title: BALF2_SARS2_PR8

first: Alexander

last: Lercher

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
Raw BCL files were converted to FASTQ usingcellranger/5.0.0mkfastq
The referencegenomewas assembled from mouse (mm10) and viral (Influenza A virus A/Puerto Rico/8/1934/H1N1/, SARS-CoV-2/MA10) genomes using cellranger/5.0.0 mkgtf
FASTQ reads were alignedto the reference genome (mm10-PR8-MA10) usingcellranger/5.0.0 count
Assembly: mm10,SARS-CoV-2/MA10 (NCBI GenBank MT952602.1), Influenza A virus A/Puerto Rico/8/1934/H1N1/ (NC_002023.1,NC_002022.1,NC_002021.1,NC_002020.1,NC_002019.1,NC_002018.1,NC_002017.1,NC_002016.1)
Supplementary files format and content: comma-separated file of gene cell matrix for each sample

extract_protocol:
Cells were isolated from bronchoalveolar lavage fluid and resuspended in PBS supplemented to contain 0.04% BSA and adjusted for a target cell recovery of 5,000 cells.
Libraries were prepared using10X Chromium NextGEM single-cell 3' sequencing (NB: Not sure if they list options to choose from, but this would be the specific library prep which we used.)according to the manufacturer's instructions.

value: BALF

value: airway-resident cells


title: BALF1_naive_PR8

status: Public on Oct 02 2024

type: SRA

city: New York

country: USA

library_source: transcriptomic single cell

molecule: total RNA

organism: Mus musculus

source_name: BALF

tag: tissue

tag: cell type

tag: genotype


title: ctrl_pic_3

library_source: transcriptomic

data_processing:
FASTQ file quality was assessed via FASTQC
Reads were aligned to the reference genome (mm10) using STAR
Assembly: mm10
Supplementary files format and content: tab-delimited file of counts per million per sample

growth_protocol: Cells were collected from bronchoalveolar lavage fluid (BALF) and cultured in RPMI medium supplemented to contain 10% fetal bovine serum, 1% penicillin/streptomycin, 1% L-Glutamine, 30 ng/mL (GM-CSF), 10 ng/mL (TGF-b), 1 µM Rosiglitazone.

extract_protocol:
Cells were collected in Trizol and RNA was extracted using the Purelink RNA Mini Kit (Thermo Fisher) according to the manufacturer's instructions.
Libraries were prepped using the SMART v4 Ultra Low Input RNA Kit (Takara #634894) according to the manufacturer's instructions.

tag: agent

value: alveolar macropahge

tag: strain

tag: treatment

value: polyIC


title: ctrl_pic_2


title: polyIC_polyIC_1


title: polyIC_ctrl_3

value: ctrl


title: polyIC_ctrl_1


title: polyIC_polyIC_3


title: polyIC_polyIC_2


title: ctrl_pic_1


title: polyIC_ctrl_2


title: MA10rec_polyIC_3

source_name: alveolar macrophage

value: wild type

tag: group

value: SARS-CoV-2 (mouse adapted strain MA10)

value: alveolar macrophage


title: ctrl_ctrl_1


title: MA10rec_polyIC_1


title: naïve_polyIC_3

value: naive


title: ctrl_ctrl_2


title: naïve_polyIC_2


title: naïve_polyIC_1


title: MA10rec_ctrl_3


title: naïve_ctrl_3


title: MA10rec_ctrl_2


title: naïve_ctrl_2


title: MA10rec_ctrl_1


title: 24M_4

city: guangzhou

first: yabing

last: xiong

address: 1838 North Guangzhou Avenue

country: China

institute: southern medical university

data_processing:
Quality control: clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5)
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes raw counts for each samples
Supplementary files format and content: tab-delimited text files includes FPKM for each samples

source_name: kidney

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer.

value: kidney

value: WT


title: 24M_2


title: MA10rec_polyIC_2


title: 2M_2


title: naïve_ctrl_1


title: 24M_3


title: 2M_1


title: TfR_2_high

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

data_processing:
Raw sequencing data (FASTQ files) were processed using Cell Ranger (v7.1.0), with the refdata-gex-mm10-2020-A reference index provided by 10X Genomics (based on GRCm38, Gencode release M23). To demultiplex cells from libraries that included pooled cells from two animals (one male, one female) a random forest classifier was trained on 6 genes with known sex-specific expression: Xist, Tsix, Ddx3y, Kdm5d, Uty, and Eif2s3y on public data from the Adolescent Mouse Brain Atlas (Zeisel et al., 2018). Cells were assigned to each sex (=animal) when on the classification probability exceeded 90%.
Normalization, variable feature selection, PCA, UMAP dimensionality reduction, and louvain clustering were all carried out in R using Seurat v4 (Hao et al., 2021). Broad cell types were predicted using Seurat's label transfer based on published snRNA-seq data from mouse brain.
Doublets were identified and removed using the scDblFinder package in R (Germain et al., 2021). More granular cell typing of immune and endothelial populations was performed using iterative subclustering and manual cell typing through marker gene analysis.
Assembly: GRCm38
Supplementary files format and content: barcodes.tsv.gz is a gzip compressed tab-separated text file with information about the cell-barcodes. It was generated by the 'cellranger aggr --normalize none' command, and contains barcodes from all samples in this submission.
Supplementary files format and content: features.tsv.gz is a gzip compressed tab-separated text file with information about the detected transcripts. It was generated by the 'cellranger aggr --normalize none' command, and contains features from all samples in this submission.
Supplementary files format and content: matrix.mtx.gz is a gzip compressed text file in Matrix Market Exchange Format, containing a (sparse) matrix of raw, unormalized counts. It was generated by the 'cellranger aggr --normalize none' command, and contains counts for all features and barcodes across all samples in this submission.
Supplementary files format and content: sample_index.csv is comma-separated text file mapping the sample index (e.g. the suffix used for cell barcodes in barcodes.tsv.gz) to the library names.
Supplementary files format and content: ElKhoury.rds is a serialized Seurat (v5) R object with demultiplexed sample and cell annotations, feature annotations, raw & scaled gene expression scores and PCA, tSNE and UMAP embeddings.

molecule: polyA RNA

source_name: brain

extract_protocol:
Brains were dissociated into single cells with the Neural Tissue Dissociation Kit (Miltenyibiotec, 130-092-628). Briefly, the brains were chopped using a razor, resuspended with HBSS, and peletted by centrifugation. The pellet was resuspended and incubated with the enzyme P mix at 37°C along with the transcriptional and translational inhibitors Actinomycin D (Cell Signaling Technology, cat. #15021, 5uM final concentration) and Anisomycin (Cell Signaling Technology, cat. #2222, 2uM final concentration) respectively. Samples were homogenized by trituration using a 5 ml serological pipette and incubated with Enzyme A at 37°C. Afterwards, the brains were triturated with a 2ml serological pipette, washed with DPBS, passed through a 100uM filter and centrifuged at 300xg for 10 min. To remove the excess myelin, cells were resuspended in 0.9M sucrose and centrifuged at 850g for 35 min. Cells were washed with the FACS buffer (1x PBS, 1% BSA, 2mM EDTA) and stained with SYTOX™ blue (ThermoFisher) to distinguish live cells. At this point, cells from 1 male and 1 female from each treatment group were pooled and processed together. (Data from individual animals were later demultiplexed based on sex-specific gene expression, see below.)  Flow cytometry revealed that ~1% of the live brain cells from the control IgG group were AF647 positive, compared to ~30% and ~20% for the ATV-TfR and ATV-CD98hc groups, respectively. We divided the AF647 positive cells from the ATV-TfR treatment group into tertiles according to fluorescence intensity, e.g. we binned them into low, medium, and high categories and applied the same FACS gates to samples from all treatment groups. In addition, AF647-negative cells were collected, generating 4 sub-populations (negative, low, medium, high intensity) for each pool. Single cells from 24 samples (3 genotypes x 2 replicates x 4 FACS bins) were captured: ~60,000 cells were sorted into a 1.5 mL centrifuge tube. To concentrate the single-cell suspensions, each sample was pelleted by centrifugation at 200xg for 10 minutes in a swing bucket rotor at 4°C, and supernatant was removed leaving only 43.3 µL volume for resuspension. The entire volume of cells was then added to the RT master mix and loaded onto Chromium Next GEM Chip G microfluidic channels per manufacturer’s protocol (10X Genomics, CG000315 Rev C). One sample (IgG, negative fluorescence) was lost due to a fluidic wetting issue, leaving 23 samples for library preparation and sequencing analysis.
Post GEM–RT Cleanup was performed using a Dynabeads cleanup mix via magnetic purification, and cDNA was generated using 12 cycles of amplification followed by cDNA purification using SPRIselect reagent. A quarter volume of the cDNA generated was used as input for 3’ gene expression library construction starting with fragmentation, end repair and A-tailing, followed by Illumina adaptor ligation and sample index PCR, with SPRIselect bead purification performed in between each step. Library quantity and quality were assessed with High Sensitivity D1000 ScreenTapes (Agilent 5067-5584). The libraries were pooled for quality control in equimolar ratios and analyzed by shallow sequencing on an Illumina MiSeq instrument (Reagent Kit v3, Illumina, MS-102-3001) to estimate the total number of cells captured for each sample. Based on this estimate, individual libraries were pooled targeting 20,000 reads per captured cell and  the sequenced deeply on an Illumina NovaSeq 6000 instrument, S2 cartridge, Paired end (28X10X10X90) by SeqMatic (Fremont, CA, USA).

treatment_protocol: Mice were IV dosed with Alexa 647 (AF647)-conjugated ATVTfR, ATVCD98hc, or control IgG via the tail vein. 24 hours after dosing, the animals were anesthetized deeply via IP injection of 2.5% Avertin, perfused with 1x PBS and whole brains (excluding olfactory bulbs as well as cerebellum, pons, and medulla) were collected.

tag: fluorescence

value: Bin 3, high for A647 signal

value: brain

tag: region

value: whole brain, excluding olfactory bulbs, cerebellum, pons and medulla

tag: replicate

value: TfR mu/hu KI

tag: pool

value: dissociated cells from 1 male and 1 female animal

tag: age

value: 3.3 months

tag: dose

value: 45 mg/kg


title: TfR_1_ low

value: Bin 1, low for A647 signal


title: TfR_2_negative

value: Bin 0, negative for A647 signal


title: TfR_2_low


title: TfR_1_ medium

value: Bin 2, mid for A647 signal


title: TfR_1_ high


title: ctrl_ctrl_3

value: alveolar macropahge

value: ctrl


title: TfR_1_ negative


title: IgG_2_negative


title: IgG_2_high


title: IgG_1_high


title: IgG_2_low


title: IgG_2_medium


title: IgG_1_low


title: CD98hc_2_medium

value: CD98hc mu/hu KI

value: DNP02 LALAPG LLB2-10-8 monovalent - Alexa647


title: IgG_1_medium


title: 24M_1


title: CD98hc_2_high


title: CD98hc_2_low


title: CD98hc_1_medium


title: CD98hc_1_high


title: CD98hc_1_negative


title: Ruvbl2fl/fl; AAV2-Cre-GFP3; 8w

city: tianjin

first: mingming

last: xing

address: Huanrui Road，Beichen District

institute: Tianjin Medical University

data_processing:
using Cutadapt to filter out unqualified sequences (sequencing joints, low quality sequences, etc.) from the original Data to obtain Clean Data
Reference genome alignment was performed using Hisat2, and based on the Hisat2 alignment results, StringTie was used to reconstruct the transcript and calculate the expression levels of all genes in each sample.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: paraventricular nucleus of hypothalamus

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1 ug of total RNA was used for the construction of sequencing libraries.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

treatment_protocol: AAV2-GFP or AAV2-Cre-GFP injected to PVH of Ruvbl2 fl/fl mice after 8 weeks of virus infection for RNA-seq

value: paraventricular nucleus of hypothalamus

value: AAV2-Cre-GFP was injected into the PVH


title: CD98hc_2_negative


title: Zfp488-HA-1

city: Cincinnati

first: Richard

last: Lu

state: Ohio

institute: CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER

library_source: genomic

data_processing:
Signals of CUT&Tag were aligned to mm10 using Bowtie (http://bowtie-bio.sourceforge.net). Peak calling was performed using MACS3 (http://liulab.dfci.harvard.edu/MACS).
Assembly: mm10
Supplementary files format and content: bed

molecule: genomic DNA

source_name: Brain

extract_protocol:
CUT&Tag assays were performed using the Hyperactive® Universal CUT&Tag Assay Kit for Illumin (Vazyme, TD903)
CUT&Tag assays were performed using the Hyperactive® Universal CUT&Tag Assay Kit for Illumin (Vazyme, TD903)

value: Brain

tag: cell line

value: Mouse OPCs


title: CD98hc_1_low

value: brain


title: TfR_2_medium

value: whole brain, excluding olfactory bulbs, cerebellum, pons and medulla


title: Ruvbl2fl/fl; AAV2--Cre-GFP1; 8w


title: Ruvbl2fl/fl; AAV2--Cre-GFP2; 8w


title: 10X scATACseq, KRN

city: Barcelona

first: Josep

last: Garnica

address: Rosselló, 149

country: Spain

institute: IDIBAPS

library_source: genomic single cell

data_processing:
Aligment - STAR, Bowtie2, Cellranger v6. TCR reconstriuction - TraCeR
PeakCalling - MACS2
Downstream - DiffBind, Seurat, Signac, GenomicRanges, Trackviewer…
Assembly: GRCm38.p6
Supplementary files format and content: Peakset; differential peaks called
Supplementary files format and content: feature count matrices

source_name: Liver

extract_protocol:
Cells were lysed in cold lysis buffer (10 mM Tris-HCl, pH 7.4,10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630), washed, and right after resuspended in transposase reaction mix.  10X single-cell RNA-seq: Alive cells were collected from untreated and aGalCer/CD1d-NP-treated 13-15 wk-old NOD mice in DMEM media (Sigma-Aldrich) supplemented with 10% FBS (Hyclone) at 4 ºC, separated into nanoscale gel beads emulsions with a 10X barcode. Cell numbers and viability were assessed using a TC20™ Automated Cell Counter (Bio-Rad Laboratories, Hercules, CA, USA), with a minimum target of 4000 cells. Later, cDNA sequencing libraries were produced using the NextGEM Single-cell 3’ mRNA kit (v3.1; 10X Genomics) following the manufacturer's instructions. These steps involved GEM-RT clean-up, cDNA Amplification for 13 cycles, and cDNA quality control and quantification using the Agilent Bioanalyzer High Sensitivity chip (Agilent Technologies). Libraries were indexed by PCR using the PN-220103 Chromium i7 Sample Index Plate. Finally, sequencing was carried out on a NovaSeq 6000 sequencer (Illumina). 10X single-cell multiome (scRNAseq+scATACseq). For 10X multiome RNA-seq+ATAC-seq, LiNKT cells were sorted from untreated (n=5; 13-15wk-old) and αGalCer/CD1d-NP-treated male NOD mice (n=4; 13-15wk-old), to obtain a total of 300.000 and 250.000 live LiNKT cells in DMEM media (Sigma-Aldrich) supplemented with 10% FBS (Hyclone). Cells were lysed at 4 ºC, and nuclei isolated. Nuclei were used for transposition of adapter sequences and processed for single-cell barcoding and library generation following the manufacturer’s instructions (CG000338; 10X Genomics). Briefly, isolated nuclei were partitioned into Gel Bead-In-Emulsions to produce barcoded cDNA from poly-adenylated mRNA as described above, as well as barcoded DNA fragments, and processed for library amplification and sequencing on a NovaSeq 6000 sequencer (Illumina), also as described above.  Smartseq2 scRNAseq: One-cell sorting of LiNKTs from untreated and αGalCer/CD1d-NP-treated mice (n=3 male mice/group; 13-15 wk-old) was performed in SMARTseq2 96-well plates (PerkinElmer, Waltham, MA, USA) containing 100 µl lysis buffer/well, consisting in 0.2% v/v Triton-100 with RNase inhibitor. Full-length single-cell RNA sequencing libraries were prepared using a modified Smart-seq protocol 64. A reverse transcription reaction was done in presence of oligo-dT30VN, betaine and template-switching oligonucleotides. Complementary DNA was then amplified with KAPA Hifi Hotsart RadyMix (Kappa Biosystems) and ISPCR primer in 25 cycles. The PCR product was purified with Agencourt Ampure XP beads (Beckman Coulter) and analyzed with a High Sensitivity DNA kit (Agilent Technologies). 200 pg of the cDNA product were fragmented with Nextera® XT (Illumina) and amplified with indexed Nextera® PCR primers. Products were purified twice with Agencourt AMPure XP beads and quantified again using a Bioanalyzer High Sensitivity DNA Kit. Sequencing of Nextera® libraries from 384 cells was carried out using one sequencing lane on an Illumina HiSeq2500 v4 or HiSeq4000 to 500K reads/cell.  ATACseq:  ATAC-seq was done on LiNKT cells isolated from untreated and αGalCer/CD1d-NP-treated mice (n=3 male mice/group; 13-15 wk-old). 7x104 cells were sorted in PBS and processed for library preparation as described 27. Briefly, cells were lysed in cold lysis buffer (10 mM Tris-HCl, pH 7.4,10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630) to isolate nuclei. The purified nuclei were washed, resuspended in the transposase reaction mix (25 μl 2x TD buffer, 2.5 μl transposase (Illumina) and 22.5 μl nuclease-free water) and incubated for 30 min at 37°C. DNA was purified with MinElute Reaction Cleanup kit (Qiagen). Libraries were generated with NEBNext® High Fidelity PCR kit (New England Biolabs, Ipswich, MA, USA) using 1x NEB Next PCR master mix (New England BioLabs) and 1.25 μM of custom Nextera PCR primers. Libraries were rendered using the barcoded primers Ad1_noMX as forward and Ad2.1-6 as reverse and purified using a PCR cleanup kit (Qiagen), yielding a final concentration of about 30 nM in 20 μl. Libraries were then analyzed on Bioanalyzer using an Agilent DNA High Sensitivity chip (Agilent Technologies, Santa Clara, CA, USA) to estimate the quantity and size distribution. Next, they were quantified by qPCR using the KAPA Library Quantification Kit before amplification with Illumina’s cBot. Libraries were finally loaded at 3.33 pM onto the flowcell and sequenced 1 x 50 on Illumina’s HiSeq 2500 to obtain 30-40 million reads/sample.  ChIP-seq: Chromatin immunoprecipitation (ChIP) and sequencing was performed on LiNKT cell samples from untreated and aGalCer/CD1d-NP-treated NOD mice (n=3/group; 13-15 wk-old) for H3K4me3, H3K27me, and H3K27Ac bound DNA via ChIP-seq following van Arensbergen’s protocols 65. LiNKT cells were sorted, fixed with 16% paraformaldehyde (PFA; Electron Microscopy Sciences, Hatfield, PA, USA) in DMEM (Sigma-Aldrich) supplemented with 10% FBS (Hyclone) and frozen at -80ºC until processed. We used 1-1.5x106 LiNKTs/sample. Cells were lysed, sheared, and sonicated using an S220 Focused-ultrasonicator (Covaris, Woburn, MA, USA) (13 min, 105 W, 2% Duty Factor, 200 cycles). This was followed by overnight incubation with the precipitating antibody: 0.5 µL of H3K4me3 (Sigma), 0.5 µL of H3K27me3 (Cell Signaling, Danvers, Massachusetts, USA), and 2 µL of H3K27Ac (Abcam, Cambridge, United Carlsbad, CA, USA) and precipitated using Protein-A-Dynabeads (Abcam). RNA was cleared using RNAse A (Qiagen) (1 hour at 65 ºC), and decrosslinking was performed overnight with proteinase K at 65 ºC. DNA was finally purified with Phenol-Chloroform and EtOH-precipitation. After quality control validation on a Bioanalyzer (Agilent Technologies), samples were sent for sequencing. Libraries were prepared using the NEB Next Ultra DNA Library Prep kit (Illumina) following the manufacturer’s protocol, analyzed with DNA High Sensitivity kit (Agilent Technologies), and quantified via qPCR using the KAPA Library Quantification Kit (Kapa Biosystems). Libraries were loaded at a concentration of 2.75 pM onto flowcells and were sequenced 1 x 50 on Illumina’s HiSeq 2500 to get 30-40 million reads/sample.  WGBS: Six replicates of LiNKTs (4-5x105 cells/sample) were obtained from untreated female NOD mice (n=7, 17wk-old) and αGalCer/CD1d-NP-treated NOD mice (n=4, 16wk-old) by cell sorting. Genomic DNA was extracted using the DNeasy Blood and Tissue kit (Qiagen) following the manufacturer’s instructions, and frozen at -20ºC. DNA was processed by Whole Genome Bisulfite Sequencing (WGBS). Briefly, DNA was sonicated to a mean size of 250 bp using a Bioruptor (Diagenode, Seraing (Ougrée), Belgium) followed by blunt-ending, dA addition to the 3'-end and ligation of methylated adaptors to protect from bisulfite conversion. Ligated DNA was bisulfite converted using the EZ DNA Methylation-Gold kit (ZYMO, Irvine, CA, USA). After treatment with sodium bisulfite, unmethylated cytosine residues were converted to uracil, leaving 5-methylcytosine (5mC) unaffected. Different insert size fragments were excised from the same lane of a 2% TAE agarose gel. Products were purified using a QIAquick PCR; after PCR amplification, uracil residues were converted to thymine. Sequencing was performed 2 x 150 bp using the NovaSeq 6000 System (Illumina).
Library fragments were amplified using 1x NEB Next PCR master mix (New England BioLabs) and 1.25 μM of custom Nextera PCR primers forward and reverse. Libraries were rendered using the barcoded primers Ad1_noMX as forward and Ad2.1-6 as reverse and purified using a PCR cleanup kit (Qiagen), yielding a final concentration of about 30 nM in 20 μL. Libraries were then analyzed on Bioanalyzer using an Agilent DNA High Sensitivity chip (Agilent Technologies, Santa Clara, CA, USA) to estimate the quantity and size distribution. Next, they were quantified by qPCR using the KAPA Library Quantification Kit before amplification with Illumina’s cBot.
Libraries were loaded at 3.33 pM onto the flowcell and sequenced 1 x 50 on Illumina’s HiSeq 2500

value: Liver

value: Liver iNKT (aGalCer/CD1d tetramer+)

value: NOD mouse

tag: chip antibody


title: 10X scATACseq, CTL

value: untreated


title: Ruvbl2fl/fl; AAV2-GFP3; 8w

value: AAV2-GFP was injected into the PVH


title: Hyp1_Input

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChlP-seq reads were trimmed from 3' end untfl the final base had a qualty score > 30, using Trimmomatic v0.33, discarding reads left with < 35 bp
ChIP-Seq reads were aligned to the GRCm38 genome using Bowtie version 2.3.4.1 Only uniquely mapping reads with at most two mismatches were retained .
To create ChIP - seq coverage plots , the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments , renormalized ( to reads per million , rpm ) and reformatted in the BED file format.
Peaks were called using MACS v2.1.0 with the significance cut-off q-value <=0.01
Assembly: BED files were generated using the ChIPseeker R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated usingMACS v2 withdefault setting.
Supplementary files format and content: m38
Supplementary files format and content: BED, narrowPeak (except for Input sample)

source_name: Hypothalamus

extract_protocol:
The hypothalamus was isolated from 8-week-old male C57BL/J mice，cross-linked with 1% formaldehyde for 10 min at room temperature, and then quenched with 125 mM glycine.
The chromatin fragments were pre-cleared and then immunoprecipitated with Protein A + G Magnetic beads coupled with anti-RUVBL2 antibody. After reverse crosslinking, CHIP and input  DNA fragments were end-repaired and A-tailed using the NEBNext End Repair/dA-Tailing Module (E7442, NEB) followed by adaptor ligation with the NEBNext Ultra Ligation Module (E7445, NEB). The DNA libraries were amplified for 15 cycles and sequenced using Illumina Hi-Seq with paired-end 2x150 as the sequencing mode.

value: Hypothalamus

value: WT


title: Ruvbl2fl/fl; AAV2-GFP2; 8w


title: Whole Genome Bisulfite Sequencing (WGBS), CTL

description: Control_vs_Treated.CG_DMR.txt, Control_vs_Treated.CG.group.site.methy_ratio.txt


title: Hyp2_RUVBL2_ChIP

value: RUVBL2(ABclonal, # A1905）


title: 10X scRNAseq, CTL

description: For 10X single-cell RNA-seq samples libraries were obtained from a single collection of cells (either CTL or KRN) sequenced in 4 different libraries in order to get enough sequencing depth.


title: Liver, DBI_CORT,H20, bio rep 5

city: PARIS

first: Guido

last: Kroemer

address: 15 rue de L'école de médecine

country: France

institute: Centre de Recherche des Cordeliers

data_processing:
QC analysis
Multilanes fasta merging just by concatenation of multilanes raw data files
HISAT2 generate .sam files
HTSeq-count to produce the final raw count file
Assembly: mm10
Supplementary files format and content: Tabulated Separated Value file with Ensembl ID, with version, the associated gene name and each sample gene raw count

growth_protocol: Experiments were conducted with 8-week-old female C57BL/6 mice. All mice were maintained in a 12-h light/dark cycles, under temperature-controlled SPF conditions with food and water ad libitum. In all experiments, mice were given one week to acclimate after their arrival before commencing the experiment.

extract_protocol: Upon euthanasia, the liver tissue is expeditiously excised, flash-frozen in liquid nitrogen, and subsequently stored at -80°C pending RNA extraction.

treatment_protocol: Corticosterone was administered as described in PMID: 31117053. Passive immunization was performed by biweekly intraperitoneal injections of anti-ACBP mAb with IgG2a isotype control antibody as control. At the end of the 5th week, the mice were sacrificed, and their tissues were collected and weighed.

tag: Sex

value: Female

value: Wild-type


title: Zfp488-HA-2


title: Liver, DBI_Veh, H15, bio rep 5


title: Liver, DBI_CORT,H17, bio rep 2


title: Liver, DBI_Veh, H14, bio rep 4


title: Liver, DBI_CORT,H16, bio rep 1


title: Liver, DBI_CORT,H19, bio rep 4


title: Liver, DBI_Veh, H13, bio rep 3


title: Liver, DBI_Veh, H12, bio rep 2


title: Whole Genome Bisulfite Sequencing (WGBS), KRN


title: Liver, IgG_CORT, H9, bio rep 4


title: Liver, IgG_CORT, H8, bio rep 3


title: Liver, IgG_CORT, H7, bio rep 2


title: Liver, IgG_CORT, H10, bio rep 5


title: Ruvbl2fl/fl; AAV2-GFP1; 8w


title: Liver, IgG_CORT, H6, bio rep 1


title: Liver, DBI_Veh, H11, bio rep 1


title: Hyp2_Input


title: Liver, IgG_Veh,H5, bio rep 5


title: 10X scRNAseq, KRN


title: Liver, IgG_Veh,H4, bio rep 4


title: Hyp1_ RUVBL2_ChIP


title: Liver, IgG_Veh,H3, bio rep 3


title: Liver, DBI_CORT,H18, bio rep 3


title: GBA mmKO, W170

city: Bethesda

first: Hannah

middle: B. D.

last: Duffy

state: MD

address: 10 Center Drive

institute: National Institutes of Health

data_processing:
Raw data processed through in-house perl scripts (Novogene Inc.) to remove reads containing adapter sequences, poly-N, and low quality reads
High quality reads were mapped to the reference genome (mm10) using Hisat2 v.2.0.5
Reads were counted with featureCounts v.1.5.0-p3
The DESeq2 R package was used to perform differential expression analysis
Assembly: mm10
Supplementary files format and content: csv files including normalized counts, raw counts, fpkm

source_name: CD11b+ cells from brain

extract_protocol:
RNeasy micro kit (Qiagen)
RNA harvested according to the manufacturer's instructions with the following kits - from whole brain: miRNeasy mini kit (Qiagen), from microglia: RNeasy micro kit (Qiagen)
Library prep performed with the NEBNext II RNA Library Prep Kit for Illumina (New England BioLabs Inc.) according to the manufacturer's instructions

value: CD11b+ cells from brain

value: F

value: 15 months

value: FloxGBA; Tmem119-CreERT2

value: Tamoxifen citrate diet


title: GBA mmKO, W168


title: GBA mmKO, W169


title: Control, GBA mmKO, W319

value: FloxGBA


title: Control, GBA mmKO, W321


title: Control, GBA mmKO, W876

value: M

value: 13 months


title: GBA nKO, E505

source_name: Brain (one hemisphere)

extract_protocol:
miRNeasy mini kit (Qiagen)
RNA harvested according to the manufacturer's instructions with the following kits - from whole brain: miRNeasy mini kit (Qiagen), from microglia: RNeasy micro kit (Qiagen)
Library prep performed with the NEBNext II RNA Library Prep Kit for Illumina (New England BioLabs Inc.) according to the manufacturer's instructions

value: Brain (one hemisphere)

value: 15 weeks

value: FloxGBA; Thy1-CreERT2,-EYFP


title: GBA nKO, E829

value: 15.7 weeks


title: GBA nKO, E153

value: 16.6 weeks


title: GBA nKO, E149

value: 16 weeks


title: GBA nKO, E507

value: 15.1 weeks


title: GBA nKO, E156


title: Control, GBA nKO, E823


title: Control, GBA nKO, E151


title: GBA mmKO, W875


title: Control, GBA nKO, E150


title: Control, GBA nKO, E155


title: Control, GBA nKO, E508


title: GBA mKO, Z982

value: 12 months


title: Liver, IgG_Veh,H2, bio rep 2

value: Liver

value: Female

value: Wild-type


title: Control, GBA nKO, E154


title: GBA mKO, X176


title: GBA mKO, Z987


title: GBA mKO, Z849

value: F


title: Control, GBA mKO, X178


title: Control, GBA mKO, Z984


title: GBA mKO, Z852

value: FloxGBA; Tmem119-CreERT2


title: Control, GBA mKO, Z847

value: Tamoxifen citrate diet


title: GBA mKO, Z850


title: Control, GBA mKO, X175

value: FloxGBA


title: Liver, IgG_Veh,H1, bio rep 1


title: Control, GBA mKO, Z988

value: M


title: Control, GBA mKO, Z986


title: PBS_5

city: Guangzhou

first: Dongmei

last: Tang

state: GuangDonng Province

address: Jingxi Street

department: pathophysiology

institute: Southern Medical University

description:
ApoE-/- mice, injected with PBS, high-fat diet for 20w
injected with PBS, high-fat diet for 20w

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: liver

extract_protocol:
Total RNA (1 µg) from mouse liver tissues was harvested using RNAiso Plus (Takara, Japan) followinng manufacture's protocols.
RNA libraries for RNA-Seq were prepared using the NEB-Next® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA)

value: liver

value: ApoE knockout


title: Control, GBA mmKO, W322

value: CD11b+ cells from brain

value: 15 months


title: Pep_A6_3

description:
ApoE-/- mice,  injected with Pep_A6 vaccine, high-fat diet for 20w
injected with Pep_A6 vaccine, high-fat diet for 20w


title: PBS_4


title: Pep_A6_2


title: PBS_3


title: Chow_5

description:
ApoE-/- mice, normal diet until sacrifice
normal diet until sacrifice


title: PBS_2


title: Chow_4


title: Chow_3


title: Chow_2


title: Chow_1


title: Mouse BM LSK sample treated by TAK-243 sample 4

city: Houston

first: Ziyi

last: Li

state: TX

address: 1400 Pressler Street

institute: MD Anderson Cancer Center

data_processing:
Sequence reads were trimmed for adaptor sequence/low quality sequence using CLC genomic benchmark.
Fastq data were aligned by STAR using reference genome mm10. The raw counts were obtained by counting the overlaps between reads and gene regions using Rsubreads.
Assembly: mm10
Supplementary files format and content: comma separated text file (csv) includes raw counts for each sample

source_name: Bone marrow

extract_protocol:
RNA was harvested using SMARTer Stranded Total RNA-seq Kit. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTer mRNA-seq Library Prep Kit following manufacturer's protocols.

value: Bone marrow

value: LSK


title: Mouse BM LSK sample treated by TAK-243 sample 1


title: Mouse BM LSK sample treated by TAK-243 sample 3


title: Mouse BM LSK sample treated by vehicle control 4

value: Vehicle


title: Mouse BM LSK sample treated by vehicle control 3


title: Mouse BM LSK sample treated by vehicle control 2


title: Mouse BM LSK sample treated by TAK-243 sample 2


title: scRNA-seq_KO_4

city: wuhan

first: zhao

last: chen

state: Hubei

address: shuiguohu

department: BIOLOGY

institute: wuhan university

description:
10x Genomics
KO_barcodes.tsv.gz
KO_features.tsv.gz
KO_matrix.mtx.gz
KO_filtered_feature_bc_matrix.h5

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: UCSC mm10 genome
Supplementary files format and content: Tab-separated values files and matrix files

source_name: small intestine crypt

extract_protocol:
Extract crypts using 8 mM EDTA and perform flow cytometry to isolate EpCAM+cells
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: small intestine crypt

value: adult


title: scRNA-seq_KO_3


title: Mouse BM LSK sample treated by vehicle control 1


title: scRNA-seq_KO_2


title: scRNA-seq_WT_4

description:
10x Genomics
WT_barcodes.tsv.gz
WT_features.tsv.gz
WT_matrix.mtx.gz
WT_filtered_feature_bc_matrix.h5


title: Pep_A6_1


title: scRNA-seq_KO_1


title: scRNA-seq_WT_3


title: scRNA-seq_WT_1


title: PBS_1


title: Tumor_KO_ rep2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt
Trimmed sequence reads were mapped to UCSC genome mm10 using Hisat2 (parameters: default)
The gene expression level was calculated by Cufflinks (version 2.2.1, http://cole-trapnell-lab.github.io/cufflinks) and normalized by fragments per kilobase of bin per million mapped reads (FPKM).
Principal component analysis (PCA) of the quality control matrices was employed to determine the presence of RNA-Seq sample outliers.
Differentially expressed genes are defined by DESeq2.
Assembly: UCSC mm10 genome
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Colon tumor

extract_protocol:
RNA isolation was performed using the RNAiso Plus (TAKARA) according to manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: Colon tumor

value: no

tag: time


title: Tumor_WT_ rep1

tag: tissue

value: APCmin/+


title: Tumor_KO_ rep1


title: scRNA-seq_WT_2


title: Tumor_WT_ rep2


title: Tumor_WT_ rep3


title: Crypt_KO_rep3


title: Crypt_KO_rep2


title: Crypt_KO_rep1


title: Crypt_WT_rep2

value: Wild type


title: Crypt_WT_rep1


title: Crypt_WT_rep3


title: vehicle, scRNAseq

city: Cambridge

first: Jonathan

last: Hsu

state: MA

address: 840 Memorial Dr 4th Floor

institute: Marengo Therapeutics

description: 10x Genomics

data_processing:
Cell Ranger v6.0.1 was used to demultiplex FASTQ reads. Data quality was checked using FastQC and MultiQC v1.9
The output from Cell Ranger was imported in R using Seurat. Empty droplets (nFeatures < 400), duplicates (nFeatures > 3500) and dead cells (percentage mitochondrial genes > 5) were removed. Data were then processed and log normalized with Seurat's standard processing steps for downstream analyses.
Assembly: mm10-2020
Supplementary files format and content: Tab-separated values files and matrix files

source_name: EMT6 tumor

growth_protocol: Isolated TIL's were maintained in RPMI media supplemented with 5 % FBS and P/S

extract_protocol:
Tissue tumor samples were gently cut to about 1 mm3 pieces placed in gentleMACS C-tubes (Miltenyi). Tissues were digested enzymatically containing 20mM HEPES(Gibco), 1mg/mL Collagenase (Sigma), 0.1mg/mL DNase (Roche) for 30 mins in a 37°C shaker with gentle agitation. The tissue pieces were gently dissociated with mechanical force using the GentleMACS Octo Dissociator (Miltenyi Biotec). Cells were then filtered through a 70μm cell strainer and suspended cells were subsequently washed and centrifuged for 5min at 300g. After tissue digestion and dissociation, CD4+ and CD8+ TILs were isolated using the mouse CD4/CD8 (TIL) MicroBeads (Miltenyi)
Samples were loaded onto a 10x Chromium instrument to generate 3’ gene expression libraries (10x Genomics), following manufacturer's protocol. Libraries were sequenced on NovaSeq to a minimum sequencing depth of 50,000 reads per cell.

treatment_protocol: Mice were implanted with 1x105 EMT6 tumor cells in PBS by subcutaneous injection. Mice were randomized into treatment group and vehicle group once tumors reached 80-150 mm3 and monitored daily for morbidity and mortality. mSTAR1302 treatment antibodies were administered for 2 cycles by IP injection once/week.

value: EMT6 tumor

tag: cell type

value: CD4 and CD8 T cells

value: BALB/c

value: 4-6 weeks


title: mSTAR1302, scRNAseq

description: 10x Genomics


title: AE0193_CBLJLANXX_Strain3_TI_nr

first: Isabelle

middle: Brun

last: Heath

state: Barcelona

address: Carrer Baldiri Reixac, 10-12

department: Molecular Modelling and Bioinformatics

institute: IRB Barcelona

data_processing:
MNase-seq paired-end reads were mapped to customized versions of the yeast genome (SacCer3, UCSC)
Output files were imported in to R where reads were trimmed to 50bp maintaining the original center and transformed to reads per million bp
Peak calling was performed, after noise filtering, with the nucleR package implemented in the Nucleosome Dynamics platform using the standard parameters for yeast: peak width of 147 bp, peak detection threshold of 35% and maximum overlap of 80 bp
Assembly: SacCer3
Supplementary files format and content: the gff files are the output files from NucleR and represent Nucleosome positioning

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol: Cells were grown in YPD rich media

extract_protocol:
The Micrococcal nuclease (MNase) digestion was performed on semi-intact yeast cells. We optimised the MNase digestion conditions for each sample to obtain about 80% of mononucleosomes
The sample preparation was done using the Illumina TruSeq DNA sample preparation kit for whole genome sequencing, following the Illumina standard protocol
The libraries (paired-end) were sequenced paired-end on a HiSeq2000, v4, 2x75bp, with approximately 10 M PE reads/sample

treatment_protocol: 1-10-phenanthroline at 100 µg/ml at 30ºC during 30min

value: Yeast

value: Strain 3 with 81bp insertion in genes TRP4 (position 1185196) and PAN5 (position 224581)

tag: genotype

value: MATa his3{delta}0 leu2{delta}0 met15{delta}0 ura3{delta}0 bar1::leu2 TRP4::81bp PAN5::81bp

value: Treated with 10.Phenanthroline


title: AE0191_CBLJLANXX_Strain1_TI_nr

value: Strain 1 with 81bp insertion in genes CKB2 (position 406248) and DGK1 (Position 899667)

value: MATa his3{delta}0 leu2{delta}0 met15{delta}0 ura3{delta}0 bar1::leu2 CKB2::81bp DGK1::81bp


title: AE0190_CBLJLANXX_Strain4_nr

value: Strain 4 with 81bp insertion in genes  UBX5 (position 1128586) and BSP1 (position 884578)

value: MATa his3{delta}0 leu2{delta}0 met15{delta}0 ura3{delta}0 bar1::leu2 UBX5::81bp BSP1::81bp

value: Not treated


title: AE0192_CBLJLANXX_Strain2_TI_nr

value: Strain 2 with 81bp insertion in genes PPT1 (position 737615)  and SLM3 (position 393462)

value: MATa his3{delta}0 leu2{delta}0 met15{delta}0 ura3{delta}0 bar1::leu2 PPT1::81bp SLM3::81bp


title: AE0189_CBLJLANXX_Strain3_nr


title: AE0194_CBLJLANXX_Strain4_TI_nr


title: Tumor_KO_ rep3

value: Colon tumor

value: no

value: adult


title: AE0188_CBLJLANXX_Strain2_nr


title: AE0187_CBLJLANXX_Strain1_nr

value: Strain 1 with 81bp insertion in genes CKB2 (position 406248) and DGK1 (position 899667)


title: 38648

type: genomic

middle: Christian

last: Harris

state: Maryland

address: 50 South Drive

department: National Human Genome Research Institute

description: KANG

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays and hybridized overnight at at 48oC.  Single-base extension and allele-specific staining was performed by hand.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing:
Image data was analyzed using GenomeStudio with GT module (Illumina).
genotypes AA, AB, BB, NC=no call

organism: Canis lupus familiaris

source_name: Whole Blood

label_protocol: 200ng of genomic DNA was amplified in an overnight reaction at 37oC. The amplified DNA was enzymatically fragmented, precipitated with isopropanol, and resuspended in hybridization buffer.

extract_protocol: Genomic DNA was extracted from whole blood or Buccal cells using Proteinase K and phenol/chloroform with standard protocols. Genomic DNA extracted from saliva using standard Performagene genotek DNA extraction protocols.

tag: breed

value: Kangal


title: 38657

description: KARA

source_name: Saliva

value: Karakachan


title: 38645

description: ASTC

value: Australian Stumpy Tail Cattle Dog


title: 38673

description: SARP

value: Sarplaninec


title: 38660

description: KARA


title: 38671

description: CASD

value: Central Asian Shepherd Dog


title: 38661

description: KARA


title: 38668

description: SARP


title: 38670

description: CASD


title: 38662

description: KARA


title: 38665

description: KANG


title: 38640

description: TATR

value: Polish Tatra Sheepdog


title: 38637

description: KARA


title: 38635

description: CASD


title: Sheep Y-chromosome methylation profile from ONT data

city: Moscow

first: Brenda

last: Murdoch

state: Idaho

address: 875 Perimeter Dr.

department: Department of Animal, Veterinary & Food Sciences

institute: University of Idaho

data_processing:
Basecalling was done for the respective sequencing platform according to the manufacturer prescribed procedure using their proprietary basecallers - Dorado for ONT and Primrose for PacBio.
Assembly: GCF_016772045.2
Supplementary files format and content: methylation call in bed format
Library strategy: WGS

organism: Ovis aries

source_name: Sheep

extract_protocol:
DNA extraction was done on standard manufacturer suggested protocol.
The respective libraries used on the sequencing platforms were made according to the specifications of the manufacturers.

value: Lung


title: Sheep Y-chromosome methylation profile from PacBio data


title: 38633

description: ILIR

value: Molosi Ilir


title: hog1∆_rep 3

city: Nutley

first: Neeraj

last: Chauhan

state: New Jersey

address: 111 ideation way

institute: Center for Discovery and Innovation, Hackensack Meridian Health

data_processing:
Quality control of raw sequencing reads was done using fastQC v0.11.8
TrueSeq (Illumina) adapters were trimmed using cutadapt v1.18
Mapping onto theC. aurisB8441 genome assembly (http://www.candidagenome.org/) used NextGenMap v0.5.5 and  Optical read duplicates were removed using Picard tools
Read counting was done using Htseq in the union mode and the genomic annotation fromC. aurisB8441
The read counts were normalized, and DESeq2 differential gene expression analysis was done using DEBrowser V1.28.0
Assembly: Genomic annotation fromC. aurisB8441
Supplementary files format and content: Tab-delimited txt file includes raw counts for each sample

organism: Candidozyma auris

source_name: hog1∆_rep 3

growth_protocol: Both parent and hog1 deletion strains grown in YPD liquid medium at 30°C with 200 rpm shaking overnight. Next day, re-inoculated in fresh media and grown for log phase (4hours)

extract_protocol:
Total RNA was purified using the TRI reagent (Sigma). Quality of RNA was assessed on a Bioanalyzer using the RNA6000 Nanochip (Agilent).
mRNA was enriched using oligo(dT) beads (NEB) and subsequently, double-stranded cDNA libraries were generated by using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions.

value: hog1∆_rep 3

value: Whole cell


title: 38632

description: ILIR


title: 38630

description: ILIR


title: 1184/P15_rep 2


title: cyp2c19 barcode-variant plasmid library

city: Seattle

first: Douglas

last: Fowler

state: WA

address: 3720 15th Ave NE, Foege Building, S320

department: Genome Sciences

institute: University of Washington

library_source: other

data_processing:
Libraries were sequenced on NextSeq 2000 instruments (Illumina) and base called using the instrument's Real Time Analysis software.
Sequencing reads were converted to fastq format and de-multiplexed with bcl2fastq.
Barcode and UMI sequencing reads for all CYP2C19  replicates were trimmed and filtered for minimum base quality Q20 using FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) and collapsed according to UMI sequences using a custom script. Barcode paired sequencing reads for all CYP2C19 abundance replicates were joined using PEAR software (https://cme.h-its.org/exelixis/web/software/pear/). FASTQ files from technical replicate amplification were concatenated for analysis with Enrich2.
The abundance scores for CYP2C19 were calculated as follows: The count for each variant in a bin was divided by the sum of counts recorded in that bin to obtain the frequency of each variant within that bin. This calculation was repeated for every bin in each replicate experiment. The summed counts of each variant in all four bins of an experiment was divided by the summed counts of all variants in all four bins of an experiment to obtain the total frequency value for each variant for each experiment. This total frequency value was used for filtering low-frequency variants out of the subsequent calculations. Next, a weighted average was calculated for each variant. Finally, for each experiment, an abundance or activity score for each variant was obtained by subjecting the weighted average of each variant to min-max normalization, using the weighted average value of synonymous variants, which was given a score of 1, and the median weighted average value for nonsense variants, which was given a score of 0. The final activity or abundance score for each variant was calculated by taking the mean of the min-max normalized scores across the replicate experiments in which it could have been observed. Only variants which were scored in two or more replicate experiments were retained in the analysis. A standard error for each score was calculated by dividing the standard deviation of the min-max normalized values for each variant by the square root of the number of replicate experiments in which it was observed.
Assembly: NONE
Supplementary files format and content: The barcode_variant_map.csv.gz processed data file is in gzip-compressed comma-separated text file format, containing the variant-barcode map determined by PacBio sequencing for the variant library.
Supplementary files format and content: The CYP2C19_data.csv.gz processed data file is in gzip-compressed comma-separated text file format, containing the CYP2C19 variant  abundance scores calculated as described above.
Supplementary files format and content: The cyp2c19_vampseq_sequencing_data.csv.gz is in gzip-compressed comma-separated text file format, containing barcode counts from all sequencing libraries processed as described above
Library strategy: DNA-seq

molecule: other

organism: synthetic construct

extract_protocol:
gDNA was extracted from FACS sorted cell pellets using a QIAGEN DNeasy Blood and Tissue kit using the manufacturer's protocol
barcode sequencing libraries were created using a nested PCR workflow. The first PCR amplified the barcode region and CYP2C19 cDNA from the gDNA of the landing pad cell line. The second PCR primed to adapters added by the first PCR and amplified the barcode region, adding Illumina sequncing adapters and a UMI

value: cyp2c19 barcode-variant plasmid library produced in E. coli


title: 1184/P15_rep 1


title: hog1∆_rep 2

source_name: hog1∆_rep 2

value: hog1∆_rep 2


title: RASJP18_C 10 U 100 Rep 3

city: Paris

first: Kyle

last: Raymond

address: 28 Rue du docteur Roux, Lwoff-22-02-03

department: Department of Virology

institute: Institut Pasteur

description: RNA JP RAS 18

data_processing:
Sequana v0.15.2
Sequences trimmed with fastp software v0.22.0
Aligned to Hg38 with STAR v2.7.10b
FeatureCounts 2.0.1 used to produce count matrix
Differential expression conducted with DESeq2
Assembly: Hg38 (Homo Sapien) Ensembl
Supplementary files format and content: .csv file of raw RNAseq reads
Supplementary files format and content: .csv file of normalized RNAseq reads

organism: Homo sapiens

source_name: HeLa

extract_protocol:
RNA was harvested using a Qiagen Rneasy Plus Kit
Libraries were constructed with the Nextseq 2000 P2 Reagent kit

value: HeLa


title: 38627

first: Alexander

description: ILIR


title: 38625

description: ILIR


title: Echinocloa_Steraia_BA

city: Godollo

first: Eva

last: Varallyay

address: 4 Szent-Györgyi Albert Street

department: Institute of Plant Protection

country: Hungary

institute: Hungarian University of Agriculture and Life Sciences

description: small RNA

data_processing:
The quality check of the sequenced small RNA libraries was done by FastQC program, embedded in CLC
Trimming of raw reads was performed using the CLC
Removing redundant reads using CLC
Supplementary files format and content: tab-delimited counts of all unique read with its number of repeats
Assembly: as small RNAs were sequences as one read no assembly was needed

organism:
Setaria viridis
Echinochloa crus-galli

source_name: plant leaf

extract_protocol:
Phenol-Kloroform extraction White and Karper (White, J.L.; Kaper, J.M. A simple method for detection of viral satellite rnas in small plant tissue samples. J. Virol. Methods 1989, 23, 83–93.)
modified Illumina Trueseq small RNA kit protocol: https://doi.org/10.1007/978-1-4939-7683-6_9

value: plant leaf

tag: species

value: pool of 6 individual plants

value: July 2021


title: RASJP15_T 30 C 10 THU 100 Rep 3

description: RNA JP RAS 15

tag: treatment


title: RASJP14_T 30 C 10 THU 100 Rep 2

description: RNA JP RAS 14


title: RASJP9_T 30 Rep 3

description: RNA JP RAS 9


title: 38624

description: ILIR


title: 38623

description: ILIR


title: 38626

description: ILIR


title: RASJP16_C 10 U 100 Rep 1

description: RNA JP RAS 16


title: RASJP12_T 10 C 10 THU 100 Rep 3

description: RNA JP RAS 12


title: 38631

description: ILIR


title: RASJP17_C 10 U 100 Rep 2

description: RNA JP RAS 17


title: RASJP13_T 30 C 10 THU 100 Rep 1

description: RNA JP RAS 13


title: RASJP10_T 10 C 10 THU 100 Rep 1

description: RNA JP RAS 10


title: RASJP11_T 10 C 10 THU 100 Rep 2

description: RNA JP RAS 11


title: RASJP6_T 10 Rep 3

description: RNA JP RAS 6


title: RASJP8_T 30 Rep 2

description: RNA JP RAS 8


title: RASJP7_T 30 Rep 1

description: RNA JP RAS 7


title: 1184/P15_rep 3


title: 38606

description: TATR


title: RASJP5_T 10 Rep 2

description: RNA JP RAS 5


title: 38593

description: KARA


title: RASJP4_T 10 Rep 1

description: RNA JP RAS 4


title: hog1∆_rep 1

source_name: hog1∆_rep 1

value: hog1∆_rep 1


title: RASJP2_Non Treated Rep 2

description: RNA JP RAS 2

value: Non Treated


title: RASJP3_Non Treated Rep 3

description: RNA JP RAS 3


title: 38592

description: KARA

value: Karakachan


title: RASJP1_Non Treated Rep 1

description: RNA JP RAS 1


title: 38588

description: KARA


title: 38589

description: KARA


title: 38621

description: ILIR


title: 38591

description: KARA


title: 100 uM NIMP 2

city: Livermore

first: Aimy

last: Sebastian

state: CA

address: 7000 East Ave

department: BBTD

institute: LLNL

data_processing:
Sequence reads were aligned against human reference genome (hg38) using STAR.  After read alignment, the number of reads per gene locus was summarized with ‘featureCounts’ from Rsubread package, using hg38 gene annotation.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes read counts for each sample .

source_name: human iPSC derived glutamatergic and GABAergic neuron co-cultured with primary human astrocytes

extract_protocol:
Co-cultures were treated with NIMP (0, 4, and 100 micromolar) for 24 hours, and cell were lysed at 6-days post exposure using RLT buffer containing β-mercaptoethanol, and the supernatant collected. Total RNA was extracted and purified from the collected supernatant using the RNAeasy mini spin columns (Qiagen).
Poly(A)+-enriched cDNA libraries were generated using the Illumina TruSeq RNA Library Prep kit v2 (Illumina Inc., Hayward, CA, USA).

treatment_protocol: Co-cultures were treated with NIMP (0, 4, and 100 micromolar) for 24 hours. NIMP was removed and replaced with fresh media and co-cultures were maintained up until  6-days post exposure

tag: t cell coculture?

value: 100  micromolar NIMP


title: 0 uM NIMP 3

value: 0 micromolar NIMP


title: 4 uM NIMP 3

value: 4 micromolar NIMP


title: 100 uM NIMP 3


title: 38582

description: AKBA

value: Akbash Dog


title: 100 uM NIMP 1

value: 100 micromolar NIMP


title: 4 uM NIMP 2


title: 0 uM NIMP 1


title: 38585

description: AKBA


title: 0 uM NIMP 4


title: 4 uM NIMP 1


title: 38581

description: AKBA


title: 0 uM NIMP 2


title: CD70-, within 1 week of aGvHD onset, 860-CD70-N_tcr

city: Birmingham

first: Paul

last: Moss

state: West Midlands

address: Vincent Drive

department: Immunology and Immunotherapy

country: United Kingdom

institute: University of Birmingham

description: QIAseq Immune Repertoire RNA

data_processing:
Raw reads were align to human TRA and TRB reference sequences using MiXCR v4.3.2
TCR clonotypes were assembled using mixcr analyze qiaseq-human-tcr-cdr3
Assembly: GRCh38
Supplementary files format and content: TCRB clonotype annotations
Library strategy: TCR-seq

source_name: PBMC

growth_protocol: PBMCs were isolated by density grade centrifugation and frozen in FCS containing 10% DMSO and stored in liquid nitrogen for later use

extract_protocol:
RNA was isolated using miRNeasy mini prep kit (Qiagen) from sorted CD70+ and CD70- T cells using BD FACS Melody according to manufacturer’s protocol.
QIAseq Immune Repertoire RNA (Qiagen) kit was used to perform TCR library preparation. Libraries were prepared according to manufacturer’s protocol using 10ng total input RNA and quantified using Qubit fluorometer

value: PBMC

value: T cells

tag: cell subset


title: CD70+, within 1 week of aGvHD onset, 860-CD70-P_tcr

description: QIAseq Immune Repertoire RNA


title: 38580

description: AKBA


title: CD70-, within 1 week of aGvHD onset, 818-CD70-N_tcr

description: QIAseq Immune Repertoire RNA


title: CD70+, within 1 week of aGvHD onset, 818-CD70-P_tcr

description: QIAseq Immune Repertoire RNA


title: 38579

description: AKBA


title: CD70-, within 1 week of aGvHD onset, 814-CD70-N_tcr

description: QIAseq Immune Repertoire RNA


title: 38578

description: CAUC

value: Caucasian Ovcharka


title: 4 uM NIMP 4


title: CD70-, within 1 week of aGvHD onset, 810-CD70-N_tcr

description: QIAseq Immune Repertoire RNA


title: 38577

description: CAUC


title: CD70-, within 1 week of aGvHD onset, 693-CD70-N_tcr

description: QIAseq Immune Repertoire RNA


title: 38575

description: KARA


title: 38574

description: KARA


title: replicate 2, sort 1, bin 2

source_name: HEK293T TetBxb1BFP iCasp9

value: HEK293T TetBxb1BFP iCasp9


title: replicate 2, sort 1, bin 3


title: CD70+, within 1 week of aGvHD onset, 693-CD70-P_tcr

description: QIAseq Immune Repertoire RNA


title: replicate 1, sort 3, bin 2


title: 38573

description: KARA


title: replicate 2, sort 1, bin 1


title: 38576

description: CAUC


title: Low conductive carbon film_1

city: Cheonan

first: Yu

middle: Meng

address: Pharmacy Bldg, Cheonan 31116, Republic of Korea

department: Department of Nanobiomedical Science

country: South Korea

institute: Institute of Tissue Regeneration Engineering (ITREN)

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to rn6 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: rn6
Supplementary files format and content: tab-delimited text files include read count values for each Sample

organism: Rattus norvegicus

source_name: neural stem/progenitor cells

growth_protocol: rNSPCs were cultured in knockout DMEM/F12 supplemented with StemPro™ Neural Supplement and antibiotics.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: rNSPCs were cultured on the different conductive carbon films.

value: neural stem/progenitor cells

value: WT

value: Stemness maintain media


title: 38572

description: SPMF

value: Spanish Mastiff


title: replicate 1, sort 2, bin 4


title: replicate 1, sort 2, bin 3


title: Medium conductive carbon film_2


title: CD70+, within 1 week of aGvHD onset, 814-CD70-P_tcr

description: QIAseq Immune Repertoire RNA


title: CD70+, within 1 week of aGvHD onset, 810-CD70-P_tcr

description: QIAseq Immune Repertoire RNA


title: Medium conductive carbon film_1


title: replicate 1, sort 2, bin 1


title: 38504

description: AFRN

value: Africanis


title: replicate 1, sort 1, bin 4


title: replicate 1, sort 1, bin 3


title: High conductive carbon film_2


title: Low conductive carbon film_2


title: replicate 1, sort 3, bin 4


title: 38297

description: BQSD

source_name: Unknown Source

value: Basque Shepherd Dog


title: 38503

description: AFRN


title: replicate 1, sort 1, bin 1


title: replicate 2, sort 1, bin 4


title: replicate 1, sort 3, bin 3


title: 38294

description: BQSD


title: CD70-, within 1 week of aGvHD onset, 860-N_rna

description:
860-CD70-N
Lexogen QuantSeq 3'
RNA_counts.csv

data_processing:
Raw reads were processed with the Dragen pipeline for quality checking and mapping to the human genome version hg38_alt_aware
Aligned reads were quantified at the gene expression level using HTSeq to produce per-sample feature count matrices
Assembly: GRCh38
Supplementary files format and content: comma separated file of raw counts for each sample

extract_protocol:
RNA was isolated using miRNeasy mini prep kit (Qiagen) from sorted CD70+ and CD70- T cells using BD FACS Melody according to manufacturer’s protocol.
Lexogen QuantSeq 3' (Illumina) kit was used to perform preparation of mRNA library. Libraries were prepared according to manufacturer’s protocol using 10ng total input RNA and quantified using Qubit fluorometer


title: CD70-, within 1 week of aGvHD onset, 848-N_rna

description:
848-CD70-N
Lexogen QuantSeq 3'
RNA_counts.csv


title: replicate 1, sort 1, bin 2


title: CD70+, within 1 week of aGvHD onset, 785-P_rna

description:
785-CD70-P
Lexogen QuantSeq 3'
RNA_counts.csv


title: High conductive carbon film_1


title: CD70-, within 1 week of aGvHD onset, 785-N_rna

description:
785-CD70-N
Lexogen QuantSeq 3'
RNA_counts.csv


title: CD70+, within 1 week of aGvHD onset, 848-P_rna

description:
848-CD70-P
Lexogen QuantSeq 3'
RNA_counts.csv


title: replicate 1, sort 2, bin 2


title: replicate 1, sort 3, bin 1


title: 38290

description: BQSD


title: CD70+, within 1 week of aGvHD onset, 704-P_rna

description:
704-CD70-P
Lexogen QuantSeq 3'
RNA_counts.csv


title: CD70-, within 1 week of aGvHD onset, 704-N_rna

description:
704-CD70-N
Lexogen QuantSeq 3'
RNA_counts.csv


title: 38286

description: BQSD


title: PLC_KO2_1

city: MEMPHIS

first: Li

last: Fan

state: Tennessee

address: 262 DANNY THOMAS PLACE, MAIL STOP 313, CHILI'S CARE CENTER

institute: St.jude Children's Research Hospital

data_processing:
Gene expression was quantified by STAR(ver. 2.6.0b) under default parameters with the human genome (GRCh37) and annotation file (Gencode v19).
Assembly: GRCh37
Supplementary files format and content: .tab files;raw counts

source_name: Hepatoma cell line

extract_protocol:
The total RNA was extracted from cells using RNeasy® Mini Kit (Qiagen, #74106) Kit following the manufacturer’s protocol.
Total RNA library was constructed using Illumina TrueSeq stranded mRNA library prep kit.

value: Hepatoma cell line

value: epithelial cells

value: HKDC1 knock out


title: CD70+, within 1 week of aGvHD onset, 953-P_atac

description:
Nextera DNA library preparation
ATAC_counts.csv

data_processing:
Reads were trimmed to remove nextera adapter sequences using Trim_Galore v0.6.5 with default parameters
Trimmed reads were aligned to the human genome reference GRCh38.genome.fa using Bowtie2 v2.3.5 (parameters: –very-sensitive-local). Alignments were filtered to keep only high quality (>q30) aligned reads from Chr1-22, ChrX and ChrY using Samtools v1.10 and duplicates removed using picard v2.21.1.
Peaks were called on the filtered alignments for each sample using MACS2 v2.2.7 with settings: --keep-dup=auto –nomodel –shift -100 –extsize 200. Peak summit files were filtered to remove peaks in known blacklisted regions (ENCFF356LFX_grch38_blacklist.bed). A union peak set across all samples was constructed using BEDtools v2.30.
The union peak set was used as the master reference peak loci to calculate the peak by sample count matrix using the annotatePeaks function from HOMER v4.11. This function also annotated peaks with closest gene (by RefSeq transcription start site) and associated genomic feature.
Assembly: GRCh38
Supplementary files format and content: comma separated file of raw counts at peak loci for each sample

extract_protocol:
Maximum of 50,000 cells were sorted on a cell sorter (FACSAria, BD) and pelleted by centrifugation at 500 × g and 4°C for 10 min. The cell pellet was washed once with cold PBS and centrifuged again. Pellets were resuspended in a 50-μl reaction cocktail containing 1 μl of 0.5% Digitonin (Promega, Madison, WI, USA), 2.5 μl of Tn5 transposase and 25 μl of TD buffer (Nextera DNA library preparation kit, Illumina, San Diego, CA, USA) and incubated for 30 min at 37°C with gentle shaking
The tagmented DNA was then purified using Minielute PCR Purification kit (Qiagen, Hilden, Germany) and eluted into 11 μl of elution buffer. The transposed DNA was then amplified using 2.5 μl of indexing primers and 25 μl of Nextera PCR master mix


title: CD70-, within 1 week of aGvHD onset, 953-N_atac


title: CD70+, within 1 week of aGvHD onset, 863-P_atac


title: 38283

description: BQSD


title: PLC_KO1_RES_2

value: HKDC1 knock out_rescue


title: CD70+, within 1 week of aGvHD onset, 818-P_atac


title: maize_BA

description: small RNA

organism: Zea mays

value: plant leaf

value: pool of 5 individual plants

value: July 2021


title: CD70-, within 1 week of aGvHD onset, 863-N_atac

value: PBMC


title: CD70-, within 1 week of aGvHD onset, 818-N_atac

value: T cells


title: 38291

description: BQSD


title: PLC_KO1_2


title: PLC_KO2_2


title: PLC_KO2_RES_2


title: CD70-, within 1 week of aGvHD onset, 814-N_atac


title: CD70+, within 1 week of aGvHD onset, 810-P_atac


title: CD70+, within 1 week of aGvHD onset, 814-P_atac


title: 38281

description: BQSD


title: 38280

description: BQSD


title: PLC_KO1_1


title: PLC_KO1_RES_1


title: CD70+, within 1 week of aGvHD onset, 720-P_atac


title: PLC_control4


title: CD70-, within 1 week of aGvHD onset, 810-N_atac


title: 38278

description: BQSD


title: 38273

description: AZWK

value: Azawakh


title: CD70-, within 1 week of aGvHD onset, 720-N_atac


title: CD70+, within 1 week of aGvHD onset, 704-P_atac


title: PLC_control3


title: 38233

description: AZWK


title: PLC_control2


title: replicate 3, sort 2, bin 4

value: HEK293T TetBxb1BFP iCasp9


title: CD70-, within 1 week of aGvHD onset, 704-N_atac


title: replicate 3, sort 2, bin 3


title: PLC_control1


title: 38231

description: AZWK


title: 38253

description: AZWK


title: RAS OUT HYP DEEP 24_10 C + 100 THU Rep 4

description: RAS OUT HYP DEEP 24

data_processing:
*library strategy: DNA-Seq
Sequencing reads were trimmed for adapters with Alientrimmer
PCR Duplicates were removed with Picard-tools v2.23.3
Single Nucleotide Variants detection was performed withbcftools mpileup V1.13
Assembly: Hg38 (Homo Sapien) Ensembl
Supplementary files format and content: .csv file of raw read counts
Supplementary files format and content: .csv file of mutation analysis at each nucleotide position of each sample

extract_protocol:
gDNA was extracted with NEB MonarchGenomic DNA Purification kit.
Library preparation was done using the NEBNext DNA Library Prep Kit and NEBNext Multiplex Oligos for Illumina

value: HeLa


title: 38229

description: AZWK


title: replicate 3, sort 2, bin 2


title: replicate 3, sort 1, bin 3


title: replicate 3, sort 1, bin 2


title: RAS OUT HYP DEEP 23_30  T + 10 C + 100 THU Rep 4

description: RAS OUT HYP DEEP 23


title: replicate 3, sort 1, bin 4


title: replicate 3, sort 1, bin 1


title: 37693

description: ASTC

value: Australian Stumpy Tail Cattle Dog


title: RAS OUT HYP DEEP 22_10 T + 10 C + 100 THU Rep 4

description: RAS OUT HYP DEEP 22


title: replicate 2, sort 2, bin 4


title: 37198

description: ASTC


title: replicate 2, sort 2, bin 3


title: replicate 2, sort 2, bin 2


title: RAS OUT HYP DEEP 21_10 C + 100 THU Rep 3

description: RAS OUT HYP DEEP 21


title: replicate 2, sort 2, bin 1


title: CD70+, within 1 week of aGvHD onset, 860-P_rna

description:
860-CD70-P
Lexogen QuantSeq 3'
RNA_counts.csv


title: replicate 3, sort 2, bin 1


title: 37187

description: DRAH

value: Drahthaar


title: 37186

description: DRAH


title: RAS OUT HYP DEEP 20_30  T + 10 C + 100 THU Rep 3

description: RAS OUT HYP DEEP 20


title: hsa_LMS, patient 3, Fer-1

city: Hannover

first: Maximilian

last: Fuchs

address: Carl-Neuberg-Str. 1

department: IMTTS

country: Germany

institute: Hanover Medical School

data_processing:
Raw data processing was conducted by use of nfcore/rnaseq (version 1.4.2)
Nextflow was used as a bioinformatics workflow tool.
It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.
The genome reference and annotation data were taken from GENCODE.org (Homo sapiens: GRCh38.p13; release 34).
Normalization and differential expression analysis was performed on the internal Galaxy (version 20.05) instance DESeq2 (Galaxy Tool Version 2.11.40.6) with default settings except for “Output normalized counts table”, which was set to “Yes” and all additional filters were disabled
Assembly: GRCh38.p13; release 34
Supplementary files format and content: trimmed raw reads in fastq format
Supplementary files format and content: raw count sin txt format

source_name: Heart failure (explanted)

growth_protocol: LMS were cultivated with medium 199 in biomimetic cultivation chambers (InVitroSys) while mechanically stretched to sarcomere length of 2.1 µm and electrically stimulated at 0.2 Hz.

extract_protocol:
RNA was extracted using miRNeasy Kit from Qiagen. 250ng of total RNA per sample were utilized as input for mRNA enrichment procedure.
Library generation was done using ‘NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina’

treatment_protocol: Ferrostatin-1 [10µM] was used to inhibit ferroptosis. Control slices were treated with 1:1000 DMSO. Treatment was given for 72 hours.

value: Heart failure (explanted)

value: WT


title: hsa_LMS, patient 4, Fer-1


title: hsa_LMS, patient 2, Fer-1


title: hsa_LMS, patient 1, Fer-1


title: 37181

description: ASTC


title: hsa_LMS, patient 4, DMSO

value: DMSO


title: 38571

description: SPMF

value: Spanish Mastiff


title: 37185

description: DRAH


title: RAS OUT HYP DEEP 17_10 T Rep 4

description: RAS OUT HYP DEEP 17


title: hsa_LMS, patient 3, DMSO


title: hsa_LMS, patient 2, DMSO


title: 37010

description: BRBT

value: Barbet


title: hsa_LMS, patient 1, DMSO


title: RAS OUT HYP DEEP 16_10 C + 100 THU Rep 2

description: RAS OUT HYP DEEP 16


title: 36581

description: BRBT


title: RAS OUT HYP DEEP 19_10 T + 10 C + 100 THU Rep 3

description: RAS OUT HYP DEEP 19


title: RAS OUT HYP DEEP 14_10 T Rep 3

description: RAS OUT HYP DEEP 14


title: RAS OUT HYP DEEP 18_30  T Rep 4

description: RAS OUT HYP DEEP 18


title: 36081

description: ARPD

value: Argentine Pila Dog


title: 36085

description: ARPD


title: Sirt6 cKO AF tissue 2

type: RNA

city: Philadelphia

first: Makarand

middle: V

last: Risbud

address: 1025 Walnut St.

institute: Thomas Jefferson University

description: Gene expression data from RNA of 24 months old mice

hyb_protocol: Affymetrix Gene chips, Mouse Clariom S, were hybridized with 2.5 μg fragmented and biotin-labeled cDNA in 100 μl of hybridization cocktail.

scan_protocol: Array scanning was performed on an Affymetrix GeneChip Scanner 3000 7G using Command Console Software (Affymetrix)

data_processing: Raw data were processed and .CHP files were generated by sst-rma normalization from Affymetrix .CEL files, and quality control of the expeirment was performed in Transcriptome Analysis Console (TAC) v4.0.2 (Affymetrix). The experimental group was compared to the control group in the TAC, including all probe sets where at least 50% of the samples had a DABG (detected above background) p < 0.05.

label: biotin

source_name: Sirt6 cKO AF

label_protocol: Single-stranded cDNA was generated, then fragmented and biotin-labeled using the GeneChip WT Plus kit according to ABI protocol (Thermo Fisher Scientific).

growth_protocol: Sirt6 fl/fl  or Sirt6 cKO mice were obtained and intevertebral discs were processed for RNA transcriptomic analysis at 24 months-of-age.

extract_protocol: NP and AF tissues were micro-dissected from caudal and lumbar intervertebral discs of four Sirt6fl/fl and four Sirt6cKO mice at 24 months of age and immediately placed in RNAlater® Reagent (INVITROGEN). Tissues were homogenized with a Pellet Pestle Motor (Sigma Aldrich, Z359971) and RNA was extracted from tissue lysates using RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions.

value: Annulus Fibrosus

value: Sirt6 cKO

value: 24 months


title: 36056

institute: National Institutes of Health

description: ARPD


title: Sirt6 cKO AF tissue 4


title: RAS OUT HYP DEEP 13_10 C + 100 THU Rep 1

description: RAS OUT HYP DEEP 13


title: RAS OUT HYP DEEP 12_Non-Treated Rep 4

description: RAS OUT HYP DEEP 12

value: Non-Treated


title: RAS OUT HYP DEEP 11_30  T + 10 C + 100 THU Rep 2

description: RAS OUT HYP DEEP 11


title: 36061

description: ARPD


title: RAS OUT HYP DEEP 15_30 T Rep 3

description: RAS OUT HYP DEEP 15


title: RAS OUT HYP DEEP 10_10 T + 10 C + 100 THU Rep 2

description: RAS OUT HYP DEEP 10


title: 36087

description: ARPD


title: 35841

description: MKRH

value: McKenzie River Husky


title: RAS OUT HYP DEEP 9_Non-Treated Rep 3

description: RAS OUT HYP DEEP 9


title: Sirt6 cKO AF tissue 1


title: 35810

description: TERV

value: Belgian Tervuren


title: Sirt6 cKO NP tissue 3

source_name: Sirt6 cKO NP

value: Nucleus Pulposus


title: Sirt6 fl/fl AF tissue 2

source_name: Sirt6 fl/fl AF

value: Sirt6 fl/fl


title: 1182 SS+

city: Minneapolis

first: Maria

last: Razzoli

state: Minnesota

department: Integrative Biology and Physiology

institute: University of Minnesota

data_processing:
FASTQ files were filtered and demultiplexed using DND2.0 with the following parameters: quality trim score = 20, adaptor trim match length = 10, adaptor trim max mismatch = 3, barcode max mismatch = 1, stitching max mismatch = 2, dedup-hd = 1
DND was used to convert the raw FASTQ files to Digital Count Conversion (DCC) file format and uploaded to the Nanostring GeoMx DSP Anaysis Suite
Limit of Quantification was derived and used to exclude genes that were not expressed at a level of LOQ raised to the power of 2 in <20% of AOIs
Individual probe counts were normalized to the median probe count for each AOI
Assembly: mm10
Supplementary files format and content: Lyons_et_al_geomix_median_norm_q_datasets2.0.csv
Library strategy: spatial transcriptomics

source_name: brain

extract_protocol:
Formalin fixed paraffin embedded tissue was sectioned at 5um and prepared using the Nanostring GeoMx workflow according to the manufacturer's instructions
Spatial transcriptomic sequencing libraries were prepared using the Nanostring GeoMx workflow according to the manufacturer's instructions

value: brain

tag: group

value: ctrl

value: high

tag: region

value: cortex

tag: subregion

value: SS

tag: mouse id


title: Sirt6 fl/fl AF tissue 3

tag: age


title: Sirt6 fl/fl AF tissue 1


title: Sirt6 cKO NP tissue 4


title: Sirt6 cKO AF tissue 3


title: Sirt6 fl/fl AF tissue 4


title: Sirt6 fl/fl NP tissue 4

source_name: Sirt6 fl/fl NP


title: Sirt6 cKO NP tissue 2


title: Sirt6 fl/fl NP tissue 3


title: Sirt6 fl/fl NP tissue 2


title: RAS OUT HYP DEEP 7_10 T + 10 C + 100 THU Rep 1

description: RAS OUT HYP DEEP 7

tag: cell line

value: HeLa


title: 35737

city: Bethesda

description: SHIK

source_name: Saliva

value: Shikoku


title: 1182 MC-

value: low

value: MC


title: 35618

description: MKRH

source_name: Whole Blood


title: 1182 CP+

value: choroid plexus

value: CP


title: Sirt6 cKO NP tissue 1

value: Sirt6 cKO

value: 24 months


title: 35616

description: MKRH

value: McKenzie River Husky


title: RAS OUT HYP DEEP 6_30  T Rep 2

description: RAS OUT HYP DEEP 6

source_name: HeLa


title: Sirt6 fl/fl NP tissue 1


title: 1182 CA3-

value: hippocampus


title: 1182 CA1+


title: RAS OUT HYP DEEP 5_10 T Rep 2

description: RAS OUT HYP DEEP 5


title: 1170 SS+

value: CSS


title: 1182 SS-


title: 1182 MC+


title: 35505

description: MKRH


title: RAS OUT HYP DEEP 8_30  T + 10 C + 100 THU Rep 1

description: RAS OUT HYP DEEP 8


title: 1170 SS-


title: 35504

description: MKRH


title: RAS OUT HYP DEEP 2_10 T Rep 1

description: RAS OUT HYP DEEP 2


title: RAS OUT HYP DEEP 4_Non-Treated Rep 2

description: RAS OUT HYP DEEP 4

value: Non-Treated


title: RAS OUT HYP DEEP 3_30  T Rep 1

description: RAS OUT HYP DEEP 3


title: 35604

description: MKRH


title: 35487

description: BELS

value: Belgian Sheepdog


title: 1170 MC-

value: brain


title: 35311

description: DNGO

value: Dingo


title: RAS OUT HYP DEEP 1_Non-Treated Rep 1

description: RAS OUT HYP DEEP 1


title: 1170 CP+

value: high


title: postnatal day 28 annulus fibrosus tissue sample 1

city: Manhattan

first: Danielle

last: D'Erminio

state: New York

address: 1 Gustave L. Levy Place

department: Orthopaedics

institute: Mount Sinai

data_processing:
The sequencing libraries were multiplexed and clustered on 4 flowcell lanes. After clustering, the flowcell was loaded on the Illumina HiSeq (4000 or equivalent) instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification.  After demultiplexing, sequence data was checked for overall quality and yield. Then, raw sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The reads were then mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate P values and Log2 fold changes. Genes with adjusted P values < 0.05 and absolute log2 fold changes >1 were called as differentially expressed genes for each comparison. Gene ontology analysis was performed on the statistically significant set of genes by implementing the software GeneSCF. The GO list was used to cluster the set of genes based on their biological process and determine their statistical significance.
assembly: GRCm38
processed data files format and content: normalized_counts.csv

source_name: annulus fibrosus

extract_protocol:
Care was taken to isolate AF tissue and discard NP and surrounding CEP. Each sample was flash-frozen in liquid nitrogen followed by homogenization using a mikro-dismembrator (Sartorius; Göttingen, Germany).
RNA extracted from homogenized AF tissue through the TRIzol/chloroform followed by RNeasy column kit (Qiagen). RNA quality and concentration analyzed using Nanodrop 2000 (ThermoFisher Scientific). DNAse treatment performed on all samples.
libraries were prepared using rRNA depletion method
The sequencing libraries were clustered on a lane of a NovaSeq 6000 S4 flowcell. After clustering, the flowcell  was  loaded  on  the  Illumina  instrument  according  to  manufacturer’s  instructions.  The samples were  sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by  the  Control  software.  Raw  sequence  data  (.bcl  files)  generated  the  sequencer  were  converted  into  fastq  files  and  de-multiplexed  using  Illumina's  bcl2fastq  2.17  software.  One  mismatch  was  allowed  for  index  sequence  The sequencing libraries were clustered on a lane of a NovaSeq 6000 S4 flowcell. After clustering, the flowcell was  loaded  on  the  Illumina  instrument  according  to  manufacturer’s  instructions.  The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the  Control  software.  Raw  sequence  data  (.bcl  files)  generated  the  sequencer  were  converted  into  fastq  files and  de-multiplexed  using  Illumina's  bcl2fastq  2.17  software.  One  mismatch  was  allowed  for  index  sequence identification.

value: annulus fibrosus

tag: strain

value: wild-type

value: postnatal day 28


title: 35309

description: DNGO

data_processing:
Image data was analyzed using GenomeStudio with GT module (Illumina).
genotypes AA, AB, BB, NC=no call

extract_protocol: Genomic DNA was extracted from whole blood or Buccal cells using Proteinase K and phenol/chloroform with standard protocols. Genomic DNA extracted from saliva using standard Performagene genotek DNA extraction protocols.


title: P6H55-12_RNA2

city: Wilmington

first: Qi

last: Zheng

state: DE

address: 1701 Rockland Road

institute: Nemours Children's Health

data_processing:
FastQC was used to assess library quality
STAR was used to map reads to the reference genome
RSEM was used to count reads mapping to annotated genes
Assembly: GRCm39
Supplementary files format and content: tab-separated values matrix files for read count of batch01 and batch02 samples

extract_protocol:
RNA was extracted by the Pediatric Genomics Laboratory at Nemours Children’s Health.
RNA libraries were constructed by the Pediatric Genomics Laboratory at Nemours Children’s Health using the Illumina Stranded Total RNA Prep with Ribo Zero Plus.

treatment_protocol: Brains were collected from pups on P7 and dissociated into a single cell solution using the Adult Brain Dissociation Kit and gentleMACS Octo Dissociator (Miltenyi Biotec). Microglia were enriched via magnetic CD11b-coated bead isolation (Miltenyi Biotec).

value: monocytes (CD11b+)

value: CF-1 wildtype

value: Control

tag: Sex

value: F


title: P6H63-7_RNA1

tag: time

value: M


title: P6H63-8_RNA1

tag: tissue


title: P6H55-7_RNA1

tag: cell type


title: 1170 CP-

value: low

value: choroid plexus

value: CP


title: 1182 CA1-

value: ctrl

value: hippocampus


title: N8-4_RNA1

tag: genotype

value: HIE


title: postnatal day 28 annulus fibrosus tissue sample 2


title: 1170 CA3+

value: brain

value: CSS


title: 35306

description: DNGO

tag: breed

value: Dingo


title: 1170 MC+

value: high

value: cortex

value: MC


title: postnatal day 28 annulus fibrosus tissue sample 3

value: annulus fibrosus

value: wild-type

value: postnatal day 28


title: 35304

description: DNGO


title: N8-3_RNA1

value: monocytes (CD11b+)

value: CF-1 wildtype


title: N5-4_RNA1

value: M


title: postnatal day 28 annulus fibrosus tissue sample 4


title: N5-3_RNA1


title: 1169 SS+

value: SS


title: 35302

description: DNGO

source_name: Unknown Tissue


title: postnatal day 21 annulus fibrosus tissue sample 2

value: postnatal day 21


title: 35303

description: DNGO


title: 1169 SS-

value: low


title: 35300

description: DNGO


title: postnatal day 21 annulus fibrosus tissue sample 4

data_processing:
The sequencing libraries were multiplexed and clustered on 4 flowcell lanes. After clustering, the flowcell was loaded on the Illumina HiSeq (4000 or equivalent) instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification.  After demultiplexing, sequence data was checked for overall quality and yield. Then, raw sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate P values and Log2 fold changes. Genes with adjusted P values < 0.05 and absolute log2 fold changes >1 were called as differentially expressed genes for each comparison. Gene ontology analysis was performed on the statistically significant set of genes by implementing the software GeneSCF. The GO list was used to cluster the set of genes based on their biological process and determine their statistical significance.
The reads were then mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. BAM files were generated as a result of this step.
assembly: GRCm38
processed data files format and content: normalized_counts.csv


title: 35215

description: BELS

value: Belgian Sheepdog


title: postnatal day 21 annulus fibrosus tissue sample 3


title: P6H8-7M_RNA1

value: Control


title: P6H7-8F_RNA2

value: brain

value: Hypoxia

value: F


title: postnatal day 14 annulus fibrosus tissue sample 1

value: postnatal day 14


title: PLC_KO2_RES_1

value: Hepatoma cell line

value: epithelial cells

value: HKDC1 knock out


title: 38285

description: BQSD

value: Basque Shepherd Dog


title: 1170 CA3-

value: CSS

value: hippocampus


title: 1169 CA3-


title: 1170 CA1-


title: 35158

description: TERV

value: Belgian Tervuren


title: P6H12-11M_RNA4

value: monocytes (CD11b+)

value: CF-1 wildtype

value: HIE

value: M


title: 1169 CA1+

value: high


title: 1169 CA3+


title: P6H12-11M_RNA3


title: 1169 MC+

value: cortex

value: MC


title: postnatal day 14 annulus fibrosus tissue sample 3

value: annulus fibrosus

value: wild-type


title: 1163 SS-

value: brain

value: low

value: SS


title: postnatal day 14 annulus fibrosus tissue sample 2

value: postnatal day 14


title: P6H12-14F_RNA2

value: F


title: 35131

description: NGSD

value: New Guinea Singing Dog


title: postnatal day 21 annulus fibrosus tissue sample 1

value: postnatal day 21


title: P6H9-15F_RNA2

value: Hypoxia


title: 1163 MC-

value: CSS


title: 35133

description: NGSD


title: 34696

description: NGSD


title: postnatal day 5 annulus fibrosus tissue sample 2

value: postnatal day 5


title: P6H8-8F_RNA3

value: monocytes (CD11b+)

value: CF-1 wildtype

value: Control


title: 35130

description: NGSD


title: P4H4-7F_RNA2


title: 34698

description: NGSD


title: 34695

description: NGSD


title: P6H9-14M_RNA2

value: M


title: postnatal day 5 annulus fibrosus tissue sample 3


title: 1163 CA3 +

value: high

value: hippocampus


title: 1163 MC+

value: cortex

value: MC


title: 34692

description: NGSD


title: postnatal day 5 annulus fibrosus tissue sample 1

value: annulus fibrosus

value: wild-type


title: 34697

description: NGSD


title: P6H7-16M_RNA2

value: brain


title: 1163 CP+

value: choroid plexus

value: CP


title: 34611

description: MKRH

value: McKenzie River Husky


title: P4H4-8M_RNA2


title: 1151 SS+

value: ctrl

value: SS


title: P4H1-6F_RNA4

value: HIE

value: F


title: postnatal day 5 annulus fibrosus tissue sample 4

value: postnatal day 5


title: P4H1-1M_RNA3

value: monocytes (CD11b+)

value: CF-1 wildtype


title: postnatal day 14 annulus fibrosus tissue sample 4

value: postnatal day 14


title: P4H1-6F_RNA3


title: 34610

description: MKRH


title: 34609

description: MKRH


title: Cattle Y-chromosome methylation profile from PacBio data

data_processing:
Basecalling was done for the respective sequencing platform according to the manufacturer prescribed procedure using their proprietary basecallers - Dorado for ONT and Primrose for PacBio.
Assembly: GCF_002263795.3
Supplementary files format and content: methylation call in bed format
Library strategy: WGS

organism: Bos taurus

source_name: Lung

extract_protocol:
DNA extraction was done on standard manufacturer suggested protocol.
The respective libraries used on the sequencing platforms were made according to the specifications of the manufacturers.

value: Lung


title: 1151 SS-

value: low

value: cortex


title: 34606

description: MKRH


title: 1151 MC-

value: MC


title: 1163 CA1-

value: CSS

value: hippocampus


title: CT1-5_rep3

city: Montreal

first: William

last: Pastor

state: Quebec

address: 3655 Promenade Sir-William-Osler rm900

department: Biochemistry

country: Canada

institute: McGill University

data_processing:
For RNA and ChIP/ATAC sequencing analysis, Genpipes 4.3.2 (https://bitbucket.org/mugqic/genpipes) provided the pipeline for basic sequencing processing.  In brief for RNAseq, sequencing quality and adaptor removal was trimmed with trimmomatic (v0.36). Trimmed fastq files alignment was performed with STAR aligner (v2.7.8a) using hg38/GRCh38 (ensembl v104). Picard (v2.9.0) was then used merged, mark duplicates, identify unique read, and sort .bam files proceeding alignment. Read counts were collected using HTseq-count and StringTie (v1.3.5). Differentially expressed gene (DEG) comparison was performed with DESeq2 package on RStudio (R v4.3.1). Correlation matrix, hierarchal gene cluster analysis, and PCA were generated in R. Gene pathway analysis were performed on ConsensusPathwayDB and EnrichR. For ChIPSeq and ATACseq, in brief, raw fastq files trimmed using trimmomatic (v.0.36). Then qualified fastq reads were mapped with BWA (v.0.7.17) with post processing with sambamda (v0.8.1) to merge replicates, mark and filter duplicates, and remove blacklist regions. Peak calling and differential-bind was performed with MACS2 (v2.2.7.1). Gene annotations and motif analysis used with Homer (v4.11). Bam to bigwig bamCoverage from deepTools (v3.5.1) was used to generate the tracks for viewing on IGV (v2.9.4).
Assembly: hg38
Supplementary files format and content: tab-delimited text includes raw counts for each sample

source_name: Trophoblast Stem Cell

growth_protocol: TSC were cultured in TSC basal media containing DMEM F-12 (GIBCO), 1x ITS-X (GIBCO), 0.3% BSA (WISENT), 1% Penicillin/Streptomyocin (GIBCO), 1% ESC qualified Fetal Bovine Serum (GIBCO), 0.1mM β-mercaptoethanol (GIBCO), 15ug/ml L-ascorbic acid (SIGMA), and 50ng/ml recombinant hEGF (GIBCO). To this, made fresh, 0.75mM valporic acid, 2uM CHIR99021 (CaymenChem), 0.5uM A8301 (CaymenChem), 1uM SB431542 (CaymenChem), and 5μM Y27632 (CaymenChem) was added to make TSCMedia. TSC were dissociated using TRYPLE (GIBCO) diluted with PBS to 30% and incubated at 37C for 10 min. Deactivation of TRYPLE was done by using 1:1 vol of 0.5mg/ml Soybean trypsin inhibitor (GIBCO) diluted in PBS. For experiments performed in figure 1-2, TSC were passaged on to 5ug/ml of Collagen IV (Corning) coated plates, but due to product availability, TSC from experiment in figure 3-6 were passaged onto Laminin 511(SIGMA) coated plates.

extract_protocol:
Total RNA isolation used manufacturing protocol indicated by Sigma-Aldrich RNAzolRT R4533. Qubit RNA BR Assay kit (Q10211) was used to accurately measure RNA concentration.
For RNA library synthesis, in brief, purified mRNA was cleaned using the NEBNext Poly(A) mRNA Magnetic Isolation Module kit (NEB E7490) and final library generation was created with the NEBNextÒ Ultra RNA Library Prep Kit for IlluminaÒ (NEB E7530) following manufacturing instructions. Barcoding came from TruSeq Unique Dual Indexes (Illumina, San Diego, CA) QubitÔ 1x dsDNA HS Assay kit (Q33231) was used to measure synthesis of the library.

treatment_protocol: StemCell Technologies Hypoxia Incubator Chamber (cat:27310) and mixed O2 and CO2 Praxiar tanks were injected into control the O2 levels.

value: Trophoblast Stem Cell

value: WT


title: RP_late-2

city: Wuhan

first: Liang

last: Hu

address: 1 Nanhu Yaoyuante, Hongshan District

institute: Hubei Academy of Agricultural Sciences

data_processing:
Data were filtered by abandoning adapter sequences and low-quality reads.
The obtained clean reads, ranging from 18 nt to 36 nt in length, underwent deduplication to generate unique reads for further exploration. These reads were matched to the Rfam (ver. 13.0) database using BLAST to identify rRNA, tRNA, snRNA, and snoRNA, adhering to a criterion of no more than two mismatches.
Unclassified reads were matched to the miRBase database (ver. 22.0) using BLAST with the same criterion to identify mature miRNA sequences.
The identified known miRNAs were classified into families by aligning them with reference miRNAs from the miRBase database.
Unmapped reads were analyzed against the genome using the Mireap online program to predict novel miRNAs.
Assembly: Rfam (ver. 13.0) database and miRBase database (ver. 22.0)
Supplementary files format and content: TXT file contain counts for each sample

organism: Oryza sativa

source_name: Leaf sheaths of rice

growth_protocol: The pyramiding line containing both BPH14/BPH15 genes (B1415) was created using the indica cartivar ‘Wushansimiao’ as the recurrent parent (RP) [12]. Rice seeds were sown in plastic contains (15 cm tall and 9 cm wide) with 15 per container and maintained in a controlled environment with 14 h light (32 ± 2°C)/10 h dark (26 ± 2°C) cycle. BPHs were reared on the susceptible cultivar ‘Taichung Native1’ (TN1, IRRI Acc. No.00105) under the same environment.

extract_protocol:
Total RNA was extracted using TRIzol from leaf sheaths of rice.
Eighteen small RNA libraries were produced using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Inc.), encompassing samples from B1415 and RP at non-infestation (B1415_0, RP_0), early infestation (B1415_early, RP_early), and late infestation (B1415_late, RP_late) stages, each with three biological replicates. The small RNA libraries underwent quantification using a high-sensitivity DNA Kit on a Bioanalyzer 2100 system (Agilent) prior to sequencing on the Illumina NovaSeq 6000 platform.

treatment_protocol: Sample collection and BPH treatments were executed following the endpoint method [33]. Despite varying start times, all treatments were concluded concurrently. Four-leaf stage seedlings of B1415 and RP were infested with eight 3rd instar BPH nymphs per seedling at 0, 3, 6, 12, 24, 48, and 72 h with 15 seedlings each in three biological replicates. Leaf sheath samples were categorized as non-infested (0 h), early infestation stage (3, 6, 12 h), or late infestation stage (24, 48, 72 h), following prior methodology [33] and designated as B1415_0, B1415_early, B1415_late, RP_0, RP_early, and RP_late, respectively. All samples were snap frozen, ground, and preserved in TRIzol (Invitrogen Life Technologies) at -80°C.

value: Leaf sheaths of rice

value: The recurrent parent (RP) 'Wushansimiao', an indica inbred rice cultivar

value: Late feeding stage


title: RP_late-3


title: CT3-20_rep3


title: RP_early-3

value: Early feeding stage


title: 34575

description: LAEK

value: Belgian Laekenois


title: CT3-2_rep3


title: 1163 CA1+

value: brain

value: high


title: BT2-5_rep3


title: 34496

description: XOLO

value: Xoloitzcuintli


title: 34541

description: BKHW

value: Bakharwal


title: 1151 MC+

value: ctrl


title: RP_late-1


title: BT2-20_rep2


title: RP_0-3

value: Non-infested by BPH


title: 1151 CA3-

value: low


title: 1151 CP+

value: choroid plexus

value: CP


title: 34314

description: AFFN

value: Affenpinscher


title: RP_early-2


title: 1151 CP-


title: RP_0-1


title: Whole Blood from BAB3225

first: Jesse

last: Bengtsson

address: 720 Broadway

institute: Pacific Northwest Research Institute

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed following the manufacturer’s protocol.

scan_protocol: Scanned on an Agilent G2600D scanner. Images were quantified using Agilent Feature Extraction Software (version 12.1.1.1)

data_processing: Agilent Feature Extraction Software (version 12.1.1.1) was used for background subtraction and normalization.

source_name: Whole Blood Extracted Genomic DNA from BAB3225

label_protocol: 1.2 ug of genomic patient and reference DNA were digested with AluI (5 U) and RsaI (5 U) (Promega, R6281 and R6371) for 2 hr at 37°C, 65°C for 20 minutes. Labeling reactions were performed according to the manufacturer’s instructions (BioPrime Array CGH Genomic Labeling Module,Invitrogen Corporation, #18095-012; Perkin-Elmer Las Inc. Cyanine Smart Pack dCTP,

extract_protocol: DNA was isolated from either peripheral blood or LCLs with a Puregene kit (Gentra Systems), following the manufacturer’s protocol

tag: sample type

value: Patient BAB3225

value: Male

value: Whole Blood

source_name: Genomic DNA extracted from Male LCL GM10851

value: Reference Sample


title: CT1-2_rep3

value: Trophoblast Stem Cell

value: WT

tag: treatment


title: 1175 SS+

value: cortex

value: SS


title: B14/15_late-3

value: Leaf sheaths of rice

value: The near isogenic lines (NILs) contain both the BPH14 and BPH15

value: Late feeding stage


title: Whole Blood from BAB3141

source_name: Whole Blood Extracted Genomic DNA from BAB3141

value: Patient BAB3141


title: 34323

last: Harris

address: 50 South Drive

description: BELS

value: Belgian Sheepdog


title: B14/15_late-2


title: 1151 CA3+

value: brain

value: ctrl

value: high

value: hippocampus