_MHCII


title: Sample_488_RORg_MHCII


title: Sample_489_RORg_MHCII


title: Sample_490_RORg_MHCII


title: Sample_510_RORg_MHCII


title: Sample_487_RORg_MHCII


title: Sample_486_RORg_MHCII


title: Sample_503_RORg_MHCII


title: Sample_485_RORg_MHCII


title: Sample_491_RORg_MHCII


title: Sample_475_RORg_MHCII


title: Sample_474_RORg_MHCII


title: Sample_480_RORg_MHCII


title: Sample_484_RORg_MHCII


title: Sample_483_RORg_MHCII


title: Sample_482_RORg_MHCII


title: Sample_481_RORg_MHCII


title: Sample_476_RORg_MHCII


title: Sample_478_RORg_MHCII


title: Sample_469_RORg_MHCII


title: Sample_477_RORg_MHCII


title: Sample_473_RORg_MHCII


title: Sample_471_RORg_MHCII


title: Sample_468_RORg_MHCII


title: Sample_472_RORg_MHCII


title: Sample_467_RORg_MHCII


title: Sample_463_RORg_MHCII


title: Sample_462_RORg_MHCII


title: Sample_464_RORg_MHCII


title: Sample_460_RORg_MHCII


title: Sample_459_RORg_MHCII


title: Sample_465_RORg_MHCII


title: Sample_458_RORg_MHCII


title: Sample_457_RORg_MHCII


title: Sample_479_RORg_MHCII


title: Sample_470_RORg_MHCII


title: Sample_454_RORg_MHCII


title: Sample_455_RORg_MHCII


title: Sample_456_RORg_MHCII


title: Sample_466_RORg_MHCII


title: Sample_447_RORg_MHCII


title: Sample_448_RORg_MHCII


title: Sample_446_RORg_MHCII


title: Sample_449_RORg_MHCII


title: Sample_461_RORg_MHCII


title: Sample_453_RORg_MHCII


title: Sample_451_RORg_MHCII


title: Sample_443_RORg_MHCII


title: Sample_444_RORg_MHCII


title: Sample_452_RORg_MHCII


title: Sample_450_RORg_MHCII


title: Sample_445_RORg_MHCII


title: Sample_439_RORg_MHCII


title: Sample_440_RORg_MHCII


title: Sample_433_RORg_MHCII


title: Sample_436_RORg_MHCII


title: Sample_441_RORg_MHCII


title: Sample_437_RORg_MHCII


title: Sample_438_RORg_MHCII


title: Sample_434_RORg_MHCII


title: Sample_435_RORg_MHCII


title: Sample_430_RORg_MHCII


title: Sample_431_RORg_MHCII


title: Sample_432_RORg_MHCII


title: Sample_429_RORg_MHCII


title: Sample_428_RORg_MHCII


title: Sample_442_RORg_MHCII


title: Sample_427_RORg_MHCII


title: Sample_426_RORg_MHCII


title: Sample_424_RORg_MHCII


title: Sample_422_RORg_MHCII


title: Sample_425_RORg_MHCII


title: Sample_419_RORg_MHCII


title: Sample_420_RORg_MHCII


title: Sample_414_RORg_MHCII


title: Sample_416_RORg_MHCII


title: Sample_417_RORg_MHCII


title: Sample_421_RORg_MHCII


title: Sample_418_RORg_MHCII


title: Sample_411_RORg_MHCII


title: Sample_410_RORg_MHCII


title: Sample_415_RORg_MHCII


title: Sample_413_RORg_MHCII


title: Sample_409_RORg_MHCII


title: Sample_404_mTEC

description:
Aire(GFP)+ medullary thymic epithelial cell from 3-week old mice
smart-seq2 protocol

source_name: Mouse Thymus Aire+  mTEC

value: thymus


title: Sample_407_mTEC

value: Aire(GFP)+ medullary thymic epithelial cell


title: Sample_412_RORg_MHCII


title: Sample_408_mTEC


title: Sample_402_mTEC


title: Sample_406_mTEC


title: Sample_403_mTEC


title: Sample_405_mTEC


title: Sample_400_mTEC


title: Sample_423_RORg_MHCII


title: Sample_398_mTEC


title: Sample_399_mTEC


title: Sample_397_mTEC


title: Sample_395_mTEC


title: Sample_396_mTEC


title: Sample_391_mTEC


title: Sample_393_mTEC


title: Sample_390_mTEC


title: Sample_387_mTEC


title: Sample_401_mTEC


title: Sample_386_mTEC


title: Sample_384_mTEC


title: Sample_383_mTEC


title: Sample_382_mTEC


title: Sample_388_mTEC


title: Sample_380_mTEC


title: Sample_381_mTEC


title: Sample_385_mTEC


title: Sample_379_RORg_MHCII


title: Sample_376_RORg_MHCII


title: Sample_377_RORg_MHCII


title: Sample_378_RORg_MHCII


title: Sample_373_RORg_MHCII


title: Sample_374_RORg_MHCII


title: Sample_372_RORg_MHCII


title: Sample_394_mTEC


title: Sample_370_RORg_MHCII


title: Sample_392_mTEC


title: Sample_371_RORg_MHCII


title: Sample_368_RORg_MHCII


title: Sample_389_mTEC


title: Sample_366_RORg_MHCII


title: Sample_365_RORg_MHCII


title: Sample_367_RORg_MHCII


title: Sample_364_RORg_MHCII


title: Sample_375_RORg_MHCII


title: Sample_363_RORg_MHCII


title: Sample_361_RORg_MHCII


title: Sample_360_RORg_MHCII


title: Sample_362_RORg_MHCII


title: Sample_358_RORg_MHCII


title: Sample_356_RORg_MHCII


title: Sample_359_RORg_MHCII


title: Sample_355_RORg_MHCII


title: Sample_357_RORg_MHCII


title: Sample_351_RORg_MHCII


title: Sample_352_RORg_MHCII


title: Sample_350_RORg_MHCII


title: Sample_354_RORg_MHCII


title: Sample_353_RORg_MHCII


title: Sample_349_RORg_MHCII


title: Sample_346_RORg_MHCII


title: Sample_348_RORg_MHCII


title: Sample_347_RORg_MHCII


title: Sample_345_RORg_MHCII


title: Sample_341_RORg_MHCII


title: Sample_343_RORg_MHCII


title: Sample_369_RORg_MHCII


title: Sample_344_RORg_MHCII


title: Sample_339_RORg_MHCII


title: Sample_342_RORg_MHCII


title: Sample_337_RORg_MHCII


title: Sample_340_RORg_MHCII


title: Sample_338_RORg_MHCII


title: Sample_336_RORg_MHCII


title: Sample_335_RORg_MHCII


title: Sample_332_RORg_MHCII


title: Sample_333_RORg_MHCII


title: Sample_331_RORg_MHCII


title: Sample_330_RORg_MHCII


title: Sample_328_RORg_MHCII


title: Sample_327_RORg_MHCII


title: Sample_329_RORg_MHCII


title: Sample_325_RORg_MHCII


title: Sample_322_RORg_MHCII


title: Sample_324_RORg_MHCII


title: Sample_323_RORg_MHCII


title: Sample_321_RORg_MHCII


title: Sample_319_RORg_MHCII


title: Sample_320_RORg_MHCII


title: Sample_317_RORg_MHCII


title: Sample_315_RORg_MHCII


title: Sample_316_RORg_MHCII


title: Sample_314_RORg_MHCII


title: Sample_334_RORg_MHCII


title: Sample_313_RORg_MHCII


title: Sample_312_RORg_MHCII


title: Sample_310_RORg_MHCII


title: Sample_311_RORg_MHCII


title: Sample_308_RORg_MHCII


title: Sample_306_RORg_MHCII


title: Sample_307_RORg_MHCII


title: Sample_303_RORg_MHCII


title: Sample_301_RORg_MHCII


title: Sample_309_RORg_MHCII


title: Sample_305_RORg_MHCII


title: Sample_326_RORg_MHCII


title: Sample_300_RORg_MHCII


title: Sample_302_RORg_MHCII


title: Sample_298_RORg_MHCII


title: Sample_318_RORg_MHCII


title: RC2_10_3

city: Hangzhou

first: Xiaoyu

last: Wang

state: Zhejiang

address: Yuhangtang Road

department: College of Life Sciences

institute: Zhejiang University

data_processing:
Raw data were firstly processed through in-house perl scripts as a quality control. Demultiplexed and quality filtered reads were then aligned to S. melonis TY genome sequence using Bowtie2-2.2.3. HTSeq 0.6.1 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions was performed using the DESeq Rpackage (1.18.0).
The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate.
Assembly: ASM176134v1
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Sphingomonas melonis TY

source_name: bacterial cells

growth_protocol: shake-flask culture, LB culture, 30℃, 200 rpm

extract_protocol:
Total bacterial samples were collected (A600 = 0.6 at the time of collected), mixed with 0.2 volumes of stop-mix (95% ethanol and 5% phenol, v/v) and snap-frozen in liquid nitrogen. Pellets were resuspended in 100 μl lysozyme solution (15 mg/ml lysozyme in TE buffer, pH = 8.0). Total RNA was isolated with Omega-E.Z.N.A.® Bacterial RNA Kit.
Briefly, RNA degradation and contamination were monitored on 1% agarose gels. The integrity of RNA sample was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, USA). Sequencing libraries were generated from rRNA-depleted RNA using the RiboMinus Bacteria 2.0 Transcriptome Isolation Kit (Thermo Scientific, USA) following the manufacturer’s recommendations.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. The library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated. Before data analysis, raw data were firstly processed through in-house perl scripts as a quality control. Demultiplexed and quality filtered reads were then aligned to S. melonis TY genome sequence using Bowtie2-2.2.3. HTSeq 0.6.1 was used to count the reads numbers mapped to each gene.

treatment_protocol: Transcriptome sequencings were carried out on S. melonis TY cultured under three levels of salt stress (0%, 1%, 2%) for 10 or 30 minutes. A total of 18 samples (6 treatments with 3 replicates) were sequenced.

value: bacterial cells

tag: treatment

value: 2% NaCl, 10 min


title: RC2_30_3

value: 2% NaCl, 30 min


title: RC2_10_2


title: RC2_30_2


title: Sample_299_RORg_MHCII


title: Sample_296_RORg_MHCII


title: Sample_295_RORg_MHCII


title: RB1_30_3

value: 1% NaCl, 30 min


title: RC2_10_1


title: RB1_30_2


title: Sample_294_RORg_MHCII


title: Sample_304_RORg_MHCII


title: Sample_293_RORg_MHCII


title: Sample_292_RORg_MHCII


title: RB1_30_1


title: Sample_291_RORg_MHCII


title: RB1_10_3

value: 1% NaCl, 10 min


title: RB1_10_2


title: RB1_10_1


title: RC2_30_1


title: Sample_290_RORg_MHCII


title: Sample_287_RORg_MHCII


title: Sample_288_RORg_MHCII


title: RA0_30_3

value: 0% NaCl, 30 min


title: Sample_289_RORg_MHCII


title: Sample_285_RORg_MHCII


title: RA0_10_3

value: 0% NaCl, 10 min


title: Sample_286_RORg_MHCII


title: RA0_30_2


title: RA0_10_2


title: Sample_297_RORg_MHCII


title: Sample_284_RORg_MHCII


title: RA0_10_1


title: Sample_283_RORg_MHCII


title: RA0_0_2

value: 0% NaCl, 0 min


title: Sample_282_RORg_MHCII


title: Sample_281_RORg_MHCII


title: RA0_0_1


title: Sample_280_RORg_MHCII


title: RA0_30_1


title: Sample_279_RORg_MHCII


title: Sample_278_RORg_MHCII


title: 21-day-old, fry1-6, replicate 2

city: Nankang

first: Ho-Ming

state: Taipei

address: No. 128, Sec. 2, Academia Road

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica

data_processing:
Adaptor sequences were trimmed using fastx_clipper of the FASTX-Toolkit (with -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCA -c).
Trimmed reads were quality-filtered using fastq_quality_filter of the FASTX-Toolkit (with -q 30 -p 90).
Trimmed reads of 20-21nt were selected and raw abundance was counted using the custom Perl scripts.
Supplementary files format and content: Tab-delimited text files contain trimmed sequences of 20-21 nt and raw abundance.

organism: Arabidopsis thaliana

source_name: rosette leave

growth_protocol: Arabidopsis thaliana was grown on soil under a 16/8-h light/dark cycle at 22°C.

extract_protocol:
Total RNA was extracted from the powder of frozen plant tissues by PureLink Plant RNA Reagent (Thermo Fisher) and MaxTract high-density gel tubes (Qiagen).
PARE libraries were constructed from 80 μg total RNA following the protocol described previously ( Zhai J, Arikit S, Simon SA, Kingham BF, Meyers BC: Rapid construction of parallel analysis of RNA end (PARE) libraries for Illumina sequencing. Methods 2014, 67:84-90).

value: rosette leave

tag: genotype

value: fry1-6 mutant

tag: growth medium

value: soil

tag: ecotype


title: RA0_0_3


title: 21-day-old, xrn4-6, replicate 2

value: xrn4-6 mutant


title: 21-day-old, fry1-6, replicate 1


title: 21-day-old, xrn3-3, replicate 2

value: xrn3-3 mutant


title: Sample_275_RORg_MHCII

value: mesenteric lymph nodes (MLN)

value: three weeks


title: Sample_276_RORg_MHCII

value: RORgt+ MHCII+


title: Sample_274_RORg_MHCII


title: 21-day-old, xrn3-3, replicate 1


title: 21-day-old, xrn2-1, replicate 2

value: xrn2-1 mutant


title: Sample_273_RORg_MHCII


title: HepaRG, day 34, 4 days DMSO removed, replicate 4

city: Vandœuvre-lès-Nancy

first: Hélène

last: Dubois-Pot-Schneider

address: Site CRAN/Faculté de Médecine - Bâtiment D, 1er étage 9 avenue de la Forêt de Haye, BP 184

department: CRAN

country: France

institute: Université de Lorraine - UMR7039 CRAN

description: Gene expression of HepaRG cells at day 34. DMSO removed from differentiated HepaRG culture (D30 + DMSO) for further 4 days

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer (HI-RPM) was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565) using one color scan setting for 8x60k array slides (profile Agilent G3-GX-1color).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using protocol GE_1-107_sep09_ssSurogates and Grid: 028004_D_F_20110325. Gene expression data were further analyzed by using the GeneSpring software (Agilent Technologies). Filtration by flag and signal intensity was applied. Briefly, were retained only the entities in which at least 100% of the values in at least one condition  had a detected flag (i.e. a positive  and significant feature as defined by GeneSpring). For the filtration by signal intensity, were retained the entities in which 100% of the values in at least one condition were within the range of interest (i.e. 20-100th percentile).

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low RNA Input Quick Amp Labelling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop (Thermo Fischer Scientific, Waltham, MA).  amplification yield was 4.04 ± 0.53 µg cRNA and specific activity was 11.97 ± 0.98 pmol Cy3 per µg cRNA.

growth_protocol: Cells were seeded at a density of 2.7 x 104/cm2 and maintained for two weeks in a William’s E medium supplemented with 10% fetal bovine serum, 100 U/ml penicillin, 100 μg/ml streptomycin, 5 μg/ml insulin, and 50 μM hydrocortisone. Then, the culture medium was or not supplemented with 2% DMSO for two additional weeks. Cells were usually collected at different stages of differentiation process: D4, D15, D30 - DMSO and D30 + DMSO. However, to determine the influence of DMSO, it was removed from differentiated HepaRG culture (D30 + DMSO) for further 4 days and cells collected at 34 days (D34 +/- DMSO)

extract_protocol: RNA extractions were performed with RNeasy mini kit (Qiagen)  following the manufacturer's recommendations. RNA was qualified using a Nanodrop 2000 spectrophotometer (Thermo Fischer Scientific, Waltham, MA).

value: HepaRG

value: hepatic stem cell

tag: day

tag: dmso

value: yes (day 15 to day 30) and no (day30 to day 34)


title: Sample_272_RORg_MHCII


title: 21-day-old, WT, replicate 2

value: wild-type


title: Sample_277_RORg_MHCII


title: 21-day-old, xrn2-1, replicate 1


title: HepaRG, day 30, plus DMSO, replicate 1

description: Gene expression of HepaRG cells at day 30 differentiated with DMSO 2%

source_name: HepaRG, day 30, plus DMSO, replicate 1

value: yes (day 15 to day 30)


title: 21-day-old, xrn4-6, replicate 1


title: HepaRG, day 15, replicate 4

description: Gene expression of HepaRG cells at day 15 of differentiation

source_name: HepaRG, day 15, replicate 4

value: no


title: HepaRG, day 30, minus DMSO, replicate 2

description: Gene expression of HepaRG cells at day 30 differentiated without DMSO

source_name: HepaRG, day 30, minus DMSO, replicate 2


title: HepaRG, day 15, replicate 3

source_name: HepaRG, day 15, replicate 3


title: HepaRG, day 30, minus DMSO, replicate 4

source_name: HepaRG, day 30, minus DMSO, replicate 4


title: HepaRG, day 34, 4 days DMSO removed, replicate 3


title: HepaRG, day 34, 4 days DMSO removed, replicate 2


title: HepaRG, day 30, plus DMSO, replicate 3

source_name: HepaRG, day 30, plus DMSO, replicate 3


title: HepaRG, day 30, plus DMSO, replicate 2

source_name: HepaRG, day 30, plus DMSO, replicate 2


title: HepaRG, day 34, 4 days DMSO removed, replicate 1


title: 21-day-old, WT, replicate 1


title: HepaRG, day 30, plus DMSO, replicate 4

source_name: HepaRG, day 30, plus DMSO, replicate 4


title: HepaRG, day 30, minus DMSO, replicate 3

source_name: HepaRG, day 30, minus DMSO, replicate 3


title: HepaRG, day 15, replicate 1

source_name: HepaRG, day 15, replicate 1


title: Sample_270_RORg_MHCII


title: HepaRG, day 15, replicate 2

source_name: HepaRG, day 15, replicate 2


title: DC2 Tumor Rep 1

description: bulk RNAseq related to Fig 1

source_name: PyMT Tumor

value: PyMT

value: PyMT Tumor

value: Type 2 Dendritic cell

value: female


title: HepaRG, day 4, replicate 3

description: Gene expression of HepaRG cells at day 4 of differentiation

source_name: HepaRG, day 4, replicate 3


title: HepaRG, day 30, minus DMSO, replicate 1

source_name: HepaRG, day 30, minus DMSO, replicate 1


title: Sample_268_RORg_MHCII

source_name: Mouse MLN RORgt+ MHCII+


title: Sample_269_RORg_MHCII


title: 14-TP-3 failed

city: San Diego

first: Peter

last: Olson

state: California

address: 3545 Cray Court

institute: Mirati Therapeutics

description:
HTG EdgeSeq Precision ImmunoOncology panel
142-1271942-4_1.failed

data_processing:
The data were analysed using HTG parser and HTG EdgeSeq Reveal software, to generate raw and normalised counts
Assembly: 1392 human gene panel
Supplementary files format and content: tab-delimited text file include raw read counts for each Sample

source_name: Kidney, NOS

extract_protocol:
formalin-fixed paraffin embedded (FFPE) samples with two 5 μm core needle biopsy sections
All samples were processed according to the manufacturer's protocol. The tissue was removed from the slides with a scalpel, lysed using proteinase K and HTG’s denaturation oil, and underwent target protection and clean up on the HTG EdgeSeq processor. Following this process, sequencing adaptors and barcodes were added and the library amplified. Amplified libraries were quantified with the Kapa library quantification kit, pooled, and sequenced on Illumina’s Miseq platform.
1392 gene HTG EdgeSeq Precision ImmunoOncology

tag: patient id

value: Kidney, NOS

tag: source

value: Fixed - FFPE

tag: disease

value: Clear Cell Renal cell carcinoma

value: Post-combination

tag: time


title: 34-NA

description:
HTG EdgeSeq Precision ImmunoOncology panel
143-1327114-5_1

tag: tissue


title: 5-TP-3

description:
HTG EdgeSeq Precision ImmunoOncology panel
S12


title: 26-Baseline failed

description:
HTG EdgeSeq Precision ImmunoOncology panel
142-1277409-1_1.failed

value: Baseline


title: 4-TP-3

description:
HTG EdgeSeq Precision ImmunoOncology panel
S9


title: HepaRG, day 4, replicate 4

source_name: HepaRG, day 4, replicate 4


title: HepaRG, day 4, replicate 2

source_name: HepaRG, day 4, replicate 2


title: 1-TP-3

description:
HTG EdgeSeq Precision ImmunoOncology panel
S3


title: DC1 Tumor Rep 1

description: bulk RNAseq related to Fig 1

extract_protocol:
RNA from sorted cells suspended in Trizol was extracted with chloroform. Isopropanol and linear acrylamide were added, and the RNA was precipitated with 75% ethanol. Sample were resuspended in RNase-free water.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 0.649-1ng total RNA with RNA integrity numbers ranging from 6.8 to 10 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech catalog # 63488), with 12 cycles of amplification. Subsequently, 15ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR

value: Type 1 Dendritic cell

tag: Sex


title: FACS sorted Blood residing Eµ-myc lymphoma cells from WT host 377

city: Parkville

first: Connie

middle: S. N.

last: Li-Wai-Suen

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

data_processing:
Libraries were sequenced on an Illumina HiSeq 2500 to produce 100bp single-end reads. Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.68  and Real Time Analysis (RTA) v1.18.66.3, running on the instrument computer. RTA  performs real-time base calling on the HiSeq instrument computer. Then the Illumina  bcl2fastq 2.19.1.403 pipeline was used to generate the sequence data.
Reads were aligned to the mouse genome mm10 using STAR version 2.5.3a.
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and Rsubread's inbuilt RefSeq annotation.
Assembly: mm10
Supplementary files format and content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

growth_protocol: mCherry+Eµ-myc 5849 2x104 cells were transplanted i.p. into age and gender matched TpoTg (overexpressing TPO) and wild-type mice (WT). CD19 mCherry double positive and fluorogold negative cells were sorted on a FACSAria II flow cytometer from blood of tumour bearing mice day 15 (1 WT, 1 TpoTg) and day 19 (3 WT, 2 TpoTg) after tumor transplant. Blood was drawn into EDTA and RBCs were depleted before sorting.

extract_protocol:
After sorting, cell pellets were frozen down and all RNA samples were prepared at the same time using RNeasy mini kit according to the RNeasy mini handbook from Qiagen.
mRNA library was prepared by Australian Genome Research Facility (AGRF) for sequencing using standard Illumina protocols.

tag: background strain

value: Wild type host

value: Blood residing E{mu}-myc lymphoma cells

value: Murine E{mu}-myc 5849 lymphoma cells

tag: host

value: Male host

tag: tissue collection date


title: Sample_266_RORg_MHCII

value: mesenteric lymph nodes (MLN)

value: three weeks

tag: cell type

value: RORgt+ MHCII+


title: FACS sorted Blood residing Eµ-myc lymphoma cells from WT host 381


title: Sample_267_RORg_MHCII

tag: age


title: 31-Baseline

description:
HTG EdgeSeq Precision ImmunoOncology panel
143-1313199-2_1

tag: treatment


title: 4-Baseline

description:
HTG EdgeSeq Precision ImmunoOncology panel
S7


title: Sample_265_RORg_MHCII


title: 22-TP-3

description:
HTG EdgeSeq Precision ImmunoOncology panel
142-1286500-8_1


title: 1-TP-4

description:
HTG EdgeSeq Precision ImmunoOncology panel
S4


title: 6-TP-2

description:
HTG EdgeSeq Precision ImmunoOncology panel
S13

value: Post-sitravatinib


title: 30-TP-2

description:
HTG EdgeSeq Precision ImmunoOncology panel
143-1306303-1_1


title: 30-Baseline

description:
HTG EdgeSeq Precision ImmunoOncology panel
143-1301543-1_1


title: Sample_264_RORg_MHCII

description:
RORgt+ MHCII+ from 3-week old mice
smart-seq2 protocol


title: FACS sorted Blood residing Eµ-myc lymphoma cells from WT host 375

tag: genotype

value: Female host


title: HepaRG, day 4, replicate 1

source_name: HepaRG, day 4, replicate 1

tag: cell line

value: HepaRG

value: hepatic stem cell

value: no


title: FACS sorted Blood residing Eµ-myc lymphoma cells from TpoTg host 386

value: Tpo transgenic host


title: 28-Baseline

description:
HTG EdgeSeq Precision ImmunoOncology panel
143-1289022-1_1

value: Kidney, NOS

value: Fixed - FFPE

value: Clear Cell Renal cell carcinoma


title: Sample_263_RORg_MHCII


title: 26-TP-2

description:
HTG EdgeSeq Precision ImmunoOncology panel
143-1281959-1_1


title: FACS sorted Blood residing Eµ-myc lymphoma cells from WT host 384


title: 26-Baseline

description:
HTG EdgeSeq Precision ImmunoOncology panel
142-1277409-1_1

value: Baseline


title: FACS sorted Blood residing Eµ-myc lymphoma cells from TpoTg host 378


title: 24-TP-3

description:
HTG EdgeSeq Precision ImmunoOncology panel
142-1287840-4_1

value: Post-combination


title: FACS sorted Blood residing Eµ-myc lymphoma cells from TpoTg host 385

value: Blood residing E{mu}-myc lymphoma cells


title: 24-Baseline

description:
HTG EdgeSeq Precision ImmunoOncology panel
142-1273537-1_1


title: Sample_271_RORg_MHCII


title: Oasl1/Apoe DKO rep3 (scRNA-Seq)

city: Seoul

first: GooTaeg

last: Oh

address: 52, Ewhayeodae-gil

department: Department of Life Sciences

country: South Korea

institute: Ewha Womans University

data_processing:
Alignment was performed using the Cell Ranger toolkit (version 3.1.0).
For each cell, filtered gene-cell-barcode matrix was obtained by appling two quality measures: mitochondrial genes (<10%) and gene count count (>200) using Seurat v4.0.3.
The doublets were detected and removed by using DoubletFinder.
The remaining data was log-normalized and then used in downstream analysis after z-transformation.
Genome_build: mm10
Supplementary_files_format_and_content: scRNA_normalized_count.txt

source_name: Aortic arch

extract_protocol:
Each cell suspension was subjected to 3’ single-cell RNA sequencing using the GemCode system (10x Genomics), following the manufacturer’s instructions. Libraries were sequenced on an Illumina HiSeq and mapped to the mouse mm10 reference genome using the Cell Ranger toolkit (version 3.1.0).
RNA libraries were prepared for sequencing using Chromium Single Cell 3’ Library v2 kit.

tag: strain

value: Apoe-/-

value: Aorta

tag: disease state

value: Atherosclerosis


title: 22-TP-2

description:
HTG EdgeSeq Precision ImmunoOncology panel
142-1276354-2_1


title: Oasl1/Apoe DKO rep2 (scRNA-Seq)


title: Sample_260_RORg_MHCII

value: mesenteric lymph nodes (MLN)

value: three weeks


title: 19-TP-2

description:
HTG EdgeSeq Precision ImmunoOncology panel
142-1266086-2_1

value: Post-sitravatinib


title: 19-TP-3

description:
HTG EdgeSeq Precision ImmunoOncology panel
142-1275717-1_1


title: 22-Baseline

description:
HTG EdgeSeq Precision ImmunoOncology panel
142-1271783-1_1


title: Sample_259_RORg_MHCII

value: RORgt+ MHCII+


title: Oasl1/Apoe DKO rep1 (scRNA-Seq)


title: 18-TP-3

description:
HTG EdgeSeq Precision ImmunoOncology panel
142-1273743-7_1


title: Sample_258_RORg_MHCII


title: 19-Baseline

description:
HTG EdgeSeq Precision ImmunoOncology panel
142-1262025-1_1


title: 18-TP-2

description:
HTG EdgeSeq Precision ImmunoOncology panel
142-1265769-1_1


title: 29-Baseline

description:
HTG EdgeSeq Precision ImmunoOncology panel
143-1295513-1_1


title: Oasl1/Apoe WT rep2 (scRNA-Seq)


title: Sample_257_RORg_MHCII


title: Sample_262_RORg_MHCII


title: Oasl1/Apoe WT rep1 (scRNA-Seq)


title: Sample_256_RORg_MHCII


title: 24-TP-2

description:
HTG EdgeSeq Precision ImmunoOncology panel
142-1279360-2_1


title: Sample_261_RORg_MHCII


title: 15-TP-2

description:
HTG EdgeSeq Precision ImmunoOncology panel
142-1265306-2_1


title: iMSBmal1-/- - 3

city: Nashville

first: Lance

last: Riley

state: TN

address: 9445 MRB4, 2213 Garland Ave

department: Biomedical Engineering

institute: Vanderbilt University

data_processing:
Sequenced reads were mapped using HISAT2 and gene counts were quantified using Htseq-count
Gene counts were quantified using HTseq-count
Differential gene expression was determined using DESeq2 using Cook's outliers to filter out low expression and alpha = 0.05 to for significance.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw counts for every gene and every sample.
Supplementary_files_format_and_content: Matrix table with DEseq2 counts for every gene and every sample.

source_name: Tibialis anterior muscle

growth_protocol: iMSBmal1fl/fl mice were maintained in 12L:12D conditions in a AAALAC approved facility until 12-16 weeks of age.

extract_protocol:
Tibialis anterior muscles were isolated and flash frozen in liquid nitrogen. Muscles were pulverized under liquid nitrogen to prevent fiber type sampling bias then homogenized in Trizol before RNA was extracted with a Qiagen RNeasy kit using the standard protocol. RNA was treated with TURBO DNase (Ambion) to remove genomic DNA.
Libraries were prepared using KAPA Stranded RNAseq Kits with RiboErase according to standard protocols.

treatment_protocol: iMSBmal1fl/fl mice were treated with either 15% ethanol in sunflower seed oil or 2 mg day-1 tamoxifen via intraperitonial injections for five days to induce recombination.

value: Skeletal muscle

value: Tamoxifen


title: 18-Baseline

description:
HTG EdgeSeq Precision ImmunoOncology panel
142-1261357-2_1


title: 14-TP-3

description:
HTG EdgeSeq Precision ImmunoOncology panel
142-1271942-4_1


title: iMSBmal1-/- - 2


title: 14-TP-2

description:
HTG EdgeSeq Precision ImmunoOncology panel
142-1263493-1_1


title: Sample_254_RORg_MHCII

description:
RORgt+ MHCII+ from 3-week old mice
smart-seq2 protocol


title: 13-TP-3

description:
HTG EdgeSeq Precision ImmunoOncology panel
142-1263665-1_1


title: 14-Baseline

description:
HTG EdgeSeq Precision ImmunoOncology panel
143-1259269-1_1


title: iMSBmal1-/- - 1


title: 13-TP-2

description:
HTG EdgeSeq Precision ImmunoOncology panel
142-1256271-1_1


title: 13-Baseline

description:
HTG EdgeSeq Precision ImmunoOncology panel
142-1252770-1_1


title: iMSBmal1+/+ - 3

value: Vehicle


title: Sample_253_RORg_MHCII


title: 12-TP-3

description:
HTG EdgeSeq Precision ImmunoOncology panel
142-1256904-4_1


title: 12-Baseline

description:
HTG EdgeSeq Precision ImmunoOncology panel
142-1246006-1_1


title: Sample_252_RORg_MHCII


title: iMSBmal1+/+ - 2


title: 15-TP-3

description:
HTG EdgeSeq Precision ImmunoOncology panel
142-1273280-2_1


title: 10-Baseline

description:
HTG EdgeSeq Precision ImmunoOncology panel
142-1230062-1_1


title: Sample_251_RORg_MHCII


title: 10-TP-3

description:
HTG EdgeSeq Precision ImmunoOncology panel
142-1244927-6_1


title: 7-Baseline

description:
HTG EdgeSeq Precision ImmunoOncology panel
S15


title: Sample_255_RORg_MHCII


title: iMSBmal1+/+ - 1


title: 8-Baseline

description:
HTG EdgeSeq Precision ImmunoOncology panel
S16


title: 2-TP-3

description:
HTG EdgeSeq Precision ImmunoOncology panel
S6


title: 6-TP-3

description:
HTG EdgeSeq Precision ImmunoOncology panel
S14


title: Sample_250_RORg_MHCII


title: 5-TP-2

description:
HTG EdgeSeq Precision ImmunoOncology panel
S11


title: 4-TP-2

description:
HTG EdgeSeq Precision ImmunoOncology panel
S8


title: Sample_249_RORg_MHCII


title: Sample_248_RORg_MHCII


title: 5-Baseline

description:
HTG EdgeSeq Precision ImmunoOncology panel
S10


title: 1-TP-2

description:
HTG EdgeSeq Precision ImmunoOncology panel
S2


title: 2-Baseline

description:
HTG EdgeSeq Precision ImmunoOncology panel
S5


title: Sample_247_RORg_MHCII

description:
RORgt+ MHCII+ from 3-week old mice
smart-seq2 protocol


title: 20.327_Tumor

city: Hershey

first: Gregory

last: Yochum

address: 700 HMC Crescent Road

institute: Penn State College of Medicine

description:
tumor tissue
20-327_L7_G821

data_processing:
Base calling with Illumina MiSeq.
Alignment with STAR version 2.7.3.
HTSeq counting of aligned reads.
DESeq2 rlog function for normalization.
Genome_build: hg38
Supplementary_files_format_and_content: *_htseq.out.txt: Count files contain raw counts for sequences aligning to each transcript.
Supplementary_files_format_and_content: raw_counts.csv: Comma-separated text file includes raw counts.

source_name: Sigmoid Colon

extract_protocol:
Tumors and adjacent colonic segments were surgically resected and aliquots were stored in RNAlater (Thermo Fisher) preservative. Samples were homogenized with a pestle and chloroform was added. The samples were centrifuged at 12,000 x g for 15 minutes. The aqueous layer was purified with RNeasy Mini Kit (Qiagen). Samples were selected for poly-adenylation, and cDNA libraries were made and sequenced on MiSeq (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: diagnosis

value: Early onset colorectal cancer

value: Tumor tissue

tag: tumor stage

tag: age at surgery


title: Sample_246_RORg_MHCII

city: New York


title: Sample_245_RORg_MHCII


title: 20.327_Normal

description:
full thickness tumor adjacent tissue
20-327_L0_G821

tag: patient id

value: Adjacent normal tissue


title: 20.146_Tumor

description:
tumor tissue
20-146_E7_G821

source_name: Rectum


title: 20.146_Normal

description:
full thickness tumor adjacent tissue
20-146_E0_G821


title: 20.002_Tumor

description:
tumor tissue
20-002_E7_G821


title: Sample_244_RORg_MHCII


title: 20.002_Normal

description:
full thickness tumor adjacent tissue
20-002_E0_G821


title: 19.253_Tumor

description:
tumor tissue
19-253_B7_G821

source_name: Ascending Colon


title: 19.253_Normal

description:
full thickness tumor adjacent tissue
19-253_B0_G821


title: 19.076_Tumor

description:
tumor tissue
19-076_B7_G821


title: Sample_242_RORg_MHCII


title: 19.076_Normal

description:
full thickness tumor adjacent tissue
19-076_B0_G821


title: Sample_240_RORg_MHCII


title: Sample_241_RORg_MHCII


title: 19.055_Tumor

description:
tumor tissue
19-055_L7_G821


title: Sample_239_RORg_MHCII


title: 19.062_Tumor

description:
tumor tissue
19-062_L7_G821


title: 19.055_Normal

description:
full thickness tumor adjacent tissue
19-055_L0_G821