title: male, chow diet, sample 487

city: Los Angeles

first: Zhengyi

last: Zhang

address: Westwood

institute: UCLA

data_processing:
Clean reads were aligned to the mouse reference genome (NCBIv37/mm9) using Bowtie2 software. Duplicated reads or those that mapped to the mitochondrial genome or aligned to unmapped contiguous regions were removed before peak calling. MACS2 was applied for peak calling. The reproducible enriched sites in each treatment time point were merged and used to obtain RPKM using SeqMonk software. Bedgraph files were generated by HOMER software. Gene annotation was performed by Homer software annotation function using the genome location of peaks.
Assembly: mm9
Supplementary files format and content: bedGraph.gz

source_name: Skeletal muscle

extract_protocol:
Nuclei were isolated from skeletal muscle of normal chow-fed, Control f/f and mERaOE mice at months of age (n=3/genotype). Briefly, 50 mg of frozen gastrocnemius muscle was minced and dounced in NIB buffer (20mM Tris-HCl, 50mM EDTA, 5mM Spermidine, 0.15mM Spermine, 0.1% mercaptoethanel, 40% glycerol pH=7.5) for 120 strokes. Homogenize samples were incubated on ice for 5 min and centrifuged at 11,00g at 4°C. The supernatants were filtered through 70 μm nylon mesh and washed with RSB buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2 pH7.4).
ATAC-seq libraries were prepared from 50,000 nuclei using the Nextera Tn5 Transposase and DNA library preparation kit (Illumina) as described with slight modifications

value: Skeletal muscle

value: Control f/f

value: Chow diet


title: male, chow diet, sample 485

status: Public on Oct 30 2024

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

treatment_protocol: normal chow-fed, Control f/f and mERaOE mice

tag: tissue

tag: genotype

value: ERaTG

tag: treatment


title: male, chow diet, sample 486


title: male, chow diet, sample 318


title: male, chow diet, sample 481


title: LN-229 MGMT-transfected cells exposed to 1 mM TMZ (1x), rep3

city: Zurich

first: Shana

middle: J.

last: Sturla

address: Schmelzbergstrasse 9

department: D-HEST

country: Switzerland

institute: ETH Zurich

data_processing:
After demultiplexing of sequencing data, each sample was represented by two fastq.gz files containing 151-nucleotide-long genomic reads. The quality of the raw sequencing data was checked via FastQC version 0.12.1.
Low-quality reads and adapter-containing reads were removed via trimmomatic version 0.39 with the following parameters: PE ILLUMINACLIP:/cluster/home/jabueche/programs/Trimmomatic-0.39/adapters/TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:151.
Reads containing the AD1B sequence, which were not removed by subtractive hybridization, were discarded using cutadapt version 4.4 and the following settings: -b "GACTGGTTCCAATTGAAAGTGCTCTTCCGATCT;e=0.1;min_overlap=15" -B "AGATCGGAAGAGCACTTTCAATTGGAACCAGTC;e=0.1;min_overlap=15" --pair-filter=any --discard-trimmed. 12 base pairs of the 5’ end of all R2 reads (not containing the site of interest) were cropped due to low quality and suboptimal per base sequence content, increasing alignment rate.
The paired reads were mapped to human reference genome GRCh38 via bowtie2 version 2.5.1, using pre-built bowtie2 index from https://genome-idx.s3.amazonaws.com/bt/GRCh38_noalt_as.zip and applying the following additional settings: --no-mixed --no-discordant.
Read duplicates were removed by gatk (version 4.2.0.0) MarkDuplicatesSpark.
Samtools version 1.17 were employed to sort, index, and generate statistics of bam files.
Bedtools2 version 2.31 were used to retrieve the coordinates of mapped and deduplicated reads and extract the sequence context of the modified nucleotides from the reference genome, while the -1 position of the read start was the modification site.
Assembly: hg38
Supplementary files format and content: The processed .tsv files are tab-separated lists of all found modification sites. Headers "Chr", "Position", "Strand", "Base", "MAPQ" are included. It contains all found sites, not only guanines.
Library strategy: O6‑MeG‑seq, a novel sequencing strategy to map O6‑methylguanine in the human genome

organism: Homo sapiens

growth_protocol: Cells were cultured in GlutaMAX™ DMEM supplemented with 10% FBS and 1% Penicillin-Streptomycin at 5% CO2 and 37°C.

extract_protocol:
Cells were detached with 0.25% Trypsin-EDTA and DNA was extracted using the QIAamp® DNA Mini Kit according to manufacturer's instructions.
Briefly, the extracted DNA was sheared, end-repaired with NEBNext Ultra II DNA Library Prep Kit and custom adapters were ligated. Fragments containing O6‑methylguanine were enriched with immunopercipitation and stalling of a high-fidelity polymerase was used to mark the site of O6‑methylguanine. Subtractive hybridisation was used to remove unwanted fragments and the library was indexed and amplified using dual indexing primers for Illumina.

treatment_protocol: LN-229 WT and MGMT-transfected cells were exposed to 1mM temozolomide in growth medium, or 1% DMSO as solvent control, once (1x) or repetitively every 4 h (3x) and DNA was extracted 24 h after first exposure. Naked DNA was allowed to react with temozolomide for 24h.

tag: cell line

tag: cell type

value: glioblastoma

value: MGMT-transfected

value: 1 mM TMZ (1x)


title: male, chow diet, sample 322


title: LAG-3 tumor 1

type: RNA

city: Providence

first: Payton

last: De La Cruz

state: Rhode Island

address: 200 Chestnut St

department: Division of Biology and Medicine

institute: Brown University

hyb_protocol: The reporter code set and capture probe set tubes were removed from -80C and thawed on ice, prior to mixing by tapping and pulse centrifugation. 70 µl hybridization buffer was added to the tube containing the reporter probe set and mixed by tapping, followed by pulse centrifugation. 8 µl of the diluted reporter probe was added to a PCR tube. Each RNA sample was diluted in water to 25 ng/µl and 2 µl final volume for 50 ng total input per sample. 5 µl RNA sample was added to each tube containing the reporter probe set and mixed by tapping, followed by pulse centrifugation. 2 µl Capture Probe Set was added to each tube, mixed by tapping, and the sample was collected by pulse centrifugation and then immediately placed in a pre-heated PCR machine, with the lid set to 70 °C and the block set to 65 °C. The hybridization was performed for 18 h at 65 °C. Samples were cooled to 4 °C and any condensation was collected by pulse centrifugation. Each sample was diluted with 18 µl hybridization buffer.

scan_protocol: An nCounter Sprint cartridge was calibrated to room temperature for 15 min prior to injection of 33 µl of each sample into one of the 12 injection ports of the cartridge, followed by the introduction of an air seal. The sample injection cartridge was sealed with provided tape and the reagent supply ports were unsealed prior to loading on the nCounter Sprint profiler. The analysis run was started immediately after loading.

data_processing:
The resulting data file in RCC format was used for data analysis in the nSolver analysis platform. Raw data in RCC format was uploaded to nSolver for automated normalization, background subtraction, and quality control (QC) check.
low count genes were filtered out for a total of 750 genes detected on the panel

label: fluorescent barcode

molecule: total RNA

source_name: tumor derived from E0771 cells

growth_protocol: E0771 cells were cultured in Dulbecco Modified Eagle Medium supplemented with 10% Fetal Bovine Serum (FBS) and 1% penicillin/streptomycin. 5x10^5 cells were injected with matrigel into the 4th mammary pad of female eight week old C57Bl/6J mice. Tumors were allowed to grow for 14 days. Mice were allocated into treatment groups once tumors were palpable.

extract_protocol: RNA extraction from flash frozen on-treatment tumors (n=3 per group) was performed using the Quick-RNA MiniPrep Kit (Zymo Research, R1054) with the manufacturer’s instructions.

treatment_protocol: Mice received 200 μg doses of mouse anti-PD-1 (clone: 29F.1A12), anti-LAG-3 (clone: C9B7W), anti-TIM-3 (clone: RMT3-23), or rat IgG2a isotype control (clone: 2A3) every 4 days via intraperitoneal injection, with treatments stopping after the third dose.

value: mouse tumor


title: LN-229 WT cells exposed to 100 μM TMZ (3x), rep3

value: WT

value: 100 μM TMZ (3x)


title: patient24_chd_sample1

city: San Francisco

first: Michael

middle: A

last: Smith

state: CA

address: 550 16th St, 5th Floor

department: Pediatrics

institute: UC San Francisco

library_source: transcriptomic

data_processing:
The workflow “QIAseq miRNA Quantification” of CLC Genomics Server with standard parameters is used to map the reads to miRBase version 22.
Assembly: miRBase version 22
Supplementary files format and content: CSV file containing raw read counts for all samples

source_name: Peripheral blood

extract_protocol:
RNA was isolated from 200 ul using the miRNeasy Serum/Plasma Advanced (QIAGEN) according to manufacturer’s instructions with an elution volume of 20 ul.
The library preparation was done using the QIAseq miRNA Library Kit (QIAGEN).

value: Peripheral blood

value: CHD


title: LN-229 WT cells exposed to 1 mM TMZ (1x), rep3


title: PD-1 tumor 3


title: LN-229 MGMT-transfected cells exposed to 100 μM TMZ (3x), rep3


title: S47_Sen+T+Coc rep2

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

data_processing:
Indexed sequences were checked quality by Fastqc
Indexed sequences were trimmed adaptor sequence by TrimGalore-0.4.5
Reads were mapped to the hg38 reference genome using STAR | version 2.7.2 with default parameters (generation of sam files)
Convert .sam files to .bam files using samtools | version: 1.5 with parameters -bh -F 3840 -q 255
Read counts over annotated genes were obtained using featureCount (subreads | version: 1.5.3) with parameters -p -B -M -O --fraction -T 10
Assembly: Rattus_norvegicus.mRatBN7.2.dna.toplevel.fa
Supplementary files format and content: tab-delimited text file includes CPM values for each Samples , treatment group avarage CPM and DEG values.

molecule: polyA RNA

organism: Rattus norvegicus

source_name: brain

growth_protocol: Primary rat fetal mixed neuronal cultures were prepared from 18-day-old Sprague-Dawley rat fetuses (Envigo Laboratories, Indianapolis, IN)  in accordance with the University of South Carolina Institutional Animal Care and Use Committee. Briefly, tissue was dissected, incubated in a solution of 0.05% Trypsin/EDTA, washed with Hank’s balanced salt solution (HBSS, Thermo Fisher Scientific), dissociated by trituration and distributed into poly-L-lysine coated 12-well plates (Costar, Cambridge, MA) with or without inserted glass coverslips containing DMEM/F12 medium with 10% fetal bovine serum. After 24 hours initial plating medium was replaced with serum-free Neurobasal medium supplemented with 2% B-27, 2 mM GlutaMAX and 0.5% D-glucose. All reagents were from Thermo Fisher Scientific. Half of the medium was replaced with freshly prepared medium once a week. Cultured cells were used for experiments at the age of 3 weeks in vitro (DIV 21).

extract_protocol:
Total RNA was extracted using  Quick-RNA™ MiniPrep Kit  (Zymo) and RNA quality was validated on RNA-1000 chip using Bioanalyzer (Agilent)
Sequencing libraries were generated using NEBNext Ultra II Directional RNA Library prep Kit

treatment_protocol: Primary cultures were treated: (i) HIV-Tat protein 1-86 (Diatheva, Italy) or control +/- small molecules for 48 h; (ii) with coaine-HCL  (Sigma Chemicals) or control  for 24 h

value: brain

value: neuron cells

value: neuron

value: Senicapoc 1uM+HIV Tat 6ng/ml+Coc 25uM


title: PD-1 tumor 2


title: S48_Sen+T+Coc rep3

value: Senicapoc 1uM+HIV Tat6ng/ml+Coc 25uM


title: LN-229 MGMT-transfected cells exposed to 1 mM TMZ (3x), rep3

value: 1 mM TMZ (3x)


title: patient20_idiohered_sample1

value: Idiohered


title: S46_Sen+T+Coc rep1


title: PD-1 tumor 1


title: S45_4OI+T+Coc rep3

value: 4-octyl-itaconate 250uM+HIV Tat 6ng/ml+Coc 25uM


title: Naked genomic DNA from LN-229 MGMT-transfected cells exposed to 1mM TMZ,  rep2

value: 1 mM TMZ on naked DNA (1x)


title: LN-229 WT cells exposed to 1 mM TMZ (3x), rep3

value: glioblastoma


title: patient23_chd_sample1


title: patient19_bpd_sample1

value: BPD


title: Naked genomic DNA from LN-229 WT cells exposed to 1mM TMZ,  rep2


title: patient28_idiohered_sample1


title: S44_4OI+T+Coc rep2


title: LN-229 MGMT-transfected cells exposed to solvent-control (1x), rep2

value: MGMT-transfected

value: solvent-control (1x)


title: patient16_bpd_sample1


title: S43_4OI+T+Coc rep1


title: S42_TAZ+T+Coc rep3

value: Tazemetostat 3uM+HIV Tat 6ng/ml+Coc 25uM


title: patient17_chd_sample1


title: patient15_bpd_sample1


title: patient26_cdh_sample1

value: CDH


title: LN-229 WT cells exposed to solvent-control (1x), rep2

value: WT


title: patient22_chd_sample1

value: Peripheral blood

value: CHD


title: LN-229 MGMT-transfected cells exposed to 100 μM TMZ (1x), rep2

value: 100 μM TMZ (1x)


title: S40_TAZ+T+Coc rep1

value: brain

value: neuron cells

value: neuron


title: patient25_cdh_sample1


title: S41_TAZ+T+Coc rep2


title: patient12_cdh_sample1


title: S38_Aml+T+Coc rep2

value: Amlexanox 25uM+HIV Tat 6ng/ml+Coc 25uM


title: patient11_idiohered_sample1

value: Idiohered


title: S39_Aml+T+Coc rep3


title: Mouse Visium liver 48h post APAP rep 2

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

description:
10x Visium
Mouse Visium liver 48h post APAP

data_processing:
Raw sequencing data for each sample was converted to matrices of expression counts using the Space Ranger software provided by 10X Genomics (version 1.1.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files including raw counts for each sample
Supplementary files format and content: h5 file including raw gene count (output Space Ranger)
Supplementary files format and content: json file including scale factors (output Space Ranger)
Supplementary files format and content: png file including tissue image (output Space Ranger)
Supplementary files format and content: csv file including tissue positions (output Space Ranger)
Library strategy: spatialVisium

source_name: liver

extract_protocol: All Methods listed in De Ponti, Buijko et al. TREM2 expression delineates spatially restricted and ontogenically distinct hepatic macrophages populations required for tissue repair. Immunity. 2024.

value: liver

tag: strain

value: APAP


title: LAM-like KCs 48h post APAP rep4

description: LAM-like KCs 48h post APAP rep4

data_processing:
FastQC v0.11.9 is used to check the quality of the samples
Sequenced reads were then mapped to mm10 transcriptome using Hisat2 v2.2.0 with parameters --max-intronlen 1000000
The mapping files were then filtered using samtools v1.10
Reads were counted using Featurecounts v2.0.0
Assembly: mm10
Supplementary files format and content: tab-delimited text files including raw counts for each sample

value: LAM-like KCs

tag: Sex

value: male

tag: time point


title: patient10_idiohered_sample1


title: Mouse Visium liver 48h post APAP rep 1


title: LN-229 MGMT-transfected cells exposed to 1 mM TMZ (1x), rep2

value: glioblastoma

value: MGMT-transfected

value: 1 mM TMZ (1x)


title: S37_Aml+T+Coc rep1


title: Mouse Visium liver PBS

description:
10x Visium
Mouse Visium liver PBS

value: PBS


title: patient9_chd_sample1


title: LAM-like KCs 48h post APAP rep2

description: LAM-like KCs 48h post APAP rep2


title: patient8_bpd_sample1

value: BPD


title: LN-229 WT cells exposed to 100 μM TMZ (3x), rep2

value: WT

value: 100 μM TMZ (3x)


title: LAM-like KCs 48h post APAP rep1

description: LAM-like KCs 48h post APAP rep1


title: LN-229 MGMT-transfected cells exposed to 100 μM TMZ (3x), rep2


title: LN-229 MGMT-transfected cells exposed to 1 mM TMZ (3x), rep2

value: 1 mM TMZ (3x)


title: LAM-like KCs 36h post APAP rep4

description: LAM-like KCs 36h post APAP rep4


title: S35_Sen+HIV Tat rep2

value: brain

value: Senicapoc 1uM+HIV Tat 6ng/ml


title: patient7_bpd_sample1

value: Peripheral blood


title: S34_Sen+HIV Tat rep1

value: neuron cells

value: neuron


title: LN-229 WT cells exposed to 100 μM TMZ (1x), rep2

value: 100 μM TMZ (1x)


title: S33_4OI+HIV Tat rep3

value: 4-octyl-itaconate 250uM+HIV Tat 6ng/ml


title: patient6_chd_sample1

value: CHD


title: LN-229 WT cells exposed to 1 mM TMZ (1x), rep2


title: LN-229 WT cells exposed to 1 mM TMZ (3x), rep2


title: LAM-like KCs 48h post APAP rep3

description: LAM-like KCs 48h post APAP rep3

value: liver

value: LAM-like KCs

value: male

value: APAP


title: LAM-like KCs 36h post APAP rep2

description: LAM-like KCs 36h post APAP rep2


title: patient5_idiohered_sample1

value: Idiohered


title: S32_4OI+HIV Tat rep2


title: LAM-like KCs 36h post APAP rep3

description: LAM-like KCs 36h post APAP rep3


title: Naked genomic DNA from LN-229 MGMT-transfected cells exposed to 1mM TMZ,  rep1

value: glioblastoma

value: MGMT-transfected

value: 1 mM TMZ on naked DNA (1x)


title: S31_4OI+HIV Tat rep1


title: patient4_chd_sample1


title: KCs 0h post PBS rep2

description: KCs 0h post PBS rep2

value: KCs

value: PBS


title: S36_Sen+HIV Tat rep3

value: brain

value: Senicapoc 1uM+HIV Tat 6ng/ml


title: LAM-like KCs 36h post APAP rep1

description: LAM-like KCs 36h post APAP rep1


title: Naked genomic DNA from LN-229 WT cells exposed to 1mM TMZ,  rep1

value: WT


title: LN-229 MGMT-transfected cells exposed to solvent-control (1x), rep1

value: solvent-control (1x)


title: LN-229 WT cells exposed to solvent-control (1x), rep1


title: S30_TAZ+HIV Tat rep3

value: neuron cells

value: neuron

value: Tazemetostat 3uM+HIV Tat 6ng/ml


title: patient1_bpd_sample1

value: Peripheral blood

value: BPD


title: KCs 0h post PBS rep1

description: KCs 0h post PBS rep1

value: liver

value: male


title: S29_TAZ+HIV Tat rep2


title: LN-229 MGMT-transfected cells exposed to 100 μM TMZ (1x), rep1

value: 100 μM TMZ (1x)


title: LN-229 WT cells exposed to 100 μM TMZ (1x), rep1

value: glioblastoma


title: S28_TAZ+HIV Tat rep1


title: KCs 96h post APAP rep4

description: KCs 96h post APAP rep4

value: APAP


title: patient2_other_sample1

value: Other


title: patient64_chd_sample1

value: CHD


title: KCs 96h post APAP rep3

description: KCs 96h post APAP rep3

value: KCs


title: S27_Aml+HIV Tat rep3

value: brain

value: Amlexanox 25uM+HIV Tat 6ng/ml


title: patient63_chd_sample1


title: KCs 96h post APAP rep2

description: KCs 96h post APAP rep2


title: S26_Aml+HIV Tat rep2


title: LN-229 WT cells exposed to 1 mM TMZ (1x), rep1

value: WT

value: 1 mM TMZ (1x)


title: patient62_chd_sample1


title: KCs 96h post APAP rep1

description: KCs 96h post APAP rep1


title: S25_Aml+HIV Tat rep1

value: neuron cells


title: KCs 72h post APAP rep4

description: KCs 72h post APAP rep4


title: patient61_idiohered_sample1

value: Idiohered


title: patient60_bpd_sample1


title: S23_Sen rep2

value: neuron

value: Senicapoc 1uM


title: S24_Sen rep3


title: LN-229 MGMT-transfected cells exposed to 100 μM TMZ (3x), rep1

value: MGMT-transfected

value: 100 μM TMZ (3x)


title: LN-229 WT cells exposed to 100 μM TMZ (3x), rep1


title: KCs 72h post APAP rep3

description: KCs 72h post APAP rep3

value: liver

value: male


title: patient65_chd_sample1

value: Peripheral blood


title: patient59_chd_sample1


title: LN-229 MGMT-transfected cells exposed to 1 mM TMZ (3x), rep1

value: glioblastoma

value: 1 mM TMZ (3x)


title: patient58_chd_sample1

value: CHD


title: KCs 72h post APAP rep1

description: KCs 72h post APAP rep1

value: KCs

value: APAP


title: S21_4OI rep3

value: brain

value: 4-octyl-itaconate 250um


title: S22_Sen rep1


title: patient57_chd_sample1


title: LN-229 WT cells exposed to 1 mM TMZ (3x), rep1

value: WT


title: LN-229 MGMT-transfected cells exposed to 1 mM TMZ (1x), rep1

value: 1 mM TMZ (1x)


title: S20_4OI rep2

value: neuron cells

value: 4-octyl-itaconate 250uM


title: KCs 6h post APAP rep4

description: KCs 6h post APAP rep4


title: patient56_cdh_sample1

value: CDH


title: PBMC, sleep restriction, participant 8, GEM well/lane 4

city: New York

first: Darwin

last: D'Souza

state: NY

address: 1470 Madison Avenue

department: ImmunoBio

institute: Human Immune Monitoring Center

library_source: transcriptomic single cell

data_processing:
Data was processed using Cellranger v6.1.2. All 8 samples were pooled using hashtag oligos across 4 10x GEM lanes. Output BAM files for each de-multiplexed sample were converted back to FASTQs for GEO upload.
Assembly: GRCh38-2020-A
Supplementary files format and content: .h5

source_name: PBMC

extract_protocol:
At baseline of each study phase, participants came to the laboratory to complete various procedures and receive their sleep assignment. Participants returned at least every other week for additional assessments, most of which are beyond the scope of this study. At each of these study visits, sleep data were reviewed with a trained study staff member to assess compliance. At study visit week 5, an evening blood draw (target time: 15:00–17:00) was collected. Peripheral blood was drawn into an EDTA tube from an antecubital vein by a trained phlebotomist. The amount of blood collected and time of draw were recorded at all visits. Whole blood was subsequently processed for collection and preservation of the viability of PBMCs. As described previously7, whole blood was transferred to a 50 ml conical tube (Corning) and PBS diluted to 1× (Thermo Fisher Scientific) was added to the blood to a final volume of 35 ml. The solution was then carefully underlaid with 15 ml of Ficoll-Paque PLUS (GE Healthcare) and spun for 30 minutes at 23°C and 1,800 rpm with the centrifuge brake off (Eppendorf 5810R; Eppendorf). The resulting white blood cell layer was aspirated and transferred to a new conical tube; PBS was added to a final volume of 50 ml and then spun for 10 minutes at 4°C (1800 rpm, brake on). After spinning, the white blood cell pellet was resuspended in freezing media (20% FBS RPMI 1640 [Thermo Fisher Scientific] with 10% DMSO [Sigma Life Sciences]) and transferred into separate 1.5 ml cryovials. The cryovials were frozen at a controlled rate of −1°C/min (Mr. Frosty; Thermo Fisher Scientific) to maintain viability of cells and were then transferred to liquid nitrogen for storage until flow cytometry analysis. Neutrophils are not included in the leukocytes isolated by Ficoll-Plaque PLUS gradient as they are pelleted and discarded.
Library was constructed according to manufacturer's protocol (10x Single Cell 3' v3 and Cell Plex)

value: PBMC

tag: 10x gem_well

value: SR


title: PBMC, sleep restriction, participant 7, GEM well/lane 4


title: S19_4OI rep1

value: neuron


title: KCs 6h post APAP rep3

description: KCs 6h post APAP rep3

value: liver

value: male


title: PBMC, sleep restriction, participant 6, GEM well/lane 4


title: PBMC, sleep restriction, participant 5, GEM well/lane 4


title: KCs 6h post APAP rep1

description: KCs 6h post APAP rep1


title: KCs 72h post APAP rep2

description: KCs 72h post APAP rep2


title: patient54_idiohered_sample1

value: Peripheral blood

value: Idiohered


title: patient13_chd_sample1

value: CHD


title: PBMC, sleep restriction, participant 8, GEM well/lane 3


title: S16_TAZ rep1

value: Tazemetostat 3uM


title: KCs 48h post APAP rep4

description: KCs 48h post APAP rep4

value: KCs

value: APAP


title: PBMC, sleep restriction, participant 7, GEM well/lane 3


title: KCs 48h post APAP rep3

description: KCs 48h post APAP rep3


title: patient53_bpd_sample1

value: BPD


title: patient52_idiohered_sample1


title: S14_Aml rep2

value: brain

value: Amlexanox 25uM


title: KCs 48h post APAP rep2

description: KCs 48h post APAP rep2


title: PBMC, sleep restriction, participant 6, GEM well/lane 3


title: S15_Aml rep3

value: neuron cells


title: patient51_chd_sample1


title: patient50_bpd_sample1


title: patient55_chd_sample1


title: PBMC, sleep restriction, participant 8, GEM well/lane 2


title: S13_Aml rep1


title: PBMC, sleep restriction, participant 5, GEM well/lane 3


title: S18_TAZ rep3


title: KCs 36h post APAP rep4

description: KCs 36h post APAP rep4


title: patient49_bpd_sample1


title: S17_TAZ rep2


title: KCs 6h post APAP rep2

description: KCs 6h post APAP rep2


title: KCs 48h post APAP rep1

description: KCs 48h post APAP rep1


title: KCs 36h post APAP rep3

description: KCs 36h post APAP rep3


title: S12_HIV Tat + Coc rep3

value: HIV Tat 6ng/ml + Coc 25uM


title: PBMC, sleep restriction, participant 6, GEM well/lane 2


title: patient48_chd_sample1


title: S10_HIV Tat + Coc rep1


title: patient47_chd_sample1


title: PBMC, sleep restriction, participant 5, GEM well/lane 2


title: KCs 36h post APAP rep2

description: KCs 36h post APAP rep2


title: S11_HIV Tat + Coc rep2


title: KCs 36h post APAP rep1

description: KCs 36h post APAP rep1


title: patient46_cdh_sample1

value: CDH


title: PBMC, sleep restriction, participant 8, GEM well/lane 1

value: PBMC


title: S08_Control rep2

value: Control


title: KCs 24h post PBS rep2

description: KCs 24h post PBS rep2

value: PBS


title: PBMC, sleep restriction, participant 7, GEM well/lane 1

value: SR


title: patient18_idiohered_sample1


title: KCs 24h post PBS rep1

description: KCs 24h post PBS rep1

value: liver

value: male


title: S07_Control rep1

value: neuron


title: PBMC, sleep restriction, participant 6, GEM well/lane 1


title: S06_HIV Tat rep3

value: HIV Tat 6ng/ml


title: KCs 24h post APAP rep4

description: KCs 24h post APAP rep4


title: patient45_chd_sample1

value: Peripheral blood

value: CHD


title: KCs 24h post APAP rep3

description: KCs 24h post APAP rep3

value: KCs

value: APAP


title: PBMC, sleep restriction, participant 5, GEM well/lane 1


title: patient44_cdh_sample1


title: S05_HIV Tat rep2

value: brain


title: KCs 24h post APAP rep2

description: KCs 24h post APAP rep2


title: PBMC, habitual sleep, participant 4, GEM well/lane 4

value: HS


title: S04_HIV Tat rep1

value: neuron cells


title: patient43_chd_sample1


title: patient42_bpd_sample1

value: BPD


title: KCs 24h post APAP rep1

description: KCs 24h post APAP rep1


title: patient41_idiohered_sample1

value: Idiohered


title: KCs 168h post APAP rep4

description: KCs 168h post APAP rep4


title: PBMC, sleep restriction, participant 7, GEM well/lane 2

value: PBMC


title: PBMC, habitual sleep, participant 3, GEM well/lane 4


title: S03_Cocaine rep3

value: Cocaine 25uM


title: S09_Control rep3

value: Control


title: S02_Cocaine rep2


title: PBMC, habitual sleep, participant 2, GEM well/lane 4


title: S01_Cocaine rep1


title: PBMC, habitual sleep, participant 4, GEM well/lane 3


title: patient40_idiohered_sample1


title: PBMC, habitual sleep, participant 1, GEM well/lane 4


title: KCs 168h post APAP rep3

description: KCs 168h post APAP rep3


title: KCs 168h post APAP rep2

description: KCs 168h post APAP rep2


title: PBMC, habitual sleep, participant 3, GEM well/lane 3


title: patient14_cdh_sample1

value: CDH


title: KCs 168h post APAP rep1

description: KCs 168h post APAP rep1

value: liver


title: patient36_cdh_sample1


title: KCs 12h post APAP rep4

description: KCs 12h post APAP rep4

value: male


title: KCs 12h post APAP rep3

description: KCs 12h post APAP rep3


title: patient35_cdh_sample1


title: PBMC, habitual sleep, participant 4, GEM well/lane 2


title: patient27_idiohered_sample1


title: KCs 12h post APAP rep2

description: KCs 12h post APAP rep2


title: PBMC, habitual sleep, participant 3, GEM well/lane 2


title: PBMC, habitual sleep, participant 2, GEM well/lane 2


title: patient34_chd_sample1


title: KCs 12h post APAP rep1

description: KCs 12h post APAP rep1


title: patient33_bpd_sample1


title: Hippocampus_rTg4510_TG [204018770001_R01C02]

type: genomic

city: Exeter

first: Emma

last: Walker

address: RILD Barrack Rd

country: United Kingdom

institute: University of Exeter

hyb_protocol: Not provided

scan_protocol: Illumina HiScan

data_processing: Normalized Average Beta calculated using the SeSame package in R

label: Cy3, Cy5

source_name: Hippocampus

label_protocol: DNA methylation was measured using the the Mammalian Methylation Array (HorvathMammalMethylChip4, GEO: GPL28271)

growth_protocol: Animals were housed under standard conditions (constant temperature and humidity) with a 12h light/dark cycle in individually ventilated cages, with free access to food (Teklad irradiated global rodent diet (Envigo, United Kingdom)) and water.

extract_protocol: Genomic DNA from all samples was isolated from the entorhinal cortex or hippocampus using the AllPrep DNA/RNA Mini Kit (Qiagen)

treatment_protocol: Mice were terminally anaesthetized with pentobarbital (intraperitoneal injection) and transcardially perfused with phosphate-buffered saline (PBS). The entorhinal cortex was dissected from the left brain hemisphere on wet ice and snap-frozen on dry ice for subsequent analysis

value: Hippocampus

tag: externalsampleid

value: F

tag: dob

tag: dod

tag: agedays

tag: mousestrain

value: Mixed

value: TG


title: Hippocampus_rTg4510_TG [204018770001_R02C02]


title: patient37_idiohered_sample1

value: Peripheral blood


title: PBMC, habitual sleep, participant 1, GEM well/lane 2


title: PBMC, habitual sleep, participant 2, GEM well/lane 3


title: patient21_other_sample1

value: Other


title: Hippocampus_rTg4510_TG [204018770001_R02C01]


title: Hippocampus_rTg4510_TG [204018770001_R01C01]


title: KCs 120h post APAP rep4

description: KCs 120h post APAP rep4

value: KCs

value: APAP


title: KCs 120h post APAP rep2

description: KCs 120h post APAP rep2


title: PBMC, habitual sleep, participant 4, GEM well/lane 1

value: HS


title: patient32_idiohered_sample1


title: Hippocampus_rTg4510_WT [204018770003_R05C02]

value: WT


title: Hippocampus_rTg4510_WT [204018770003_R06C02]


title: PBMC, habitual sleep, participant 1, GEM well/lane 3


title: patient31_idiohered_sample1

value: Idiohered


title: PBMC, habitual sleep, participant 3, GEM well/lane 1

value: PBMC


title: KCs 120h post APAP rep1

description: KCs 120h post APAP rep1


title: Hippocampus_rTg4510_TG [204018770003_R03C02]


title: Mouse, male sample2, sublibrary1

city: St. Louis

first: Lite

last: Yang

state: MO

address: 4922 Parkview Place

institute: Washington University in St. Louis

data_processing:
Raw sequencing data from individual libraries were processed and mapped to the reference genome and the gene-cell counts matrices from all snRNA-seq libraries of the same species were concatenated using 10X Genomics cellranger-v6.1.2 or cellranger-v7.0.1
Assembly: mouse: mm10, baboon: Panubis1.0, and macaque: Mmul_10
Supplementary files format and content: Gene matrix.rds contains gene-cell counts for all libraries, metadata.csv contains meta data for all libraries

source_name: Ventral pallidum, bilateral, pooled from 5 mice

extract_protocol:
Nuclear extraction for both mice and primates was performed with density gradient centrifugation according to the protocol described previously with modifications to scale down the reaction volume (85). Samples were moved from -80 ̊C and thawed on ice for 2 minutes. Tissues were transferred to a dounce homogenizer (Millipore Sigma, D8938-1SET) in homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris-HCl, pH 8.0, 5 µg/mL actinomycin, 1% BSA, and 0.08 U/µl RNase inhibitor, 0.01% NP40) on ice. Samples were homogenized for 10 strokes with the loose pestle in a total volume of 1 mL, followed by 10 additional strokes with the tight pestle. The tissue homogenate was then passed through a 50 µm filter and diluted 1:1 with working solution (50% iodixanol, 25 mM KCl, 5 mM MgCl2, and 10 mM Tris-HCl, pH 8.0). Nuclei were layered onto an iodixanol gradient after homogenization and ultracentrifuged as described previously. After ultracentrifugation, nuclei were collected between the 30 and 40% iodixanol layers and diluted with resuspension buffer (1xPBS with 1% BSA, and 0.08 U/µl RNase inhibitor). Nuclei were centrifuged at 500 g for 10 min at 4°C and resuspended in resuspension buffer with 5 ng/µl of 7-AAD. FACS was carried out to further remove cellular debris. 7-AAD+ events were collected using a 100 µm nozzle on a BD FACSAria III instrument into a 1.5 mL microcentrifuge tube.
Nuclei were processed according to the manufacturer’s manual of 10X Genomics Chromium Single Cell Gene Expression 3’ V3.1 Assay.


title: PBMC, habitual sleep, participant 1, GEM well/lane 1


title: KCs 120h post APAP rep3

description: KCs 120h post APAP rep3


title: patient3_chd_sample1

value: CHD


title: Hippocampus_rTg4510_TG [204018770003_R04C02]


title: Mouse, female sample2, sublibrary1

value: Ventral pallidum, bilateral, pooled from 5 mice


title: patient29_chd_sample1


title: Mouse, female sample1, sublibrary1


title: patient30_other_sample1


title: Hippocampus_rTg4510_WT [204018770003_R01C02]


title: Mouse, male sample1, sublibrary2


title: S508 96h

city: Coventry

first: Jan

middle: J

last: Brosens

address: University Hospital Coventry and Warwickshire

department: Warwick Medical School

institute: University of Warwick

data_processing:
Sequencing reads were mapped to the hg38 human genome assembly using STAR2 v2.5.3a using default settings and gencode.v38 annotation file Ensembl.
Assembly: hg38
Supplementary files format and content: Decidualization_timecourse_RNAseq_counts_matrix.txt: counts matrix in .TXT format

source_name: Endometrial stromal cell

extract_protocol:
RNA was purified using QIAGEN RNeasy AllPrep kits according to manufacturer's instructions.
Libraries were constructed using Illumina Nextera Library Prep Kit with i7 indexes. Concentrations were measured using Qubit HS DNA Assay (Thermo Fisher Scientific, Paisley, United Kingdom). Library sizes were assessed on an Agilent Technologies 2100 Bioanalyzer before sequencing on the Illumina Nextseq platform paired-end reads (42 bp (R1) and 42 bp (R2)). One cartridge was used per 2 patients i.e. 20 multiplexed samples per cartridge.

treatment_protocol: Endometrial biopsies were collected in DMEM-F12 media and processed for primary EnSC culture as described (Brosens 1999). Monolayers of stromal cells were cultured (in DMEM-F12 media, 10 % dextra-coated charcoal-stripped FBS, 1× Antibiotic-Antimycotic, L-Glutamine, Insulin and E2, at 37 ˚C with 5 % CO2) until confluent. Confluent cells were incubated for 12 hours in differentiation base media (phenol red-free DMEM/F-12, 2 % dextran-coated charcoal-stripped FBS, 1× Antibiotic-Antimycotic, L-Glutamine) before the addition of 0.5 mM 8-bromo-cAMP and 1M medroxyprogesterone acetate (MPA) to induce decidualization.

value: Endometrial stromal cell

tag: batch

value: Batch 2


title: S508 48h


title: PBMC, habitual sleep, participant 2, GEM well/lane 1


title: xpc-1 RNA-seq R2

city: Chapel Hill

first: Cansu

last: Kose

state: NC

address: 120 Mason Farm Rd.

department: Biochemistry and Biophysics

institute: UNC-Chapel Hill

description: raw files are adaptor-trimmed

data_processing:
Reads were aligned using STAR, followed by a filtering step to remove unmapped reads, reads with unmapped mates, reads that do not pass quality controls, reads that are unpaired, and reads that are not properly paired.. We only kept the first read from the mate pair to ensure independent measures. Read counts for each gene (ensemble: Caenorhabditis_elegans.WBcel235.105.gtf) were obtained using FeatureCounts.
Assembly: Caenorhabditis elegans (Ensembl Version 105)
Supplementary files format and content: Tab-delimited text files include read numbers for each gene.

organism: Caenorhabditis elegans

source_name: whole-organism

growth_protocol: L1 worms were grown on NGM plates and fed with E. coli bacteria

extract_protocol:
L1 wildtype, csb-1, xpc-1 1 stage  C. elegans were collected in M9 and washed until the supernatant was clear, followed by incubation with TRIzol and chloroform. After centrifugation at 14,000g for 15 minutes at 4°C, the aqueous phase was mixed with an equal volume of isopropanol. Following centrifugation, the RNA pellet was washed several times and then resuspended in RNase-free water. Next steps, stranded and poly(A) enriched library preparation and sequencing were performed by Novogene.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

treatment_protocol: untreated

tag: line

value: whole-organism

value: untreated


title: csb-1 RNA-seq R2

description: raw files are adaptor-trimmed


title: csb-1 RNA-seq R1

description: raw files are adaptor-trimmed


title: Hippocampus_rTg4510_WT [204018770003_R02C02]

value: Hippocampus

value: F


title: S508 36h


title: MEF, Gliocidin 12 hr, replicate 3

first: Mungunsarnai

last: Ganbold

state: NYC

address: 417 East 68st

department: Brain Tumor Center

institute: MSKCC

data_processing:
Raw reads were aligned to GRCm38 mouse reference genome in a Linux environment using STAR (v.2.7.8a) and gene-level counts were generated with “quantMode GeneCounts" parameter.
Assembly: mm10; GRCm38
Supplementary files format and content: FASTQ as raw files
Supplementary files format and content: Comma-separated gene level MEF and HTS counts and RDS file of Seurat Integrated  Vehicle, Temozolomide, Gliocidin and Combo single cell RNAseq counts as processed 3 files

source_name: mouse embryonic fibroblasts

extract_protocol:
HTS cells and MEFs were treated with DMSO or Gliocidin (1μM) for 12 hours. Cells were harvested and RNA extracted using Direct-zol RNA Microprep kit (Zymo Research).
polyA selected, non-strand specific

value: mouse embryonic fibroblasts

value: fibroblast

value: mouse tumor cells

value: wildtype

value: Gliocidin


title: N2 RNA-seq R2

description: raw files are adaptor-trimmed


title: Hippocampus_rTg4510_WT [204018770003_R05C01]

value: Mixed


title: Hippocampus_rTg4510_WT [204018770003_R06C01]

value: WT


title: Hippocampus_rTg4510_TG [204018770003_R04C01]

value: TG


title: S508 24h


title: Hippocampus_rTg4510_TG [204018770003_R03C01]


title: S508 18h


title: xpc-1 RNA-seq R1

description: raw files are adaptor-trimmed


title: N2 RNA-seq R1

description: raw files are adaptor-trimmed


title: MEF, Gliocidin 12 hr, replicate 1


title: Hippocampus_rTg4510_WT [204018770003_R02C01]


title: Mouse, male sample1, sublibrary1


title: SKOV3 CAF, rep 3

city: Sioux Falls

first: Pilar

last: de la Puente

state: South Dakota

address: 2301 E 60th St N

institute: Sanford Research

data_processing:
Raw data files received from Novogene. Reads aligned using STAR v 2.7.10 and mapped to human genome build 38.
Assembly: hg38
Supplementary files format and content: tab delimited data files include raw gene counts for each Sample

source_name: SKOV3 conditioned uCAF

extract_protocol:
RNA was collected using QIAgen RNeasy mini columns and confirmed for quality.
RNA was extracted and sent to Novogene for sequencing. RNA libraries for RNA-seq was prepared using standard Illumina protocols through Novogene.

value: SKOV3 conditioned uCAF

value: cancer associated fibroblasts


title: S508 9h


title: S508 12h


title: SKOV3 CAF, rep 2


title: MEF, DMSO 12 hr, replicate 2

value: DMSO


title: S508 6h

value: Endometrial stromal cell


title: Hippocampus_rTg4510_TG [203877620100_R05C02]


title: Hippocampus_rTg4510_WT [204018770003_R01C01]


title: Normal HUF, rep 3

source_name: HUF

value: HUF

value: normal fibroblasts


title: MEF, Gliocidin 12 hr, replicate 2


title: Hippocampus_rTg4510_TG [203877620100_R06C02]


title: HTS, Gliocidin 12 hr, replicate 3

source_name: tumor, HTS

value: tumor, HTS

value: GBM


title: S508 3h

value: Batch 2


title: S508 0h


title: Normal HUF, rep 2


title: HTS, Gliocidin 12 hr, replicate 2


title: MEF, DMSO 12 hr, replicate 3

value: mouse embryonic fibroblasts


title: S506 96h


title: Kuramochi CAF, rep 3

source_name: Kuramochi conditioned uCAF

value: Kuramochi conditioned uCAF


title: Hippocampus_rTg4510_WT [203877620100_R03C02]

value: Hippocampus

value: F


title: Normal HUF, rep 1


title: Kuramochi CAF, rep 2


title: MEF, DMSO 12 hr, replicate 1

value: fibroblast

value: mouse tumor cells

value: wildtype


title: HTS, Gliocidin 12 hr, replicate 1

value: Gliocidin


title: Hippocampus_rTg4510_TG [203877620100_R02C02]

value: Mixed

value: TG


title: S506 36h


title: Hippocampus_rTg4510_TG [203877620100_R01C02]


title: SKOV3 CAF, rep 1

value: SKOV3 conditioned uCAF

value: cancer associated fibroblasts


title: S506 48h

value: Endometrial stromal cell


title: HTS, DMSO 12 hr, replicate 3

value: DMSO


title: HTS, DMSO 12 hr, replicate 2

value: tumor, HTS


title: Hippocampus_rTg4510_WT [203877620100_R04C02]

value: WT


title: Hippocampus_rTg4510_WT [203877620100_R04C01]


title: Hippocampus_rTg4510_TG [203877620100_R05C01]


title: HTS, DMSO 12 hr, replicate 1

value: GBM


title: Hippocampus_rTg4510_WT [203877620100_R03C01]


title: S506 18h

value: Batch 2


title: Primary CAF, rep 2

source_name: Primary OC CAF

value: Primary OC CAF


title: S506 12h


title: mouse 10, ALY+LPS

city: TORONTO

first: Gary

last: Sweeney

state: ON

address: 4700 Keele street

country: Canada

institute: York University

data_processing:
featureCounts v1.5.0-p3
Assembly: Hisat2 v2.0.5
Supplementary files format and content: tab-deilimited text file includes raw counts for each sample

source_name: blood

extract_protocol:
RNA was extracted using PureLink™ RNA Mini Kit (Thermo 12183018). 1 ug of RNA was used for the construction of sequencing libraries.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

value: blood


title: Hippocampus_rTg4510_TG [203877620100_R02C01]

value: Hippocampus

value: F


title: Primary CAF, rep 3


title: Primary CAF, rep 1


title: mouse 8, ALY+LPS


title: mouse 7, ALY+LPS


title: S506 9h


title: Hippocampus_rTg4510_WT [204027420011_R06C02]


title: Hippocampus_rTg4510_TG [203877620100_R01C01]


title: mouse 6, ALY+LPS


title: Kuramochi CAF, rep 1

value: Kuramochi conditioned uCAF


title: S506 3h


title: mouse 4, ALY+LPS


title: S506 24h


title: S506 6h


title: S506 0h


title: SANLPC, CITE-seq adt

city: Toronto

first: Stephanie

last: Protze

state: Ontario

address: 101 College Street

department: McEwen Stem Cell Institute

institute: University Health Network

description: antibody-derived oligotag (ADT)

library_source: other

data_processing:
The demultiplexing, barcoded processing, and gene counting were made using Cell Ranger software v6.1.2 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix file
Library strategy: CITE-seq

molecule: protein

extract_protocol:
SANLPCs were dissociated into single cells, barcoded CD34 antibody was added and the cells were FACS sorted for live singlets using DAPI
Library construction was performed according to manufacturers instruction (single cell 3' v3 protocol, 10x Genomics)

value: SANLPC differentiation

tag: adt

value: TotalSeq A0054 anti-human CD34


title: SANLPC, CITE-seq gex

description: polyA RNA


title: SANLPC, scRNAseq

description: 10x genomics

data_processing:
The demultiplexing, barcoded processing, and gene counting were made using Cell Ranger software v2.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix file

extract_protocol:
SANLPCs were dissociated into single cells and FACS sorted for live singlets using DAPI.
Library construction was performed according to manufacturers instruction (single cell 3' v2 protocol, 10x Genomics)


title: mouse 3, ALY+LPS

tag: tissue


title: Hippocampus_rTg4510_WT [204027420011_R05C02]

value: Mixed

tag: genotype


title: fetal SAN, snRNAseq

description: 10x genomics

data_processing:
The demultiplexing, barcoded processing, and gene counting were made using Cell Ranger software v3.1.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: GRCh38-1.2.0_premrna-
Supplementary files format and content: Tab-separated values files and matrix file

source_name: dissected fetal SAN gestatio week 19

extract_protocol:
SAN tissue was dissected from the heart. The tissue was immediately frozen using liquid nitrogen and stored at -80°C. The frozen tissue was retrieved and dissociated using lysis buffer containing: 0.32M sucrose (Sigma, S0389), 5mM CaCl2 (Fluka, 21114), 3mM Mg(AC)2 (Sigma, 228648), 20mM Tris-HCl (ThermoFisher, 15567-027), 0.1%Triton X-100 (MilliporeSigma, X100), 0.1mM EDTA (ThermoFisher, AM9260G) in DNase/RNase free water (Qiagen, 129115). A douncer was used to mechanically homogenize the tissue until single nuclei were obtained. Homogenate was washed twice with PBS containing 1% BSA and 0.2U/ul RNAseOUT (ThermoFisher, 10777019) and filtered through a 40um cell strainer. Nuclei were stained with DAPI (10g/ml) and sorted for DAPI+ single-nuclei on a FACSAria (BD) sorter at the SickKids-UHN Flow Cytometer Facility.
Library construction was performed according to manufacturers instruction (single cell 3' v3 protocol, 10x Genomics)

value: dissected fetal SAN gestatio week 19


title: S170 96h

value: Batch 1


title: mouse 1, ALY+LPS

tag: treatment


title: Hippocampus_rTg4510_WT [204027420011_R02C02]


title: Hippocampus_rTg4510_TG [204027420011_R03C02]

value: TG


title: S170 48h

value: Endometrial stromal cell


title: S170 36h


title: mouse 7, LPS

value: LPS


title: HAP1parental cell_VacV_polysomes_7

city: Chicago

first: Chorong

last: Park

address: 303 E Chicago Ave

institute: Northwestern Univeristy

data_processing:
Raw reads quality check with FastQC
reads trimming with Trimmomactic
reads aligning with STAR
gene counts with Htseq
Assembly: GRCh38 and VacV (AY243312.1)
Supplementary files format and content: for signaling output, Bigwig format files were created
Supplementary files format and content: for gene counts, txt files were created
Library strategy: Ribosome profiling

growth_protocol: HAP1 parental cells (Horizon, C859) and RACK1 knockout HAP1 cells were cultured in Iscove’s Modified Dulbecco’s medium (IMDM; Fisher Scientific) containing 5% fetal bovine serum (FBS), 100 IU penicillin-streptomycin, 4mM L-glutamine and 25 mM HEPES.

extract_protocol:
cell lysates were prepared for sucrose gradient centrifugation and polysome fractionation then RNA was extracted from total, 80S and polysome pooled fractions using RNA extraction kits (QIAGEN, 74104).
mRNA samples were prepared using NEB ultraII non-directional kit with polyA selection kit (NEB, #E7775)

treatment_protocol: cells were infected with Vaccinia virus at MOI 25

tag: cell line

value: wild type

value: Haploid

tag: infection

value: VacV


title: HAP1parental cell_VacV_total_7


title: S170 24h


title: HAP1parental cell_VacV_80s ribosome_7


title: mouse 6, LPS

value: WT


title: S170 18h


title: Hippocampus_rTg4510_TG [204027420011_R04C02]


title: HAP1_RACK1KO_VacV_total_3

value: RACK1 knock out


title: S170 12h


title: Hippocampus_rTg4510_WT [204027420011_R05C01]


title: Hippocampus_rTg4510_WT [204027420011_R06C01]


title: Hippocampus_rTg4510_TG [204027420011_R04C01]


title: mouse 4, LPS

value: blood


title: HAP1_RACK1KO_VacV_polysome_3


title: mouse 3, LPS


title: HAP1parental cell_VacV_total_6


title: mouse 8, LPS


title: S170 9h


title: Hippocampus_rTg4510_WT [204027420011_R01C02]

value: Hippocampus


title: S170 6h


title: mouse 2, LPS


title: Hippocampus_rTg4510_TG [204027420011_R03C01]

value: F


title: Hippocampus_rTg4510_WT [204027420011_R01C01]


title: Hippocampus_rTg4510_WT [204027420011_R02C01]


title: HAP1parental cell_VacV_80s ribosome_6


title: HAP1parental cell_VacV_polysomes_6


title: mouse 5, LPS


title: mouse 10, ALY


title: HAP1_RACK1KO_VacV_80s ribosome_3


title: S170 0h


title: Hippocampus_J20_TG [204027420021_R06C02]


title: mouse 9, ALY


title: S169 96h


title: HAP1_RACK1KO_VacV_total_2


title: mouse 8, ALY


title: S169 48h


title: mouse 7, ALY


title: HAP1_RACK1KO_VacV_polysome_2


title: S170 3h


title: HAP1_RACK1KO_VacV_80s ribosome_2


title: S169 36h


title: mouse 6, ALY


title: Hippocampus_J20_WT [204027420021_R04C02]


title: S169 24h


title: HAP1parental cell_VacV_total_5


title: Hippocampus_J20_WT [204027420021_R03C02]


title: HAP1parental cell_VacV_polysomes_5


title: S169 18h


title: Hippocampus_J20_TG [204027420021_R01C02]


title: Hippocampus_J20_TG [204027420021_R02C02]


title: mouse 4, ALY


title: Hippocampus_J20_TG [204027420021_R05C02]


title: HAP1parental cell_VacV_80s ribosome_5


title: S169 12h


title: S169 9h


title: HAP1_RACK1KO_VacV_total_1


title: mouse 3, ALY


title: mouse 2, ALY


title: Hippocampus_J20_TG [204027420021_R06C01]


title: mouse 5, ALY


title: S169 6h


title: HAP1_RACK1KO_VacV_polysome_1


title: Hippocampus_J20_TG [204027420021_R05C01]


title: mouse 10, PBS

value: PBS


title: S169 3h


title: HAP1_RACK1KO_VacV_80s ribosome_1


title: Hippocampus_J20_WT [204027420021_R03C01]


title: Hippocampus_J20_WT [204027420021_R04C01]


title: S169 0h


title: Hippocampus_J20_TG [204027420021_R02C01]


title: HAP1parental cell_VacV_polysomes_4


title: mouse 9, PBS


title: LIHDIIV14 at 0h

city: Esch-sur-Alzette

first: Feng

middle: Q.

last: Hefeng

address: 29, rue Henri Koch

department: Department of Infection and Immunity

country: Luxembourg

institute: Luxembourg Institute of Health

description:
column name description
HFHJYBGXC_V14T0Th2_19s000188-1-1_He_lane119s000188_sequence.txt.gz

data_processing:
Quality control of the raw sequencing data was conducted using the FastQC software (v0.11.7-Java-1.8.0_162) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were mapped to the reference human genome 38 (http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/) and summarized to genes using the R Bioconductor Rsubread package (v1.32.4). In addition to those already failed with RNA extraction steps due to technical issues, one sample was also excluded for further analysis because CD127 Ab was forgotten to add before sorting. Genes that consistently had zero or very low counts were first removed using the Bioconductor edgeR package (v3.24.3). Trimmed Mean of M-values (TMM) normalization was performed on the filtered data with the edgeR package. The normalized data were voom-transformed to enable differential expression analysis with the Bioconductor limma package (v3.38.3).
Assembly: reference human genome 38
Supplementary files format and content: Excel table summary file for all the samples; each row represents one gene (gene name is based on HGNC to avoid Excel conversion errors), while each column represents the normalized read counts of the corresponding gene for the given sample; the column name of each sample is equal to the raw sequence file name.

extract_protocol:
Following the PBMC isolation from fresh blood of different participants at various time points/visits, CD4+ T cells were first enriched with human CD4 microbeads (130-045-101, Miltenyl Biotec) following the manufacture’s recommendations while the remaining fractions of PBMC were immediately cryopreserved as described in other sections of the manuscript. The CD4+ T cells were then immediately shipped to our sorting flow-cytometry facility at 4°C. The CD4+ T cells were first stained in Brilliant Stain Buffer (563794, BD) using all the Abs with specified dilution factors listed in Table S4 (of the manuscript). Incubate for 30 min at 4°C in the dark, briefly vortex once after 15 min. Wash the cells twice: centrifuge at 350g, 10 min, 4°C. Re-suspend the cells at a concentration of 10 million per ml. Proceed to aseptic sorting 20 PSI, with 100 um nozzle and Purity mode in a BD Aria III sorter (for the FACS gating strategy, please refer to Figure S6A of the manuscript). After sorting, cells were centrifuged at 350g, 10 min, 4°C, pelleted and lysated in 700 ul of the Qiazol buffer (Qiagen). Transfer the samples into 1.5 ml Eppendorf tubes and immediately freeze at -80°C until RNA extraction. RNA was extracted using RNeasy Micro kit (Qiagen) following the manufacture’s recommendations.
RNA-seq was performed at the EMBL Genomics Core Facility (Heidelberg, Germany) using single-read 75bp by NextSeq 500 with ~ 50 Million reads/sample. The NEBNext Ultra II RNA Library Prep Kit was used and the rRNA depletion step was included.

value: PBMC

tag: cell type

value: CD4 Th2 cells

tag: disease state

value: Venom allergy patients

value: Venom allergy AIT

tag: time


title: mouse 8, PBS


title: HAP1parental cell_VacV_80s ribosome_4


title: Hippocampus_J20_TG [204027420021_R01C01]

tag: Sex


title: LIHDIIP16 at 0h

description:
column name description
H37VCBGXC_P16T0Th2_19s000205-1-1_He_lane119s000205_sequence.txt.gz

value: Pollen allergy patients

value: Pollen allergy AIT


title: Hippocampus_J20_WT [204027420041_R06C02]

tag: externalsampleid


title: HAP1parental cell_mock_polysomes_4

value: mock


title: mouse 1, ALY


title: LIHDIIP12 at 12W

description:
column name description
H37VCBGXC_P12T4Th2_19s000332-1-1_He_lane119s000332_sequence.txt.gz


title: mouse 7, PBS


title: mouse 6, PBS


title: LIHDIIP11 at 12W

description:
column name description
H37VCBGXC_P11T4Th2_19s000331-1-1_He_lane119s000331_sequence.txt.gz


title: HAP1parental cell_VacV_total_3


title: Hippocampus_J20_WT [204027420041_R05C02]

tag: dob


title: HAP1parental cell_mock_80s ribosome_4


title: mouse 4, PBS


title: HAP1parental cell_VacV_80s ribosome_3


title: Hippocampus_J20_TG [204027420041_R04C02]

tag: dod

value: TG


title: LIHDIIP08 at 6W

description:
column name description
H37VCBGXC_P08T3Th2_19s000306-1-1_He_lane119s000306_sequence.txt.gz


title: Hippocampus_J20_WT [204027420041_R02C02]

tag: agedays


title: mouse 5, PBS


title: mouse 3, PBS


title: Hippocampus_J20_TG [204027420041_R03C02]

tag: mousestrain


title: HAP1parental cell_VacV_polysomes_3

value: wild type


title: LIHDIIP03 at 12W

description:
column name description
H37VCBGXC_P03T4Th2_19s000327-1-1_He_lane119s000327_sequence.txt.gz


title: mouse 2, PBS


title: Hippocampus_J20_WT [204027420041_R01C02]


title: Hippocampus_J20_WT [204027420041_R05C01]


title: Hippocampus_J20_WT [204027420041_R06C01]


title: mouse 1, PBS


title: Hippocampus_J20_TG [204027420041_R04C01]


title: HAP1parental cell_mock_80s ribosome_3

value: Haploid


title: LIHDIIC08 at 2W

description:
column name description
H37VCBGXC_C08T4Th2_19s000344-1-1_He_lane119s000344_sequence.txt.gz

value: Healthy controls

value: no any AIT treatment


title: mCCDcl1 cells, TMPRSS2 knockout, rep6

city: Erlangen

first: Alexandr

middle: V

last: Ilyaskin

address: Waldstr. 6

department: Institute of Cellular and Molecular Physiology

country: Germany

description:
278738
rlogcounts2023.txt

data_processing:
quality trimming using cutadapt v3
alignment to GRCm38 using STAR v2.7
feature counting with subRead featureCounts v2.0.1 and Ensembl annotation 102
differential expression analysis using DESeq2
Assembly: GRCm38.102
Supplementary files format and content: tab-separated text containing rlog-normalized counts

growth_protocol: TMPRSS2 knockout mCCDcl1 cells were generated using CRISPR/Cas9 technique. sgRNA sequence targeting firefly luciferase, which is not expressed in murine cells, was used to generate nontargeting control mCCDcl1 cells. TMPRSS2 knockout and control mCCDcl1 cells were seeded on permeable supports (Millicell PCF membrane inserts; Merck-Millipore) in a standard culture medium (phenol-red free DMEM/F12 medium supplemented with 2% fetal bovine serum, 1 nM triiodothyronine, 60 nM sodium selenite, 5 µg/ml apotransferrin, 10 ng/ml epidermal growth factor, 5 µg/ml insulin, 50 nM dexamethasone, 100 units/ml penicillin, 100 µg/ml streptomycin) and maintained in a 5% CO2 atmosphere at 37 °C. After five days, cells were fed with modified medium lacking apotransferrin, epidermal growth factor, and fetal bovine serum. 24 h before experiments, dexamethasone was removed from the supplemented medium, and medium was exchanged for the last time.

extract_protocol:
RNA was isolated from cells harvested from each individual permeable support using the NucleoSpin RNA kit (Machery-Nagel).
mRNA libraries were prepared using the Illumina Truseq Stranded mRNA kit according to the manufacturer's instructions.

value: renal cortical collecting duct cells

value: TMPRSS2 knockout


title: LIHDIIC07 at 12W

description:
column name description
H37VCBGXC_C07T6Th2_19s000363-1-1_He_lane119s000363_sequence.txt.gz


title: LIHDIIP08 at 12W

description:
column name description
H37VCBGXC_P08T4Th2_19s000328-1-1_He_lane119s000328_sequence.txt.gz


title: mCCDcl1 cells, TMPRSS2 knockout, rep5

description:
278737
rlogcounts2023.txt


title: HAP1parental cell_VacV_total_2

value: VacV


title: LIHDIIV07 at D7

description:
column name description
H35GTBGXC_V07T3Th2_19s000292-1-1_He_lane119s000292_sequence.txt.gz


title: LIHDIIV07 at 0h

description:
column name description
H35GTBGXC_V07T0Th2_19s000181-1-1_He_lane119s000181_sequence.txt.gz


title: HAP1parental cell_VacV_polysomes_2


title: mCCDcl1 cells, TMPRSS2 knockout, rep4

description:
278736
rlogcounts2023.txt


title: HAP1parental cell_VacV_80s ribosome_2


title: mCCDcl1 cells, TMPRSS2 knockout, rep3

description:
278735
rlogcounts2023.txt


title: HAP1parental cell_mock_total_2


title: HAP1parental cell_mock_polysomes_3


title: LIHDIIP10 at 24h

description:
column name description
H35GTBGXC_P10T1Th2_19s000237-1-1_He_lane119s000237_sequence.txt.gz


title: HAP1parental cell_mock_total_3


title: mCCDcl1 cells, TMPRSS2 knockout, rep2

description:
278732
rlogcounts2023.txt


title: Hippocampus_J20_WT [204027420041_R02C01]

value: Hippocampus

value: F

value: WT


title: Hippocampus_J20_TG [204027420041_R03C01]


title: Hippocampus_J20_TG [204027420043_R06C02]


title: LIHDIIP01 at 6W

description:
column name description
H37VCBGXC_P01T3Th2_19s000302-1-1_He_lane119s000302_sequence.txt.gz

value: PBMC

value: CD4 Th2 cells


title: Hippocampus_J20_WT [204027420041_R01C01]


title: Hippocampus_J20_TG [204027420043_R05C02]


title: HAP1parental cell_mock_80s ribosome_2


title: HAP1parental cell_mock_polysomes_2


title: mCCDcl1 cells, TMPRSS2 knockout, rep1

description:
278730
rlogcounts2023.txt


title: mCCDcl1 cells, nontargeting control, rep6

description:
278728
rlogcounts2023.txt

value: nontargeting contol (WT)


title: LIHDIIP08 at 2W

description:
column name description
H35GTBGXC_P08T2Th2_19s000270-1-1_He_lane119s000270_sequence.txt.gz

value: Pollen allergy patients


title: HAP1parental cell_VacV_polysomes_1


title: Hippocampus_J20_WT [204027420043_R03C02]


title: LIHDIIP08 at 0h

description:
column name description
H35GTBGXC_P08T0Th2_19s000197-1-1_He_lane119s000197_sequence.txt.gz

value: Pollen allergy AIT


title: Hippocampus_J20_WT [204027420043_R04C02]


title: HAP1parental cell_VacV_80s ribosome_1


title: mCCDcl1 cells, nontargeting control, rep5

description:
278726
rlogcounts2023.txt


title: LIHDIIC03 at 24h

description:
column name description
H35GTBGXC_C03T2Th2_19s000282-1-1_He_lane119s000282_sequence.txt.gz


title: LIHDIIP03 at 2W

description:
column name description
H35GTBGXC_P03T2Th2_19s000268-1-1_He_lane119s000268_sequence.txt.gz


title: HAP1parental cell_mock_polysomes_1

value: mock


title: mCCDcl1 cells, nontargeting control, rep2

description:
278723
rlogcounts2023.txt


title: LIHDIIC06 at 8h

description:
column name description
H35GTBGXC_C06T1Th2_19s000249-1-1_He_lane119s000249_sequence.txt.gz


title: HAP1parental cell_mock_80s ribosome_1


title: mCCDcl1 cells, nontargeting control, rep3

description:
278724
rlogcounts2023.txt


title: mCCDcl1 cells, nontargeting control, rep1

description:
278722
rlogcounts2023.txt


title: LIHDIIP14 at 6W

description:
column name description
HJT7NBGXB_P14T3Th2_19s000312-1-1_He_lane119s000312_sequence.txt.gz


title: PCOS22

city: Zhongshan

first: Yuezhou

last: Chen

address: East 2 Sunwen Road

department: Center for Reproductive Medicine

country: China

institute: Zhongshan City People's Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

source_name: cumulus cells

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Life Technologies, Carlsbad, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

value: cumulus cells

value: pcos


title: PCOS21


title: Hippocampus_J20_TG [204027420043_R02C02]

value: TG


title: mCCDcl1 cells, nontargeting control, rep4

description:
278725
rlogcounts2023.txt


title: LIHDIIP13 at 6W

description:
column name description
HJT7NBGXB_P13T3Th2_19s000311-1-1_He_lane119s000311_sequence.txt.gz


title: PCOS23


title: mCCDcl1 cells, vehicle 24h, rep7

description:
275347
rlogcounts2022.txt

growth_protocol: Wildtype mCCDcl1 cells were seeded on permeable supports (Millicell PCF membrane inserts; Merck-Millipore) in a standard culture medium (phenol-red free DMEM/F12 medium supplemented with 2% fetal bovine serum, 1 nM triiodothyronine, 60 nM sodium selenite, 5 µg/ml apotransferrin, 10 ng/ml epidermal growth factor, 5 µg/ml insulin, 50 nM dexamethasone, 100 units/ml penicillin, 100 µg/ml streptomycin) and maintained in a 5% CO2 atmosphere at 37 °C. After five days, cells were fed with modified medium lacking apotransferrin, epidermal growth factor, and fetal bovine serum. 24 h before experiments, dexamethasone was removed from the supplemented medium, and medium was exchanged for the last time.

treatment_protocol: mCCDcl1 cells were treated with 3 nM aldosterone or vehicle (0.9% NaCl) for 24 h. To minimize ENaC-mediated Na+ influx, apical amiloride (2 µM) was present during the treatments and removed shortly before RNA-isolation.

value: vehicle (0.9% NaCl), 24 h


title: Hippocampus_J20_TG [204027420043_R05C01]


title: LIHDIIV17 at D7

description:
column name description
HJT7NBGXB_V17T3Th2_19s000301-1-1_He_lane119s000301_sequence.txt.gz

value: Venom allergy patients

value: Venom allergy AIT


title: Hippocampus_J20_WT [204027420043_R03C01]


title: Hippocampus_J20_TG [204027420043_R01C02]


title: mCCDcl1 cells, vehicle 24h, rep6

description:
275346
rlogcounts2022.txt

value: renal cortical collecting duct cells


title: PCOS20


title: Hippocampus_J20_TG [204027420043_R06C01]


title: LIHDIIP12 at 6W

description:
column name description
HJT7NBGXB_P12T3Th2_19s000310-1-1_He_lane119s000310_sequence.txt.gz


title: Hippocampus_J20_TG [204027420043_R02C01]


title: Hippocampus_J20_WT [204027420043_R04C01]


title: LIHDIIP11 at 6W

description:
column name description
HJT7NBGXB_P11T3Th2_19s000309-1-1_He_lane119s000309_sequence.txt.gz


title: mCCDcl1 cells, vehicle 24h, rep4

description:
275344
rlogcounts2022.txt


title: LIHDIIP10 at 6W

description:
column name description
HJT7NBGXB_P10T3Th2_19s000308-1-1_He_lane119s000308_sequence.txt.gz


title: Hippocampus_J20_TG [204027420043_R01C01]


title: PCOS18


title: PCOS19


title: PCOS17


title: PCOS15


title: Hippocampus_J20_WT [204027420001_R06C02]


title: mCCDcl1 cells, vehicle 24h, rep1

description:
275341
rlogcounts2022.txt


title: LIHDIIP03 at 6W

description:
column name description
HJT7NBGXB_P03T3Th2_19s000304-1-1_He_lane119s000304_sequence.txt.gz


title: PCOS16


title: mCCDcl1 cells, aldosterone 24h, rep7

description:
275340
rlogcounts2022.txt

value: aldosterone, 3 nM, 24 h


title: mCCDcl1 cells, aldosterone 24h, rep6

description:
275339
rlogcounts2022.txt


title: PCOS14


title: mCCDcl1 cells, vehicle 24h, rep5

description:
275345
rlogcounts2022.txt


title: PCOS13


title: mCCDcl1 cells, vehicle 24h, rep2

description:
275342
rlogcounts2022.txt


title: Hippocampus_J20_WT [204027420001_R05C02]

value: Hippocampus


title: LIHDIIP06 at 6W

description:
column name description
HJT7NBGXB_P06T3Th2_19s000305-1-1_He_lane119s000305_sequence.txt.gz


title: mCCDcl1 cells, vehicle 24h, rep3

description:
275343
rlogcounts2022.txt


title: Cortex Entorhinalis_rTg4510_WT [204027420001_R02C02]

source_name: Cortex Entorhinalis

value: Cortex Entorhinalis

value: F

value: Mixed


title: LIHDIIP16 at 2W

description:
column name description
HTGLVBGXB_P16T2Th2_19s000279-1-1_He_lane119s000279_sequence.txt.gz

value: PBMC

value: CD4 Th2 cells


title: LIHDIIP02 at 6W

description:
column name description
HJT7NBGXB_P02T3Th2_19s000303-1-1_He_lane119s000303_sequence.txt.gz

value: Pollen allergy patients


title: Cortex Entorhinalis_rTg4510_TG [204027420001_R03C02]


title: PCOS12


title: Cortex Entorhinalis_rTg4510_TG [204027420001_R04C02]


title: mCCDcl1 cells, aldosterone 24h, rep4

description:
275337
rlogcounts2022.txt

value: WT


title: LIHDIIP03 at 0h

description:
column name description
HTGLVBGXB_P03T0Th2_19s000194-1-1_He_lane119s000194_sequence.txt.gz

value: Pollen allergy AIT


title: Hippocampus_J20_WT [204027420001_R06C01]


title: mCCDcl1 cells, aldosterone 24h, rep5

description:
275338
rlogcounts2022.txt


title: LIHDIIP09 at 6W

description:
column name description
HJT7NBGXB_P09T3Th2_19s000307-1-1_He_lane119s000307_sequence.txt.gz


title: Hippocampus_J20_WT [204027420001_R05C01]


title: PCOS11

value: cumulus cells


title: Cortex Entorhinalis_rTg4510_WT [204027420001_R01C02]


title: LIHDIIC10 at 12W

description:
column name description
HTGLVBGXB_C10T6Th2_19s000366-1-1_He_lane119s000366_sequence.txt.gz

value: Healthy controls

value: no any AIT treatment


title: mCCDcl1 cells, aldosterone 24h, rep2

description:
275335
rlogcounts2022.txt


title: PCOS10

value: pcos


title: LIHDIIC09 at 12W

description:
column name description
HTGLVBGXB_C09T6Th2_19s000365-1-1_He_lane119s000365_sequence.txt.gz


title: Cortex Entorhinalis_rTg4510_TG [204027420001_R04C01]

value: TG


title: PCOS9


title: LIHDIIC08 at 12W

description:
column name description
HTGLVBGXB_C08T6Th2_19s000364-1-1_He_lane119s000364_sequence.txt.gz


title: mCCDcl1 cells, aldosterone 24h, rep3

description:
275336
rlogcounts2022.txt


title: PCOS8


title: mCCDcl1 cells, aldosterone 24h, rep1

description:
275334
rlogcounts2022.txt


title: LIHDIIC08 at 24h

description:
column name description
HTGLVBGXB_C08T2Th2_19s000287-1-1_He_lane119s000287_sequence.txt.gz


title: LIHDIIC06 at 12W

description:
column name description
HTGLVBGXB_C06T6Th2_19s000362-1-1_He_lane119s000362_sequence.txt.gz


title: PCOS7


title: Ery2

city: Hangzhou

first: Jiang

last: Penglei

address: Yuhangtang Road 866

department: School of basic medicine science

institute: Zhejiang University

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw reads were trimmed for adaptor sequences and low quality bases using trimmomatic (0.38)
The trimmed reads length less than 17 bp were removed. Clean reads for each sample were aligned by bowtie2 (2.3.4.1) with parameter “--very-sensitive-local” to the artificial small ncRNA reference which include ENSEMBL annotated small ncRNAs (miRNA, misc_RNA, Mt_rRNA, Mt_tRNA, snoRNA, snRNA, tRNA) and 45S pre-rRNA (NR_046233.2).
Read counts per ncRNA were calculated by a perl script.
Assembly: GRCm38
Supplementary files format and content: Comma separated text files with raw gene counts for every gene and every sample

source_name: bone marrow

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen).
1~3 μg total RNA per sample was used for library construction, which was generated using NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB) following manufacturer’s instructions. After synthesis of first strand cDNA, PCR amplification was performed using LongAmp Taq 2X Master Mix, SR Primer for illumina and index primer. PCR products were purified on a 8% polyacrylamide gel (100V, 80 min). DNA fragments corresponding to 170~370 bp (the length of snoRNA plus adaptors) were recovered and dissolved in 8 μL elution buffer. At last, library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips. After clustering of the index-coded samples, the library preparations were sequenced on an Illumina NovaSeq platform.

treatment_protocol: Single cells dissected from mouse tissues (BM) were first stained with surface markers for 30 min in a dark cool room (4°C) and then washed with PBS+2%FBS buffer. Samples were then incubated with fluorescent dye conjugated antibodies for 30 min and analyzed by flow cytometry. For cell surface phenotyping, a lineage cocktail (Lin) was used, including CD3, CD4, CD8, CD11b (Mac-1), Gr1, CD45R (B220), IgM and Ter119 (eBioscience). Monoclonal antibodies against Sca-1, c-Kit, CD34, Flk2, CD49b, CD127, CD16/32 were also used to isolate hematopoietic progenitors and mature cells by FACS.

value: bone marrow

value: Erythroid


title: Cortex Entorhinalis_rTg4510_TG [204027420001_R03C01]


title: My2

value: Myloid


title: LIHDIIC01 at 24h

description:
column name description
HTGLVBGXB_C01T2Th2_19s000280-1-1_He_lane119s000280_sequence.txt.gz


title: PCOS5


title: Ery1


title: Cortex Entorhinalis_rTg4510_WT [204027420001_R01C01]


title: My1


title: PCOS6


title: Cortex Entorhinalis_rTg4510_TG [204027420008_R06C02]


title: PCOS4


title: LIHDIIP15 at 2W

description:
column name description
HJTCNBGXB_P15T2Th2_19s000277-1-1_He_lane119s000277_sequence.txt.gz


title: T2

value: T


title: Cortex Entorhinalis_rTg4510_TG [204027420008_R05C02]

value: Cortex Entorhinalis


title: Cortex Entorhinalis_rTg4510_WT [204027420008_R03C02]

value: F


title: LIHDIIP14 at 2W

description:
column name description
HJTCNBGXB_P14T2Th2_19s000276-1-1_He_lane119s000276_sequence.txt.gz


title: T1


title: PCOS3


title: Cortex Entorhinalis_rTg4510_WT [204027420001_R02C01]

value: Mixed


title: PCOS2


title: LIHDIIP13 at 2W

description:
column name description
HJTCNBGXB_P13T2Th2_19s000275-1-1_He_lane119s000275_sequence.txt.gz

value: PBMC


title: B2

value: B


title: PCOS1


title: LIHDIIP12 at 2W

description:
column name description
HJTCNBGXB_P12T2Th2_19s000274-1-1_He_lane119s000274_sequence.txt.gz

value: CD4 Th2 cells

value: Pollen allergy patients


title: LIHDIIC05 at 12W

description:
column name description
HTGLVBGXB_C05T6Th2_19s000361-1-1_He_lane119s000361_sequence.txt.gz


title: LIHDIIP08 at 24h

description:
column name description
H35GTBGXC_P08T1Th2_19s000235-1-1_He_lane119s000235_sequence.txt.gz

value: Pollen allergy AIT


title: Cortex Entorhinalis_rTg4510_TG [204027420008_R01C02]


title: B1


title: Control17

value: cumulus cells

value: control


title: Cortex Entorhinalis_rTg4510_TG [204027420008_R02C02]


title: LIHDIIP11 at 2W

description:
column name description
HJTCNBGXB_P11T2Th2_19s000273-1-1_He_lane119s000273_sequence.txt.gz


title: Control16


title: Cortex Entorhinalis_rTg4510_WT [204027420008_R04C02]

value: WT


title: MEP1

value: MEP


title: Control15


title: Cortex Entorhinalis_rTg4510_TG [204027420008_R06C01]

value: TG


title: LIHDIIC06 at 24h

description:
column name description
HJTCNBGXB_C06T2Th2_19s000285-1-1_He_lane119s000285_sequence.txt.gz

value: Healthy controls

value: no any AIT treatment


title: Cortex Entorhinalis_rTg4510_TG [204027420008_R05C01]


title: LIHDIIC05 at 24h

description:
column name description
HJTCNBGXB_C05T2Th2_19s000284-1-1_He_lane119s000284_sequence.txt.gz


title: GMP1

value: bone marrow

value: GMP


title: Control13


title: CMP2

value: CMP


title: MEP2


title: Cortex Entorhinalis_rTg4510_WT [204027420008_R03C01]

value: Cortex Entorhinalis

value: F


title: Cortex Entorhinalis_rTg4510_WT [204027420008_R04C01]

value: Mixed


title: Control12


title: Cortex Entorhinalis_rTg4510_TG [204027420008_R01C01]


title: LIHDIIC02 at 24h

description:
column name description
HJTCNBGXB_C02T2Th2_19s000281-1-1_He_lane119s000281_sequence.txt.gz

value: PBMC


title: LIHDIIC07 at 24h

description:
column name description
HJTCNBGXB_C07T2Th2_19s000286-1-1_He_lane119s000286_sequence.txt.gz

value: CD4 Th2 cells


title: CMP1


title: Control11


title: Cortex Entorhinalis_rTg4510_TG [204027420008_R02C01]


title: CLP2

value: CLP


title: LIHDIIV16 at D7

description:
column name description
H77KFBGXB_V16T3Th2_19s000300-1-1_He_lane119s000300_sequence.txt.gz

value: Venom allergy patients

value: Venom allergy AIT


title: LIHDIIV15 at D7

description:
column name description
H77KFBGXB_V15T3Th2_19s000299-1-1_He_lane119s000299_sequence.txt.gz


title: Control14

value: cumulus cells

value: control


title: GMP2


title: LIHDIIV14 at D7

description:
column name description
H77KFBGXB_V14T3Th2_19s000298-1-1_He_lane119s000298_sequence.txt.gz


title: CLP1


title: Control10


title: WT-Kc_rep4

city: Brisbane

first: Janin

last: Chandra

state: Queensland

address: 37 Kent st., Woolloongabba

department: Faculty of Medicine

country: Australia

institute: The University of Queensland

data_processing:
Raw sequences were qualified using FastQC
Low-quality and adapter bases were removed using fastp and mapped to the mouse genome GRCm38 (mm10) using Bowtie2
BAM files were generated by using SAMtools and Picard
Peaksets were derived by using MACS3 peak caller
A consensus peakset was established by restricting analysis to peaks identified consistently in all replicates. Differential analysis was executed by default using DESeq2 interrogated in DiffBind package
Assembly: mm10
Supplementary files format and content: csv, normalized read counts

source_name: skin

extract_protocol:
Cells were sorted from mice then lysed using cold lysis buffer. The nuclei-containing pellets were collected and fragmented by Illumina Tn5 transposition buffer.
Fragmented chromatin was purified using the MinElute PCR Purification Kit (Qiagen) and amplified by PCR using 25 μL HotStart KAPA readymix (2x) and 2.5 μL of both the Forward and Reverse Indexing primers (25 μM)

value: skin

value: Keratinocytes

value: wild type


title: Control8


title: LIHDIIC04 at 24h

description:
column name description
HJTCNBGXB_C04T2Th2_19s000283-1-1_He_lane119s000283_sequence.txt.gz

source_name: PBMC

value: Healthy controls

value: no any AIT treatment


title: Cortex Entorhinalis_rTg4510_WT [204027420007_R06C02]

value: WT


title: Cortex Entorhinalis_rTg4510_WT [204027420007_R05C02]


title: E7-Kc_rep4


title: Control9


title: Control7


title: LIHDIIV12 at D7

description:
column name description
H77KFBGXB_V12T3Th2_19s000297-1-1_He_lane119s000297_sequence.txt.gz


title: WT-LC_rep4

value: Langerhans cells


title: Cortex Entorhinalis_rTg4510_TG [204027420007_R03C02]

value: Cortex Entorhinalis

value: TG


title: E7-LC_rep4


title: Cortex Entorhinalis_rTg4510_WT [204027420007_R02C02]

value: F

value: Mixed


title: Control5


title: LIHDIIV06 at D7

description:
column name description
H77KFBGXB_V06T3Th2_19s000291-1-1_He_lane119s000291_sequence.txt.gz

value: PBMC

value: CD4 Th2 cells


title: LIHDIIV09 at D7

description:
column name description
H77KFBGXB_V09T3Th2_19s000294-1-1_He_lane119s000294_sequence.txt.gz

value: Venom allergy patients


title: Control4


title: E7-LC_rep3


title: E7-LC_rep2


title: LIHDIIV04 at D7

description:
column name description
H77KFBGXB_V04T3Th2_19s000290-1-1_He_lane119s000290_sequence.txt.gz

value: Venom allergy AIT


title: Cortex Entorhinalis_rTg4510_WT [204027420007_R06C01]


title: Cortex Entorhinalis_rTg4510_TG [204027420007_R04C02]


title: Control3

value: cumulus cells


title: Control2

value: control


title: LIHDIIC09 at 24h

description:
column name description
H77KFBGXB_C09T2Th2_19s000288-1-1_He_lane119s000288_sequence.txt.gz


title: E7-Kc_rep2

value: skin


title: LIHDIIC10 at 24h

description:
column name description
H77KFBGXB_C10T2Th2_19s000289-1-1_He_lane119s000289_sequence.txt.gz


title: Cortex Entorhinalis_rTg4510_WT [204027420007_R05C01]


title: E7-Kc_rep3

value: Keratinocytes


title: LIHDIIV11 at D7

description:
column name description
H77KFBGXB_V11T3Th2_19s000296-1-1_He_lane119s000296_sequence.txt.gz


title: Cortex Entorhinalis_rTg4510_WT [204027420007_R01C02]


title: WT-LC_rep3

value: wild type


title: LIHDIIV11 at 24h

description:
column name description
HG3GKBGXB_V11T2Th2_19s000260-1-1_He_lane119s000260_sequence.txt.gz


title: Control1


title: Cortex Entorhinalis_rTg4510_TG [204027420007_R04C01]


title: Cortex Entorhinalis_rTg4510_WT [204027420007_R02C01]


title: WT-LC_rep2


title: LIHDIIV10 at 24h

description:
column name description
HG3GKBGXB_V10T2Th2_19s000259-1-1_He_lane119s000259_sequence.txt.gz


title: PDX-161010-1, Combo

source_name: tumor

value: tumor

value: GBM

value: human tumor cells

value: Gliocidin plus Temozolomide


title: Cortex Entorhinalis_rTg4510_WT [204027420007_R01C01]

value: Cortex Entorhinalis

value: WT


title: Cortex Entorhinalis_rTg4510_TG [204027420007_R03C01]

value: F

value: TG


title: WT-Kc_rep3


title: Cortex Entorhinalis_rTg4510_TG [204027420014_R06C02]

value: Mixed


title: PDX-161010-1, Gliocidin

value: Gliocidin


title: LIHDIIV08 at 24h

description:
column name description
HG3GKBGXB_V08T2Th2_19s000257-1-1_He_lane119s000257_sequence.txt.gz

value: PBMC

value: CD4 Th2 cells

value: Venom allergy patients


title: PDX-161010-1, vehicle

value: Vehicle


title: E7-Kc_rep1

value: skin


title: E7-LC_rep1

value: Langerhans cells


title: LIHDIIV06 at 24h

description:
column name description
HG3GKBGXB_V06T2Th2_19s000255-1-1_He_lane119s000255_sequence.txt.gz

value: Venom allergy AIT


title: Cortex Entorhinalis_rTg4510_TG [204027420014_R05C02]


title: Cortex Entorhinalis_rTg4510_WT [204027420014_R04C02]


title: IR 1051 CM

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.20
Alignment to mouse genome using STAR spliced read aligner
Counting reads using HTSeq with homo sapiens  genome GRCh38 as reference
Normalization using trimmed mean of M values method, and differential expression analysis using Biocoductor packages.
Assembly: GRCh38
Supplementary files format and content: counts

growth_protocol: Patient-derived 1051 GBM cells were growni in Neurosphere media (DEMEMf12, B27, Penn strep, Heparin, EGF, bFGF)

extract_protocol:
Cells were collected as pelletes, washed 2x with PBS . Qiagen Rneasy Plus kit was used for RNA extraction. Nanodrop was used to measure RNA concentration.
Library was prepared using TruSeq Stranded RNA
RNA samples were barded into cDNA libraries and sequencing was carried out as paired end
Novaseq S4

treatment_protocol: Cells were grown as neurospheres and treated with rEndocan (10ng/ml) or HBEC-5i conditon media or just PBS control for 72 hours.

value: IR 1051 CM


title: WT-LC_rep1

value: wild type


title: IR 1051 control

value: IR 1051 control


title: Cortex Entorhinalis_rTg4510_WT [204027420014_R03C02]

data_processing: Normalized Average Beta calculated using the SeSame package in R

extract_protocol: Genomic DNA from all samples was isolated from the entorhinal cortex or hippocampus using the AllPrep DNA/RNA Mini Kit (Qiagen)


title: LIHDIIC09 at 8h

description:
column name description
HG3GKBGXB_C09T1Th2_19s000252-1-1_He_lane119s000252_sequence.txt.gz

value: Healthy controls

value: no any AIT treatment


title: LIHDIIC10 at 8h

description:
column name description
HG3GKBGXB_C10T1Th2_19s000253-1-1_He_lane119s000253_sequence.txt.gz


title: WT-Kc_rep1

value: Keratinocytes


title: LIHDIIV09 at 24h

description:
column name description
HG3GKBGXB_V09T2Th2_19s000258-1-1_He_lane119s000258_sequence.txt.gz


title: 1051 CM


title: PDX-161010-1, Temozolomide

value: tumor

value: GBM

value: human tumor cells

value: Temozolomide


title: 1051 ESM1


title: LIHDIIV07 at 24h

description:
column name description
HG3GKBGXB_V07T2Th2_19s000256-1-1_He_lane119s000256_sequence.txt.gz

value: PBMC


title: LIHDIIC08 at 8h

description:
column name description
HG3GKBGXB_C08T1Th2_19s000251-1-1_He_lane119s000251_sequence.txt.gz

value: CD4 Th2 cells


title: WT-Kc_rep2


title: Cortex Entorhinalis_rTg4510_TG [204027420014_R06C01]

value: Cortex Entorhinalis

value: F

value: Mixed

value: TG


title: Cortex Entorhinalis_rTg4510_TG [204027420014_R05C01]


title: Cortex Entorhinalis_J20_TG [204027420014_R01C02]


title: Cortex Entorhinalis_J20_TG [204027420014_R02C02]


title: M12RPF-JC_A1-RPI47_4th

city: Beijing

first: Xu

middle: jia

last: yue

address: NO.3 Dongdan street, Beijing

institute: Peking Union Medical College

data_processing:
Sequenced reads were first trimmed for adaptor sequences and low quality bases using trimmomatic. rRNA, tRNA and mitochondrial were trimmed from clean data. Trimmed reads were aligned to the reference genome using STAR (2.7.3a). Aligned reads were deduplicated and sorted.
Assembly: GENCODE (vM22) mouse genome (mm10)
Supplementary files format and content: TXT format data
Library strategy: Ribo-seq

extract_protocol:
160 cells were sorted and lysed on ice with 22 mM Tris-HCl (pH 7.4), 1% Triton X-100, 100 µg/mL cycloheximide, 165 mM NaCl, 16.5 mM MgCl2, 5.5 mM CaCl2, 2.2 U/µL RNase inhibitor. Exposed RNA was digested by 10500 U/mL micrococcal nuclease at 37°C for 30 min and then ribosome-protected footprints (RPFs) were generated.
The extracted RPFs for subsequent small RNA library construction was performed including end repair, adapter ligation, cDNA synthesis and PCR amplification. The purified library was sequenced with Illumina NovaSeq 6000 platform.

value: bone marrow

value: WT

value: low-input Ribo-seq (160 cells/type)


title: 1051 control

value: 1051 control


title: IR 1051 ESM1

value: IR 1051 ESM1


title: LIHDIIV04 at 24h

description:
column name description
HG3GKBGXB_V04T2Th2_19s000254-1-1_He_lane119s000254_sequence.txt.gz

value: Venom allergy patients

value: Venom allergy AIT


title: M12RPF-JC_A1-RPI46_4th

value: MPP


title: Cortex Entorhinalis_rTg4510_WT [204027420014_R04C01]


title: M12RPF-JC_A1-RPI48_4th

value: Mat-KO


title: Cortex Entorhinalis_rTg4510_WT [204027420014_R03C01]


title: LIHDIIP15 at 12W

description:
column name description
H773KBGXB_P15T4Th2_19s000335-1-1_He_lane119s000335_sequence.txt.gz

value: Pollen allergy patients

value: Pollen allergy AIT


title: M12RPF-JC_A1-RPI45_4th

value: LT-HSC


title: PDGFBB rep3

growth_protocol: Patient-derived 1079GBM cells were growni in Neurosphere media (DEMEMf12, B27, Penn strep, Heparin, EGF, bFGF)

treatment_protocol: Cells were grown as neurospheres and treated with rEndocan (10ng/ml) or rPDGFBB (10ng/ml) or PBS for control for 72 hours.

value: PDGFBB


title: LIHDIIP10 at 12W

description:
column name description
H773KBGXB_P10T4Th2_19s000330-1-1_He_lane119s000330_sequence.txt.gz

value: PBMC

value: CD4 Th2 cells


title: PDGFBB rep2


title: M12RPF-JC_A1-RPI44_4th

value: CLP


title: M12RPF-JC_A1-RPI43_4th

value: CMP


title: LIHDIIP09 at 12W

description:
column name description
H773KBGXB_P09T4Th2_19s000329-1-1_He_lane119s000329_sequence.txt.gz


title: PDGFBB rep1


title: Cortex Entorhinalis_J20_TG [204027420014_R02C01]

value: Cortex Entorhinalis

value: F

value: TG


title: Cortex Entorhinalis_J20_TG [204027420014_R01C01]


title: M12RPF-JC_A1-RPI42_4th

value: bone marrow

value: GMP

value: low-input Ribo-seq (160 cells/type)


title: LIHDIIP01 at 12W

description:
column name description
H773KBGXB_P01T4Th2_19s000325-1-1_He_lane119s000325_sequence.txt.gz


title: PDGFBB rep4


title: Endocan rep4

value: Endocan


title: LIHDIIP02 at 12W

description:
column name description
H773KBGXB_P02T4Th2_19s000326-1-1_He_lane119s000326_sequence.txt.gz


title: Cortex Entorhinalis_J20_WT [204027420037_R05C02]

value: WT


title: LIHDIIC10 at D7

description:
column name description
H773KBGXB_C10T3Th2_19s000324-1-1_He_lane119s000324_sequence.txt.gz

value: Healthy controls

value: no any AIT treatment


title: LIHDIIC09 at D7

description:
column name description
H773KBGXB_C09T3Th2_19s000323-1-1_He_lane119s000323_sequence.txt.gz


title: M12RPF-JC_A1-RPI39_4th

value: Myeloid cell


title: Endocan rep1


title: LIHDIIC02 at 2W

description:
column name description
H773KBGXB_C02T4Th2_19s000338-1-1_He_lane119s000338_sequence.txt.gz


title: Cortex Entorhinalis_J20_TG [204027420037_R03C02]


title: Endocan rep3


title: LIHDIIP16 at 12W

description:
column name description
H773KBGXB_P16T4Th2_19s000336-1-1_He_lane119s000336_sequence.txt.gz

value: Pollen allergy patients

value: Pollen allergy AIT


title: M12RPF-JC_A1-RPI38_4th

value: B cell


title: Cortex Entorhinalis_J20_WT [204027420037_R06C02]


title: LIHDIIC01 at 2W

description:
column name description
H773KBGXB_C01T4Th2_19s000337-1-1_He_lane119s000337_sequence.txt.gz

value: PBMC

value: CD4 Th2 cells


title: M12RPF-JC_A1-RPI37_4th

value: T cell


title: Control rep4

value: Control


title: M12RPF-JC_A1-RPI40_4th

value: Erythoid cell


title: M12RPF-JC_A1-RPI41_4th

value: MEP


title: Endocan rep2


title: M12RPF-JC_A1-RPI48_3rd

value: bone marrow

value: Mat-KO


title: Control rep3


title: Cortex Entorhinalis_J20_WT [204027420037_R02C02]

value: Cortex Entorhinalis

value: F


title: Control rep2


title: LIHDIIC10 at 6W

description:
column name description
HJT7VBGXB_C10T5Th2_19s000356-1-1_He_lane119s000356_sequence.txt.gz


title: Cortex Entorhinalis_J20_WT [204027420037_R01C02]

value: WT


title: Cortex Entorhinalis_J20_TG [204027420037_R04C02]

value: TG


title: Cortex Entorhinalis_J20_WT [204027420037_R06C01]


title: LIHDIIC09 at 6W

description:
column name description
HJT7VBGXB_C09T5Th2_19s000355-1-1_He_lane119s000355_sequence.txt.gz

value: Healthy controls

value: no any AIT treatment


title: Cortex Entorhinalis_J20_WT [204027420037_R05C01]


title: M12RPF-JC_A1-RPI47_3rd

value: low-input Ribo-seq (160 cells/type)


title: LIHDIIC08 at 6W

description:
column name description
HJT7VBGXB_C08T5Th2_19s000354-1-1_He_lane119s000354_sequence.txt.gz


title: GATA6 KD 2

city: Larissa

first: Antonis

last: Giakountis

address: Biopolis, Mezourlo

department: Biochemistry and Biotechnology

country: Greece

institute: University of Thessaly

data_processing:
HISAT2-BOWTIE2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic
Trimmed sequence reads were mapped to GRCh37/hg19 using hisat2 (parameters -un, --add-chrname). Hisat2 unaligned reads were mapped with BOWTIE2 (parameters --local –very-sensitive-local). Hisat2 and Bowtie2 aligned reads were merged.
Read count extraction and normalization were performed using the metaseqR2 Bioconductor package
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: AGS

growth_protocol: AGS cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol (MRC). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using Illumina's RNA-seq library Prep kit protocol following manufacturer's protocols.

treatment_protocol: 3x10^5 AGS cells  were cultured with and without Doxycycline treatment (1 ug/ml) for 72 hr prior to RNA isolation

value: AGS

value: Gastric cancer cell

value: Doxycycline, 1 ug/ml

value: 72 hrs


title: GATA6 KD 1


title: M12RPF-JC_A1-RPI43_3rd

value: CMP


title: Cortex Entorhinalis_J20_TG [204027420037_R04C01]

first: Emma

last: Walker

address: RILD Barrack Rd


title: M12RPF-JC_A1-RPI42_3rd

value: GMP


title: Control rep1

value: Control


title: Control6

value: cumulus cells

value: control


title: M12RPF-JC_A1-RPI46_3rd

value: bone marrow

value: MPP


title: LIHDIIC06 at 6W

description:
column name description
HJT7VBGXB_C06T5Th2_19s000352-1-1_He_lane119s000352_sequence.txt.gz

value: PBMC

value: CD4 Th2 cells


title: GATA4 KD 2

value: WT


title: M12RPF-JC_A1-RPI44_3rd

value: CLP


title: LIHDIIC07 at 6W

description:
column name description
HJT7VBGXB_C07T5Th2_19s000353-1-1_He_lane119s000353_sequence.txt.gz

value: Healthy controls

value: no any AIT treatment


title: LIHDIIC04 at 12W

description:
column name description
HJT7VBGXB_C04T6Th2_19s000360-1-1_He_lane119s000360_sequence.txt.gz


title: Cortex Entorhinalis_J20_TG [204027420037_R03C01]

value: Cortex Entorhinalis

value: F

value: TG


title: LIHDIIC04 at 6W

description:
column name description
HJT7VBGXB_C04T5Th2_19s000350-1-1_He_lane119s000350_sequence.txt.gz


title: GATA6 Control 2

value: AGS

value: Gastric cancer cell

value: no treatment

value: 72 hrs


title: Cortex Entorhinalis_J20_WT [204027420037_R01C01]


title: Cortex Entorhinalis_J20_WT [204027420037_R02C01]


title: M12RPF-JC_A1-RPI41_3rd

value: MEP

value: low-input Ribo-seq (160 cells/type)


title: LIHDIIC05 at 6W

description:
column name description
HJT7VBGXB_C05T5Th2_19s000351-1-1_He_lane119s000351_sequence.txt.gz


title: LIHDIIC03 at 12W

description:
column name description
HJT7VBGXB_C03T6Th2_19s000359-1-1_He_lane119s000359_sequence.txt.gz


title: Cortex Entorhinalis_J20_TG [204027420027_R06C02]


title: M12RPF-JC_A1-RPI45_3rd

value: bone marrow

value: LT-HSC


title: M12RPF-JC_A1-RPI40_3rd

value: Erythoid cell


title: GATA4 KD 1

value: Doxycycline, 1 ug/ml


title: GATA6 Control 1

value: WT


title: Cortex Entorhinalis_J20_TG [204027420027_R05C02]


title: Cortex Entorhinalis_J20_WT [204027420027_R04C02]


title: GATA4 Control 2


title: LIHDIIC02 at 12W

description:
column name description
HJT7VBGXB_C02T6Th2_19s000358-1-1_He_lane119s000358_sequence.txt.gz

value: PBMC

value: CD4 Th2 cells


title: Cortex Entorhinalis_J20_WT [204027420027_R03C02]


title: M12RPF-JC_A1-RPI39_3rd

value: Myeloid cell


title: LIHDIIV10 at D7

description:
column name description
HN2K3BGX9_V10T3Th2_19s000295-1-1_He_lane119s000295_sequence.txt.gz

value: Venom allergy patients

value: Venom allergy AIT


title: GATA4 Control 1


title: M12RPF-JC_A1-RPI38_3rd

value: B cell


title: Case2 tumor, post-treatment

city: Nagoya

first: Hiromichi

last: Ebi

state: Aichi

address: 1-1, Kanokoden, Chikusa-ku

department: Division of Molecular Therapeutics

country: Japan

institute: Aichi Cancer Center Research Institute

data_processing:
First, fastp (v0.23.4) 4 software for trimming adapter sequences from sequencing reads was applied to paired-end RNA-seq fastq files for each sample.
Second, ribosomal RNA derived reads were removed by RiboDetector (https://github.com/hzi-bifo/RiboDetector).
Third, kallisto (v0.46.2) 5 software was used to estimate a transcript-level abundance from the trimmed reads with known transcript sequences and annotations in GENCODE Release 33.
Third, gene-level abundance values in transcripts per million (TPM) were estimated by summarizing the transcript-level estimates with the R package tximport (v1.22.0) in the R environment (v4.1.2) using a matching list between transcript ids and gene ids based on the annotations of GENCODE.
Assembly: GENCODE Release 33
Supplementary files format and content: A tab-delimited text file includes TPM values for each sample.

source_name: small cell lung cancer

extract_protocol:
Total RNA was extracted from FFPE samples using the RNeasy Mini Kit.
An RNA-seq library was prepared using the SMARTer® Stranded Total RNA-Seq Kit v3 -Pico Input Mammalian (Takara Bio, Japan) following the manufacturer's protocol.

value: small cell lung cancer

tag: case

value: post

value: EGFR tyrosine kinase inhibitors


title: LIHDIIV10 at 0h

description:
column name description
HN2K3BGX9_V10T0Th2_19s000184-1-1_He_lane119s000184_sequence.txt.gz


title: M12RPF-JC_A1-RPI37_3rd

value: T cell


title: Case2 tumor, pre-treatment

source_name: lung adenocarcinoma

value: lung adenocarcinoma

value: pre


title: Cortex Entorhinalis_J20_TG [204027420027_R01C02]

city: Exeter

institute: University of Exeter

value: Cortex Entorhinalis

value: F

value: TG


title: LIHDIIV08 at D7

description:
column name description
HN2K3BGX9_V08T3Th2_19s000293-1-1_He_lane119s000293_sequence.txt.gz


title: M12RPF_A1-RPI48_2nd

value: bone marrow

value: Mat-KO

value: low-input Ribo-seq (160 cells/type)


title: Cortex Entorhinalis_J20_TG [204027420027_R02C02]


title: LIHDIIV08 at 0h

description:
column name description
HN2K3BGX9_V08T0Th2_19s000182-1-1_He_lane119s000182_sequence.txt.gz

value: PBMC

value: CD4 Th2 cells


title: M12RPF_A1-RPI47_2nd

value: WT


title: Case1 tumor, post-treatment


title: Cortex Entorhinalis_J20_TG [204027420027_R06C01]


title: Case1 tumor, pre-treatment


title: M12RPF_A1-RPI46_2nd

value: MPP


title: M12RPF_A1-RPI45_2nd

value: LT-HSC


title: LIHDIIP14 at 0h

description:
column name description
HN2K3BGX9_P14T0Th2_19s000203-1-1_He_lane119s000203_sequence.txt.gz

value: Pollen allergy patients

value: Pollen allergy AIT


title: CD8_VDJ.MPS12349777

city: Montreal

first: Naglaa

last: Shoukry

state: QC

address: Tour Viger, Local 09.414, 900 rue St-Denis

institute: CRCHUM

data_processing:
Raw files were processed using 10x genomics cellranger multi pipeline using default parameters
Assembly: GRCh38 Human Genome + VDJ reference, from Ensembl (As per the cellranger multi tutorial)
Supplementary files format and content: Pertinent files for downstream analysis using Seurat and scRepertoire, in R

molecule: other

growth_protocol: PBMCs were thawed and washed twice with RPMI-5 (RPMI medium supplemented with 5% human Serumand 1% penicillin/streptomycin). Cells (average 2.5 × 106) were then incubated in 1 ml of RPMI-5 for 3 hours at 37°C, 5% CO2 in 5 ml polypropylene snap cap tubes followed by the addition of 5 µl of CD40 blocking antibody to prevent the interaction of CD40L with CD40 and its subsequent downregulation.

extract_protocol:
AIM+ CD4 (CD69+ CD40L+) and AIM+ CD8 T cells (CD69+ 4-1BB+) were FACS-sorted at 18 hours post-stimulation with HCV non-structural protein (NS5B) peptides pool
Single-cell RNA-seq libraries were prepared according to the 10X Genomics chromium single-cell protocol for the Next GEM Single Cell 5' Reagent Kits v2 (Dual Index)

treatment_protocol: Cells were stimulated for 6, 9, 18 or 24 hours at 37°C, 5% CO2 with 1 µg/ml of HCV overlapping peptides pool representing non-structural protein NS5B

value: CD8 T-cell

tag: sample type

value: HCV-specific AIM+ TCR


title: CD8_GEX.MPS12349973

value: HCV-specific AIM+ scRNA


title: Cortex Entorhinalis_J20_TG [204027420027_R05C01]


title: Cortex Entorhinalis_J20_WT [204027420027_R04C01]


title: LIHDIIP13 at 0h

description:
column name description
HN2K3BGX9_P13T0Th2_19s000202-1-1_He_lane119s000202_sequence.txt.gz


title: M12RPF_A1-RPI44_2nd

value: CLP


title: Cortex Entorhinalis_J20_WT [204027420027_R03C01]

value: Cortex Entorhinalis


title: LIHDIIP13 at 12W

description:
column name description
HN2K3BGX9_P13T4Th2_19s000333-1-1_He_lane119s000333_sequence.txt.gz


title: CD4_VDJ.MPS12349777

value: CD4 T-cell


title: M12RPF_A1-RPI43_2nd

value: CMP


title: LIHDIIC01 at 12W

description:
column name description
HN2K3BGX9_C01T6Th2_19s000357-1-1_He_lane119s000357_sequence.txt.gz

value: Healthy controls

value: no any AIT treatment


title: Cortex Entorhinalis_J20_TG [204027420027_R02C01]

value: F

value: TG


title: Cortex Entorhinalis_J20_TG [204027420027_R01C01]


title: CD4_GEX.MPS12349973-E12

value: PBMC


title: LIHDIIP14 at 12W

description:
column name description
HN2K3BGX9_P14T4Th2_19s000334-1-1_He_lane119s000334_sequence.txt.gz

value: CD4 Th2 cells


title: M12RPF_A1-RPI41_2nd

value: bone marrow

value: MEP

value: low-input Ribo-seq (160 cells/type)


title: LIHDIIC01 at 0h

description:
column name description
HN2K3BGX9_C01T0Th2_19s000206-1-1_He_lane119s000206_sequence.txt.gz


title: BNIP3-Doxo-3

city: Tokyo

first: Takao

last: Fujisawa

address: 7-3-1, Hongo, Bunkyo-ku

institute: The University of Tokyo

data_processing:
Sequence reads were trimmed for adaptor sequence/lowquality sequence using trim-galore (parameters: default, version 0.6.7).
Raw paired-end 150 bp reads were aligned to the reference genome (GRCh38) using HISAT2 (version 2.2.1).
The number of mapped reads to each gene was determined by featureCounts (version 2.0.6).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for each sample.

extract_protocol:
RNA was harvested using ISOGEN (Wako). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760L) and NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs Set 4) (NEB, E6446S).

value: siRNA BNIP3, doxorubicin


title: M12RPF_A1-RPI42_2nd

value: GMP


title: BNIP3-Doxo-2


title: M12RPF_A1-RPI40_2nd

value: Erythoid cell


title: BNIP3-Doxo-1


title: Cortex Entorhinalis_J20_WT [204027420024_R05C02]

value: WT


title: LIHDIIP16 at 24h

description:
column name description
HK257BGXB_P16T1Th2_19s000243-1-1_He_lane119s000243_sequence.txt.gz

value: Pollen allergy patients

value: Pollen allergy AIT


title: Cortex Entorhinalis_J20_WT [204027420024_R06C02]

value: Cortex Entorhinalis


title: LIHDIIP15 at 24h

description:
column name description
HK257BGXB_P15T1Th2_19s000242-1-1_He_lane119s000242_sequence.txt.gz


title: M12RPF_A1-RPI39_2nd

value: Myeloid cell


title: Cortex Entorhinalis_J20_TG [204027420024_R03C02]