title: I047&I041_Naïve samples

city: Esch-sur-Alzette

first: Kamil

last: Grzyb

email: kamilgen@gmail.com, kamil.grzyb@uni.lu

address: 2, avenue de l'Université

country: Luxembourg

institute: University of Luxembourg - LCSB

data_processing:
Bcl2fastq ver 2.0 was used for the base calling
Paired end sequencing reads were trimmed for adaptor sequence. Based on the original Dropseq implementation (Macosko et al; 2015), the reads were demultiplexed for the cell barcode and UMI. The genes mapped to GRCm38.87 using STAR genome aligner - with default parameters
Genome_build: GRCm38.87 (mm10)
Supplementary_files_format_and_content: tab-delimited text files include raw counts

source_name: brain single cell suspension

growth_protocol: Mouse glioma 261 (GL261) cells were maintained at 37ºC with 5% CO2 in serum medium. 1µl containing 500 GL261 cells were implanted into the right striatum of the brain and the mice were monitored weekly for the first 2 weeks and daily from day 21 post-implantation. Magnetic resonance imaging (MRI) was performed weekly upon 21 post-implantation to assess tumour volume and the brains were isolated at respective volume: early stage (5-10mm3); intermediate stage (20-25mm3) and late stage (30-35mm3).

extract_protocol:
Single cell RNA seq using Dropseq - 3' bead based enrichment technique, using SMART synthesis (Macosko et al, 2015 doi: 10.1016/j.cell.2015.05.002)
Libraries were prepared according to Drop-seq methods (Macosko et al, 2015 doi: 10.1016/j.cell.2015.05.002). After cDNA tagmenation, PCR amplification was performed using Illumina primers (N701,N702,N707,N710, A501). The purified cDNA fragments of ~600 bp were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.

value: brain

tag: tumour stage

value: Irg1/Acod1 +/+

value: No treatment


title: THP1_NoLPS_RNAseq_1

status: Public on Sep 16 2020

type: SRA

city: Stanford

first: Jesse

middle: M

last: Engreitz

state: CA

address: Biomedical Innovation Building Rm 3700

country: USA

institute: Stanford University

description: PolyA mRNA from THP1 cells

library_source: transcriptomic

data_processing:
Pseudo-align reads to hg19 transcriptome index using kallisto
Aggregate TPM values over all isoforms for the same gene
Genome_build: hg19
Supplementary_files_format_and_content: Expression level (TPM) for each gene

molecule: polyA RNA

organism: Homo sapiens

source_name: monocytic cell line

growth_protocol: The human monocyte THP1 cell line was obtained from ATCC (ATCC, TIB-202). Cells were maintained in RPMI 1640 Medium (Corning, 10-040-CM) supplemented with 10% fetal bovine serum (Life Technologies, 16140071) and 1% penicillin-streptomycin (Life Technologies Inc., 15140163). Cell lines were cultured at 37°C with 5% CO₂ and were subcultured twice a week by aspirating off all cell culture medium except 0.5 ml in a T-75 flask and 1 ml in a T-175 flask, and refreshing the flasks with 13 ml and 49 ml of medium respectively.

extract_protocol:
RNA was extracted from 20 million THP1 cells in thre biological replicates.
RNA-seq libraries were prepared using the Smart-seq2 protocol in bulk

treatment_protocol: THP1 cells were stimulated using cell culture medium with LPS at a final concentration of 0.5 µg/ml, diluted from a 5 mg/ml LPS stock (Millipore Sigma, L3024), for 20 hours.

tag: cell type

tag: stimulation

value: LPS -


title: I040_GBM Late stage

molecule: total RNA

organism: Mus musculus

tag: tissue

value: Late stage

tag: strain

tag: genotype

tag: treatment

value: GBM implanted cells


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B2_ad007

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: DG

tag: Sex

value: male

tag: age


title: I029&I030_Naïve samples

value: Irg1/Acod1 -/-


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B11_ad006


title: Muscle_Ni_03mo_rep1

type: RNA

city: Lexington

first: Yuan

last: Wen

state: Kentucky

address: 760 Press Ave

institute: University of Kentucky

hyb_protocol: Standard Affyemtrix protocol

scan_protocol: Standard Affyemtrix protocol

data_processing: Raw signal intensity data was background corrected, log2 transformed and normalized with robust multi-array average (RMA) from the Affymetrix data bank using the “oligo” package in R v4.0.1 (8). Each Affymetrix chip contains 25,117 probesets, including 2163 control and unmapped probesets.

label: biotin

organism: Rattus norvegicus

source_name: gastrocnemius, nickel, 3 months, replicate 1

label_protocol: Standard Affyemtrix protocol

growth_protocol: Male Sprague-Dawley rats (Rattus norvegicus; age, approximately 30 d; weight, 75 to 100 g) were purchased from Envigo (Barrier 208A, Frederick, MD). Rats were allowed to acclimate in the AFRRI vivarium for at least 2 weeks prior to the start of experiments. The room was maintained at standard temperature (21 ± 2°C) and humidity (30% to 70%), with a 12:12-h light:dark cycle (lights on, 0600) and access to standard rat chow (Teklad Global Rodent Diet 8604, Envigo) and water ad libitum. Rats were pair-housed in plastic microisolation cages (23.8 × 45.4 cm) with filter tops and bedding (Teklad Sani-Chips, Envigo), changed 2 or 3 times weekly. All procedures involving animals were conducted to achieve maximal possible wellbeing of the rats, were IACUC-approved (protocol no. 2016-05-006) prior to the start of the study, and were performed in compliance with the guidelines set forth in the Guide for the Care and Use of Laboratory Animals in an AAALAC-accredited facility.

extract_protocol: Total RNA was isolated from gastrocnemius muscle using TRIzol® reagent (Invitrogen, Carlsbad, CA) following manufacturer’s protocol. For each metal and time point, three Affymetrix chips (Clariom S Rats) were used with 250 ng of total RNA derived from a pooled sample from 2-3 animals.

treatment_protocol: Pellets were surgically implanted into the gastrocnemius muscle, and each animal received 2 pellets per limb for a total of 4 pellets per rat. Prior to use, pellets were cleaned and chemically sterilized as previously described (https://doi.org/10.1177%2F1091581814565038)

tag: gender

value: Male

value: Sprague-Dawley

value: Skeletal Muscle

value: Ni

tag: time


title: Muscle_Ni_01mo_rep2

source_name: gastrocnemius, nickel, 1 month, replicate 2


title: Muscle_Ni_01mo_rep1

source_name: gastrocnemius, nickel, 1 month, replicate 1


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B11_ad002


title: Muscle_Fe_12mo_rep3

source_name: gastrocnemius, iron, 12 months, replicate 3

value: Fe


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B10_ad001


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B1_ad012


title: I034_GBM Intermediate stage

value: Intermediate stage


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B11_ad001


title: Muscle_Ni_03mo_rep3

source_name: gastrocnemius, nickel, 3 months, replicate 3


title: Muscle_Fe_03mo_rep3

source_name: gastrocnemius, iron, 3 months, replicate 3


title: CHD8_ChIP_rep2

first: Christopher

middle: Michael

last: Weber

address: B209 Beckman Center

department: Pathology

data_processing:
Reads were aligned to mm9 genome build using Bowtie 2.1.0
Reads that contained more than a single mismatch and duplicates were discarded, leaving only unique reads.
Comparing to input samples for each cell type, peak calling was performed by MACS 2.1.1
Genome_build: mm9
Supplementary_files_format_and_content: peaks (bed) and bigWig

source_name: ES cells

growth_protocol: Cells were grown on gelatin coated dishes in 2i media.

extract_protocol: tagmentation on beads

tag: antibody

value: Sigma ANTI-FLAG M2 #F1804

value: ES cells


title: Muscle_Fe_12mo_rep2

source_name: gastrocnemius, iron, 12 months, replicate 2


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B10_ad006


title: I056_GBM Early stage

value: brain

value: Early stage


title: Muscle_Fe_06mo_rep2

source_name: gastrocnemius, iron, 6 months, replicate 2


title: Muscle_Fe_03mo_rep2

source_name: gastrocnemius, iron, 3 months, replicate 2


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B1_ad010


title: Muscle_Fe_12mo_rep1

source_name: gastrocnemius, iron, 12 months, replicate 1


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B10_ad004


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B10_ad002


title: Muscle_Fe_01mo_rep3

source_name: gastrocnemius, iron, 1 month, replicate 3


title: Muscle_Fe_01mo_rep2

source_name: gastrocnemius, iron, 1 month, replicate 2


title: I027_GBM Early stage


title: Input_CHD8_rep2

value: none (input)


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B1_ad008


title: Muscle_Fe_06mo_rep1

source_name: gastrocnemius, iron, 6 months, replicate 1


title: Muscle_Fe_06mo_rep3

source_name: gastrocnemius, iron, 6 months, replicate 3


title: I039_GBM Intermediate stage

source_name: brain single cell suspension

value: Irg1/Acod1 +/+


title: Input_CHD8_rep1


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B1_ad007

source_name: C57BL/6J Male P56 Mouse Brain


title: I028_GBM Late stage

value: Late stage


title: CHD8_ChIP_rep1


title: Muscle_Fe_01mo_rep1

source_name: gastrocnemius, iron, 1 month, replicate 1


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B1_ad006


title: HFD.Ang.Rep4

city: Utrecht

first: Cornelis

middle: J.

last: Boogerd

address: Uppsalalaan 8

department: Developmental Biology and Stem Cell Research

country: Netherlands

institute: Hubrecht Institute

data_processing:
aligment - STAR 2.4.2a
readcount analysis - HTSEQ COUNT 0.6.1
Genome_build: mm10
Supplementary_files_format_and_content: AW_readCounts_raw_geo.txt -> Matrix table with raw readcounts per gene for all samples

source_name: left ventricle

extract_protocol:
Standard Trizol totalRNA extraction
TruSeq mRNA stranded (illumina)

treatment_protocol: Aged (18-22 months old) female C57BL/6J mice were fed a standardized chow (CTRL) or high fat diet (HFD) for 12 weeks. After 8 weeks HFD, Angiotensin-II (ANGII), was administered for 4 weeks via osmotic mini-pumps.

value: female

value: left ventricle

tag: diet

value: High fat diet (HFD)

value: ANGII

value: 18-22 months


title: HFD.Ang.Rep2


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B1_ad001

value: DG

value: male


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A9_ad012


title: LFD.Ctrl.Rep4

value: control diet (LFD)

value: Saline


title: Muscle_DU_06mo_rep3

source_name: gastrocnemius, depleted uranium, 6 months, replicate 3

value: Male

value: Sprague-Dawley

value: Skeletal Muscle

value: DU


title: Muscle_Fe_03mo_rep1

source_name: gastrocnemius, iron, 3 months, replicate 1

value: Fe


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A9_ad006


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B1_ad004


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A9_ad004


title: Muscle_DU_12mo_rep3

source_name: gastrocnemius, depleted uranium, 12 months, replicate 3


title: LFD.Ctrl.Rep2


title: LFD.Ctrl.Rep1


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A9_ad001


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A8_ad012


title: HFD.Ang.Rep1


title: Muscle_DU_03mo_rep3

source_name: gastrocnemius, depleted uranium, 3 months, replicate 3


title: CEMBA190625_10F_1_CEMBA190625_10F_2_B1_ad002


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A8_ad010


title: RNA_CHD8_KO_NPC_rep1

description: rRNA depleted total RNA

data_processing:
Genome build: mm9
The first three bases of read 1 were trimmed with cutadapt 1.16 using -u 3 option. Transcripts were quantified using Kallisto against UCSC mm9 reference.
Supplementary_files_format_and_content: Kallisto abundance estimates.

source_name: neural progenitor cells

extract_protocol: Libraries were prepared using the SMARTer kit (Takara Bio # 634874), which produces stranded libraries from rRNA depleted total RNA.

value: ES derived neural progenitor cells


title: Muscle_DU_12mo_rep1

source_name: gastrocnemius, depleted uranium, 12 months, replicate 1


title: Muscle_DU_01mo_rep2

source_name: gastrocnemius, depleted uranium, 1 month, replicate 2


title: Muscle_DU_01mo_rep3

source_name: gastrocnemius, depleted uranium, 1 month, replicate 3


title: Muscle_DU_12mo_rep2

source_name: gastrocnemius, depleted uranium, 12 months, replicate 2


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A8_ad006


title: LFD.Ctrl.Rep3


title: Muscle_DU_06mo_rep1

source_name: gastrocnemius, depleted uranium, 6 months, replicate 1


title: RNA_CHD8_KO_NPC_rep2

description: rRNA depleted total RNA


title: Muscle_DU_06mo_rep2

source_name: gastrocnemius, depleted uranium, 6 months, replicate 2


title: Muscle_DU_01mo_rep1

source_name: gastrocnemius, depleted uranium, 1 month, replicate 1


title: 3rdWTCD4Tcells0h

city: Tampa

first: Sungjune

last: Kim

address: 12902 USF Magnolia Driv

institute: RADIATION ONCOLOGY

data_processing:
Illumina NextSeq 500 pair-end reads from RNA-Seq libraries were first adaptor trimmed
STAR (2.6.0c) was utilized for alignment  to the reference genome.
To analyze gene expression, DESeq was applied for gene normalization
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include log2 transformed gene expression values for each sample

growth_protocol: Spleens were collected from C57BL/6J and Sirt2-/- mice and were processed into single-cell suspensions. CD4+ T cells were negatively enriched using Mouse CD4+ T cell isolation kits™ according to the manufacturer’s instructions. The purity of the isolated cells was confirmed by flow cytometry (>95%, not shown). CD4+ purified T cells were either followed directly by RNA extraction (naïve = 0 hour) or stimulated for 24 hours.  CD4+ purified T cells were cultured in complete RPMI 1640 medium (Thermo Fisher Scientific) supplemented with 10% (vol/vol) fetal bovine serum (FBS, Biowest) and 1% (vol/vol) penicillin/streptomycin (P/S, Thomas Scientific Inc.). WT and Sirt2-/- CD4+ T cells were activated with plate-bound anti-CD3 antibody (5 μg/ml, 145-2C11, BioXCell) for 24 hours.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen; cat. #74106) according to the manufacturer’s instructions
Total RNA-seq libraries were generated from 100 ng of RNA using the NuGen Ovation Mouse RNA-seq System according to the manufacturer's protocol. rRNA transcripts were selectively reduced using the NuGen probe-based AnyDeplete strategy according to the protocol.

treatment_protocol: Non stimulated ( naïve = 0h) or stimulated with anti-CD3 antibody (5 μg/ml, 145-2C11, BioXCell) for 24 hours

tag: strain background

tag: genotype/variation

value: wild type

value: Spleen

value: CD4+ T cells

value: non-stimulated (naïve = 0h)


title: 3rdWTCD4Tcells24h

value: stimulated with anti-CD3 antibody for 24hrs


title: Muscle_DU_03mo_rep1

source_name: gastrocnemius, depleted uranium, 3 months, replicate 1


title: RNA_CHD8_Het_NPC_rep2

description: rRNA depleted total RNA


title: 3rdSIRT2KOCD4Tcells0h


title: RNA_WT_NPC_rep1

description: rRNA depleted total RNA

value: WT


title: 3rdSIRT2KOCD4Tcells24h


title: RNA_CHD8_Het_NPC_rep1

description: rRNA depleted total RNA


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A7_ad012


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A7_ad010


title: RNA_CHD8_KO_ESC_rep1

description: rRNA depleted total RNA

source_name: embryonic stem cells

value: embryonic stem cells


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A8_ad004

source_name: C57BL/6J Male P56 Mouse Brain

value: DG


title: Muscle_DU_03mo_rep2

source_name: gastrocnemius, depleted uranium, 3 months, replicate 2


title: 2ndWTCD4Tcells24h


title: 2ndSIRT2KOCD4Tcells24h


title: RNA_WT_NPC_rep2

description: rRNA depleted total RNA


title: 2ndWTCD4Tcells0h


title: RNA_CHD8_Het_ESC_rep2

description: rRNA depleted total RNA


title: 2ndSIRT2KOCD4Tcells0h


title: Muscle_Cu_12mo_rep3

source_name: gastrocnemius, copper, 12 months, replicate 3

value: Cu


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A7_ad006

value: male


title: RNA_CHD8_KO_ESC_rep2

description: rRNA depleted total RNA


title: 1stWTCD4Tcells24h


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A8_ad001


title: Muscle_Cu_03mo_rep3

source_name: gastrocnemius, copper, 3 months, replicate 3


title: Muscle_Cu_06mo_rep3

source_name: gastrocnemius, copper, 6 months, replicate 3


title: RNA_CHD8_Het_ESC_rep1

description: rRNA depleted total RNA


title: RNA_WT_ESC_rep2

description: rRNA depleted total RNA


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A8_ad002


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A6_ad006


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A7_ad002


title: RNA_WT_ESC_rep1

description: rRNA depleted total RNA


title: ATAC_CHD8_KO_NPC_rep2

data_processing:
Basecalls performed using Illumina CASAVA version 1.8.2
Reads were trimmed to remove adapters, then aligned to the mm9 genome assembly using bowtie version 2.1.0, requiring mapping qualities > 10. Duplicate reads were discarded.
Peaks were called by creating pseudofragments of length 200 bp around each ATAC-seq fragment end, then using MACS 2.1.0 with with default settings.
Peaks with less than 10 reads per million were discarded to ensure high-quality peak calls.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated by creating pseudofragments of length 200 bp centered over all ATAC-seq read fragments, then calculating the basepair coverage for each replicate using Bedtools, normalizing by the total number of reads within called peaks. For samples with multiple replicates, values in the bigWig files represent coverage calculated in this way averaged across both replicates using bwtool.

growth_protocol: ES Cells were grown on gelatin coated dishes in 2i media and differentiated NPCs were grown on laminin-coated plates in N2B27 media supplemented with 5 ng/mL EGF and bFGF

extract_protocol: ATAC-seq was performed as previously described (PMID: 24097267).


title: Muscle_Cu_12mo_rep2

source_name: gastrocnemius, copper, 12 months, replicate 2


title: Muscle_Cu_01mo_rep3

source_name: gastrocnemius, copper, 1 month, replicate 3


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A7_ad004


title: 1stSIRT2KOCD4Tcells0h


title: 1stSIRT2KOCD4Tcells24h


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A6_ad004


title: ATAC_CHD8_KO_NPC_rep1

source_name: neural progenitor cells


title: IDS KO/TfR KI + vehicle, microglia_13

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

description:
DRN-17029
IDS KO/TfR KI + vehicle, microglia
processed data file: dst133_processed_data.xlsx

data_processing:
Sequencing adapters were trimmed from the raw reads with skewer. Reads were aligned to the mouse genome version GRCm38_p6. A STAR index (version 2.7.1a) was built with the –sjdbOverhang=50 argument. Splice junctions from Gencode gene models (release M17) were provided via the –sjdbGTFfile argument. STAR alignments were generated with the following parameters: –outFilterType BySJout, –quantMode TranscriptomeSAM, –outFilterIntronMotifs RemoveNoncanonicalUnannotated, –outSAMstrandField intronMotif, –outSAMattributes NH HI AS nM MD XS and –outSAMunmapped Within. Alignments were obtained with the following parameters: –readFilesCommand zcat –outFilterType BySJout –outFilterMultimapNmax 20 –alignSJoverhangMin 8 –alignSJDBoverhangMin 1 –outFilterMismatchNmax 999 –outFilterMismatchNoverLmax 0.6 –alignIntronMin 20 –alignIntronMax 1000000 –alignMatesGapMax 1000000 –quantMode GeneCounts –outSAMunmapped Within –outSAMattributes NH HI AS nM MD XS –outSAMstrandField intronMotif –outSAMtype BAM SortedByCoordinate –outBAMcompression 6. Gene level counts were obtained using feature Counts from the subread package (version 1.6.2). Gene symbols and biotype information were extracted from the Gencode GTF file.
To calculate normalized counts per million (CPM) TMM normalization was applied across all genes annotated as protein_coding with the edgeR R package.
Genome_build: GRCm38
Supplementary_files_format_and_content: dst133_processed_data.xlsx: Excel (XLSX) file with sample annotations, raw counts and TMM-normalized counts per million (CPM).

source_name: brain

growth_protocol: To prepare a single cell suspension for sorting CNS cells, mice were perfused with PBS, brains dissected and processed into a single cell suspension according to the manufacturers’ protocol using the adult brain dissociation kit (Miltenyi Biotec 130-107-677). Cells were Fc blocked (Biolegend #101320, 1:100) and stained for flow cytometric analysis with Fixable Viability Stain BV510 (BD Biosciences #564406, 1:100) to exclude dead cells, CD11b-BV421 (BD Biosciences 562605, 1:100), CD31-PerCP Cy5.5 (BD Biosciences #562861, 1:100), O1-488 (Thermo/eBio #14-6506-82, 1:37.5), Thy1-PE (R&D #FAB7335P, 1:100), and EAAT2-633 (Alomone #AGC-022-FR, 1:50). Cells were washed with PBS/1% BSA and strained through a 100μm filter before sorting CD11b+ microglia, EAAT2+ astrocytes, and Thy1+ neurons on a FACS Aria III (BD Biosciences) with a 100 μm nozzle. In order to achieve pure populations of astrocytes, microglia, and neurons negative gates were set to remove O1+ and CD31+ cells which are predominantly oligodendrocytes and endothelial cells respectively.

extract_protocol:
Live cells were sorted directly in 350uL RLT-plus buffer (Qiagen, Hilden, Germany) with 1:100 beta-mercaptoethanol. RNA was extracted using the RNeasy Plus Micro Kit (Qiagen, 74034) and resuspended in 14μL nuclease-free water. RNA quantity and quality were assessed with a RNA 6000 Pico chip (Agilent 5067-1513) on a 2100 Bioanalyzer (Agilent).
For Illumina Next Generation Sequencing, samples were processed using the Clontech SMART-Seq® v4 3′ DE (Takara Bio USA, Inc. 635040 ) kit for cDNA synthesis and the Nextera XT DNA Library Prep Kit (Illumina FC-131-1096) for library generation. Up to 1 ng of total RNA per sample was used for reverse transcription followed by 13 cycles of cDNA amplification to produce full length cDNA. After purification, cDNA quantification was performed using Bioanalyzer High Sense DNA chip (Agilent 5067-4626) and normalized to 300 pg of input for library preparation. The tagmentation step simultaneously fragmented and introduced adaptors to the DNA strands, followed by 12 cycles of PCR amplification. Library quantity and quality were assessed with Qubit 1X dsDNA HS Assay Kits (Invitrogen Q33231) and Bioanalyzer High Sense DNA chip. Libraries were pooled in equimolar ratios for sequencing on two Illumina NextSeq flowcells at SeqMatic, 76 bases single end reads.

tag: strain/background

value: IDS KO/TfR KI

value: Microglia

value: 3 months

value: Vehicle

value: 10 mg/kg

value: 4 weeks

tag: group

value: Group 5, mouse 13

tag: batch

value: day 2

value: 202 pg/uL

value: TRUE


title: ATAC_CHD8_HET_NPC_rep2

tag: cell type

value: ES derived neural progenitor cells


title: IDS KO/TfR KI + vehicle, neurons_13

description:
DRN-17025
IDS KO/TfR KI + vehicle, neurons
processed data file: dst133_processed_data.xlsx

value: Neurons

value: Male

value: 64 pg/uL

value: FALSE


title: IDS KO/TfR KI + vehicle, astrocytes_13

description:
DRN-17027
IDS KO/TfR KI + vehicle, astrocytes
processed data file: dst133_processed_data.xlsx

value: Astrocytes

value: 222 pg/uL


title: Muscle_Cu_01mo_rep2

source_name: gastrocnemius, copper, 1 month, replicate 2

value: Sprague-Dawley

tag: tissue

value: Skeletal Muscle

value: Cu


title: 1stWTCD4Tcells0h

value: wild type

value: Spleen

value: CD4+ T cells

value: non-stimulated (naïve = 0h)


title: Muscle_Cu_12mo_rep1

source_name: gastrocnemius, copper, 12 months, replicate 1

tag: strain


title: ATAC_CHD8_HET_NPC_rep1

tag: genotype


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A5_ad012

value: DG

value: male


title: ATAC_WT_NPC_rep2

value: WT


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A5_ad010


title: IDS KO/Tfr KI + ETV:IDS, microglia_16

description:
DRN-17021
IDS KO/Tfr KI + ETV:IDS, microglia
processed data file: dst133_processed_data.xlsx

value: IDS KO/Tfr KI

value: Microglia

value: 3 months

tag: treatment

value: 10 mg/kg

value: 4 weeks

value: Group 6, mouse 16

value: day 2

value: 22 pg/uL

value: TRUE


title: IDS KO/TfR KI + vehicle, input_13

description:
DRN-17023
IDS KO/TfR KI + vehicle, input
processed data file: dst133_processed_data.xlsx

value: IDS KO/TfR KI

value: Input

value: Male

value: Vehicle

value: Group 5, mouse 13

value: 161 pg/uL


title: Muscle_Cu_06mo_rep2

source_name: gastrocnemius, copper, 6 months, replicate 2

value: Sprague-Dawley

value: Skeletal Muscle

value: Cu


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A7_ad001

tag: brain region

value: DG

value: male


title: Muscle_Cu_03mo_rep1

source_name: gastrocnemius, copper, 3 months, replicate 1


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A5_ad008

tag: Sex


title: Muscle_Cu_06mo_rep1

source_name: gastrocnemius, copper, 6 months, replicate 1


title: Muscle_Cu_03mo_rep2

source_name: gastrocnemius, copper, 3 months, replicate 2


title: ATAC_CHD8_KO_ESC_rep2

value: embryonic stem cells


title: Muscle_Cu_01mo_rep1

source_name: gastrocnemius, copper, 1 month, replicate 1


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A6_ad002

tag: age


title: IDS KO/Tfr KI + ETV:IDS, neurons_16

description:
DRN-17017
IDS KO/Tfr KI + ETV:IDS, neurons
processed data file: dst133_processed_data.xlsx

value: IDS KO/Tfr KI

value: Neurons

value: 3 months

value: 10 mg/kg

value: 4 weeks

value: 39 pg/uL

value: FALSE


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A5_ad007


title: Muscle_Co_12mo_rep3

source_name: gastrocnemius, cobalt, 12 months, replicate 3

tag: gender

value: Male

value: Co


title: Muscle_Co_06mo_rep3

source_name: gastrocnemius, cobalt, 6 months, replicate 3

tag: time


title: IDS KO/Tfr KI + ETV:IDS, input_16

description:
DRN-17015
IDS KO/Tfr KI + ETV:IDS, input
processed data file: dst133_processed_data.xlsx

value: Input

value: Group 6, mouse 16

value: day 2

value: 192 pg/uL

value: TRUE


title: ATAC_WT_NPC_rep1

value: ES derived neural progenitor cells

value: WT


title: Muscle_Co_03mo_rep3

source_name: gastrocnemius, cobalt, 3 months, replicate 3

value: Sprague-Dawley

value: Skeletal Muscle


title: ATAC_CHD8_HET_ESC_rep1

source_name: embryonic stem cells

value: embryonic stem cells


title: IDS KO/Tfr KI + ETV:IDS, astrocytes_16

description:
DRN-17019
IDS KO/Tfr KI + ETV:IDS, astrocytes
processed data file: dst133_processed_data.xlsx

value: IDS KO/Tfr KI

value: Astrocytes

value: 3 months

value: 50 pg/uL


title: ATAC_CHD8_HET_ESC_rep2


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A5_ad001

source_name: C57BL/6J Male P56 Mouse Brain

value: DG

value: male


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A4_ad010


title: IDS KO/TfR KI + vehicle, neurons_12

description:
DRN-17009
IDS KO/TfR KI + vehicle, neurons
processed data file: dst133_processed_data.xlsx

value: IDS KO/TfR KI

value: Neurons

value: Male

value: Vehicle

value: 10 mg/kg

value: 4 weeks

value: Group 5, mouse 12

value: 35 pg/uL

value: FALSE


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A4_ad012


title: ATAC_WT_ESC_rep1

value: WT


title: IDS KO/TfR KI + vehicle, microglia_12

description:
DRN-17013
IDS KO/TfR KI + vehicle, microglia
processed data file: dst133_processed_data.xlsx

value: Microglia

value: day 2

value: 329 pg/uL

value: TRUE


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A4_ad008


title: IDS KO/TfR KI + vehicle, astrocytes_12

description:
DRN-17011
IDS KO/TfR KI + vehicle, astrocytes
processed data file: dst133_processed_data.xlsx

value: Astrocytes

value: 3 months

value: 100 pg/uL


title: ATAC_WT_ESC_rep2

value: embryonic stem cells


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A5_ad006

value: DG

value: male


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A4_ad007


title: WT 5

city: London

first: Aida

last: Martinez-Sanchez

address: Du Cane Road

country: United Kingdom

institute: Imperial College London

data_processing:
Paired Reads (_R1, R2) were aligned to the index Mus_musculus.GRCm38.cdna.ncrna.index using Salmon/0.12.0 with parameters salmon quant –p 20 --gcBias ISR  --validateMappings. Salmon outputs are quant.sf.txt files containing TPM (transcript per million)
Genome_build: GRCm38
Supplementary_files_format_and_content: Plain text, tab-delimited file with single header line naming columns. Columns are Name, length, Effective leght, TPM and NumReads

source_name: Pancreatic Islets

extract_protocol:
pancreas was isolated and Pancreatic Islets were purified by centrifugation through a histopaque gradient. RNA extraction was performed using trizol reagent. mRNA enrichment starting from 0.8-1 μg of total RNA was obtained using a NEBNext Poly(A) mRNA Magnetic Isolation Kit (NEB).
RNA libraries were prepared for sequencing using standard Illumina protocols (using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB))

value: pancreatic islets

value: 22 weeks post natal

value: wild type


title: Muscle_Co_01mo_rep3

source_name: gastrocnemius, cobalt, 1 month, replicate 3

value: Male

value: Sprague-Dawley

value: Skeletal Muscle

value: Co


title: IDS KO/TfR KI + vehicle, input_12

description:
DRN-17007
IDS KO/TfR KI + vehicle, input
processed data file: dst133_processed_data.xlsx

value: IDS KO/TfR KI

value: Input

value: Vehicle

value: 10 mg/kg

value: 4 weeks

value: Group 5, mouse 12

value: 183 pg/uL


title: Muscle_Co_03mo_rep2

source_name: gastrocnemius, cobalt, 3 months, replicate 2


title: ATAC_CHD8_KO_ESC_rep1

value: embryonic stem cells


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A4_ad006

value: DG


title: Muscle_Co_12mo_rep2

source_name: gastrocnemius, cobalt, 12 months, replicate 2


title: TfR KI + vehicle, astrocytes_10

description:
DRN-17003
TfR KI + vehicle, astrocytes
processed data file: dst133_processed_data.xlsx

source_name: brain

value: TfR KI

value: Astrocytes

value: 3 months

value: Group 4, mouse 10

value: day 2

value: 147 pg/uL

value: TRUE


title: TfR KI + vehicle, microglia_10

description:
DRN-17005
TfR KI + vehicle, microglia
processed data file: dst133_processed_data.xlsx

value: Microglia

value: Male

value: 77 pg/uL


title: WT 4

value: pancreatic islets

value: 22 weeks post natal

value: wild type


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A4_ad004

value: male


title: WT 2


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A4_ad001


title: C2CD4B KO 4


title: IDS KO/Tfr KI + ETV:IDS, microglia_15

description:
DRN-16997
IDS KO/Tfr KI + ETV:IDS, microglia
processed data file: dst133_processed_data.xlsx

value: IDS KO/Tfr KI

value: 10 mg/kg

value: 4 weeks

value: Group 6, mouse 15

value: 250 pg/uL


title: C2CD4B KO 3


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A3_ad012

value: DG


title: IDS KO/Tfr KI + ETV:IDS, astrocytes_15

description:
DRN-16995
IDS KO/Tfr KI + ETV:IDS, astrocytes
processed data file: dst133_processed_data.xlsx

value: Astrocytes

value: 3 months

value: 171 pg/uL


title: Muscle_Co_01mo_rep2

source_name: gastrocnemius, cobalt, 1 month, replicate 2

value: Sprague-Dawley

value: Skeletal Muscle

value: Co


title: Muscle_Co_03mo_rep1

source_name: gastrocnemius, cobalt, 3 months, replicate 1

value: Male


title: Muscle_Co_01mo_rep1

source_name: gastrocnemius, cobalt, 1 month, replicate 1


title: Muscle_Al_12mo_rep3

source_name: gastrocnemius, aluminum, 12 months, replicate 3

value: Al


title: WT 3

value: pancreatic islets

value: 22 weeks post natal


title: Muscle_Co_06mo_rep1

source_name: gastrocnemius, cobalt, 6 months, replicate 1


title: C2CD4B KO 2


title: IDS KO/Tfr KI + ETV:IDS, neurons_15

description:
DRN-16993
IDS KO/Tfr KI + ETV:IDS, neurons
processed data file: dst133_processed_data.xlsx

value: Neurons

value: day 2

value: 130 pg/uL

value: FALSE


title: WT 1

value: wild type


title: IDS KO/Tfr KI + ETV:IDS, input_15

description:
DRN-16991
IDS KO/Tfr KI + ETV:IDS, input
processed data file: dst133_processed_data.xlsx

value: IDS KO/Tfr KI

value: Input

value: 10 mg/kg

value: 4 weeks

value: Group 6, mouse 15

value: 103 pg/uL

value: TRUE


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A3_ad008

value: DG

value: male


title: Muscle_Al_06mo_rep3

source_name: gastrocnemius, aluminum, 6 months, replicate 3

value: Male

value: Sprague-Dawley

value: Skeletal Muscle

value: Al


title: HFD.Ang.Rep3

source_name: left ventricle

value: female

value: left ventricle

value: High fat diet (HFD)

value: ANGII

value: 18-22 months


title: TfR KI + vehicle, neurons_10

description:
DRN-17001
TfR KI + vehicle, neurons
processed data file: dst133_processed_data.xlsx

value: TfR KI

value: Neurons

value: 3 months

value: Vehicle

value: Group 4, mouse 10

value: day 2

value: 89 pg/uL

value: FALSE


title: C2CD4B KO 1

value: pancreatic islets

value: 22 weeks post natal


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A3_ad007

value: DG

value: male


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A4_ad002


title: TfR KI + vehicle, input_10

description:
DRN-16999
TfR KI + vehicle, input
processed data file: dst133_processed_data.xlsx

value: Input

value: Male

value: 10 mg/kg

value: 4 weeks

value: 175 pg/uL

value: TRUE


title: IDS KO/Tfr KI + ETV:IDS, microglia_14

description:
DRN-16989
IDS KO/Tfr KI + ETV:IDS, microglia
processed data file: dst133_processed_data.xlsx

value: IDS KO/Tfr KI

value: Microglia

value: Group 6, mouse 14

value: 222 pg/uL


title: E11-FL-2L

city: New Haven

first: Mingyu

last: Yang

state: CT

address: 55 Prospect St., Room 103

department: Biomedical Engineering

institute: Yale

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
The processed read was trimmed, mapped against the mouse genome(GRCh38), demultiplexed and annotated(Gencode release M11) using the ST pipeline v1.7.2
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include counts for each pixels for each Sample

source_name: mouse embryo, day 11

extract_protocol:
The freshly dissected embryos were immersed into OCT and snapped frozen with liquid nitrogen. Before sectioning, the frozen tissue block was warmed to the temperature of cryotome cryostat (-20°C). Tissue block was then sectioned into thickness of <7 µm and placed in the center of a poly-L-lysine coated glass slide (CatLog no. 63478-AS, electron microscopy sciences). The slide was kept at -80 °C until use.
The sequencing library was built with a Nextera XT kit (Illumina) and sequenced using a HiSeq 4000 sequencer using a pair-end 100x100 mode.

value: embryo

tag: developmental stage

value: Embryonic Day 11

tag: resolution

value: 10 micron


title: Muscle_Co_06mo_rep2

source_name: gastrocnemius, cobalt, 6 months, replicate 2

value: Sprague-Dawley

value: Skeletal Muscle

value: Co


title: Muscle_Al_03mo_rep3

source_name: gastrocnemius, aluminum, 3 months, replicate 3

value: Al


title: Muscle_Al_01mo_rep3

source_name: gastrocnemius, aluminum, 1 month, replicate 3


title: Muscle_Al_12mo_rep2

source_name: gastrocnemius, aluminum, 12 months, replicate 2


title: E11-FL-1L


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A3_ad010

source_name: C57BL/6J Male P56 Mouse Brain

value: DG

value: male


title: IDS KO/Tfr KI + ETV:IDS, astrocytes_14

description:
DRN-16987
IDS KO/Tfr KI + ETV:IDS, astrocytes
processed data file: dst133_processed_data.xlsx

value: Astrocytes

value: Male

value: 3 months

value: 10 mg/kg

value: day 2

value: 134 pg/uL


title: Muscle_Al_06mo_rep2

source_name: gastrocnemius, aluminum, 6 months, replicate 2


title: Muscle_Co_12mo_rep1

source_name: gastrocnemius, cobalt, 12 months, replicate 1


title: IDS KO/Tfr KI + ETV:IDS, input_14

description:
DRN-16983
IDS KO/Tfr KI + ETV:IDS, input
processed data file: dst133_processed_data.xlsx

value: IDS KO/Tfr KI

value: Input

value: 4 weeks

value: Group 6, mouse 14

value: 431 pg/uL

value: TRUE


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A3_ad006


title: IDS KO/TfR KI + vehicle, astrocytes_11

description:
DRN-16979
IDS KO/TfR KI + vehicle, astrocytes
processed data file: dst133_processed_data.xlsx

value: IDS KO/TfR KI

value: Vehicle

value: Group 5, mouse 11

value: 98 pg/uL


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A3_ad004

value: DG

value: male


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A2_ad008


title: IDS KO/TfR KI + vehicle, neurons_11

description:
DRN-16977
IDS KO/TfR KI + vehicle, neurons
processed data file: dst133_processed_data.xlsx

value: Neurons

value: Male

value: 77 pg/uL

value: FALSE


title: 0725e10aL

data_processing:
Library strategy: CITE-seq
Illumina Casava 1.8.2 software used for basecalling.
The processed read was trimmed, mapped against the mouse genome (GRCh38), demultiplexed and annotated (Gencode release M11) using the ST pipeline v1.7.2.
Genome_build: GRCh38
Supplementary_files_format_and_content: *tsv: Tab-delimited text files include counts for each pixels for each Sample.

source_name: mouse embryo, day 10

value: Embryo

value: Embryonic day 10

value: 50 micron


title: E11-2L

value: embryo

value: Embryonic Day 11

value: 25 micron


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A2_ad006


title: IDS KO/Tfr KI + ETV:IDS, neurons_14

description:
DRN-16985
IDS KO/Tfr KI + ETV:IDS, neurons
processed data file: dst133_processed_data.xlsx

source_name: brain

value: IDS KO/Tfr KI

value: 3 months

value: 10 mg/kg

value: 4 weeks

value: Group 6, mouse 14

value: day 2

value: 64 pg/uL


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A2_ad007

value: DG

value: male


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A2_ad002


title: Muscle_Al_01mo_rep2

source_name: gastrocnemius, aluminum, 1 month, replicate 2

value: Male

value: Sprague-Dawley

value: Skeletal Muscle

value: Al


title: Muscle_Al_03mo_rep2

source_name: gastrocnemius, aluminum, 3 months, replicate 2


title: IDS KO/TfR KI + vehicle, microglia_11

description:
DRN-16981
IDS KO/TfR KI + vehicle, microglia
processed data file: dst133_processed_data.xlsx

value: IDS KO/TfR KI

value: Microglia

value: Vehicle

value: Group 5, mouse 11

value: 292 pg/uL

value: TRUE


title: E11-1L

value: embryo

value: Embryonic Day 11

value: 25 micron


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A2_ad010


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A2_ad012


title: IDS KO/TfR KI + vehicle, input_11

description:
DRN-16975
IDS KO/TfR KI + vehicle, input
processed data file: dst133_processed_data.xlsx

value: Input

value: 3 months

value: 10 mg/kg

value: 4 weeks

value: day 2

value: 239 pg/uL


title: 0719aL

value: Embryo

value: Embryonic day 10

value: 10 micron


title: 0713aL


title: 0702aL

value: 50 micron


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A12_ad004

value: DG

value: male


title: Porphyromonas gingivalis Cas3 KO in human serum KO3

city: Gainesville

first: Jose

last: Solbiati

state: Florida

address: 1395 Center Drive

department: Oral biology

institute: University of Florida

description: Matrix_genes_counts_Pg_planktonic_growth_KO.csv

data_processing:
We used the PATRIC annotation for genome ID 431947.7 of P. gingivalis sequences 33277  for our analysis. Low-quality sequences were removed from the query files using Trimmomatic .
Cleaned files were aligned against the P. gingivalis ATCC 33277 genome database using bowtie2 .
Eukaryotic sequences, human and G. mellonella, were aligned against genome release 33 (GRCh38.p13) in GenCode (https://www.gencodegenes.org/) and RefSeq assembly accession GCF_003640425.2, respectively. Alignment for eukaryotic sequences was performed using STAR . Read counts from the BAM files were obtained using featureCounts.
In the case of THP-1 infection experiments, differential expression analysis was performed using NOISeqBio (102). After exploratory analysis with NOISeqBio, we selected RPKM normalization for THP-1 cells data, tmm normalization with length correction for P. gingivalis intracellular transcriptome, and tmm normalization without length correction for was P. gingivalis planktonic transcriptome. Only with significant differential expression and log changes > 2 were used in posterior analyses.
Genome_build: human:  release 33 (GRCh38.p13), Porphyromonas gingivalis genome ID 431947.7 of P. gingivalis sequences 33277 , galleria mellonella: GCF_003640425.2.
Supplementary_files_format_and_content: tab-delimited text files
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Porphyromonas gingivalis

growth_protocol:
Bacterial growth conditions. Porphyromonas gingivalis ATCC 33277 was cultured anaerobically at 37°C. Cells maintained on BHI-Blood agar plates supplemented with 5 μg/ml hemin, and 1 μg/ml menadione (vitamin K). Two different liquid growth media were used in the experiments. For the construction of the mutant and the infection experiments, we used TSB broth supplemented with 1 mg/ml yeast extract, 5 μg/ml hemin, and 1 μg/ml menadione. For the transcriptome experiments, we grew P. gingivalis in 20% heat-inactivated human serum (Sigma-Aldrich H3667-20ML) supplemented with 5 μg/ml hemin as describe in Grenier et al.
THP-1 cells culture. The human monocyte/macrophage cell line THP-1 (ATCC®, TIB-202) was cultured at 37°C in a 5% CO2 incubator in RPMI-1640 supplemented with 10% heat-inactivated fetal bovine serum, L-glutamine (2 mM), penicillin/streptomycin (100 U/100 µg/ml), HEPES (10 mM), sodium pyruvate (1 mM), glucose (4.5 mg/ml), sodium bicarbonate (1.5 mg/ml) and 2-mercaptoethanol (0.05 mM; Sigma-Aldrich, St. Louis, MO). Cells were adjusted to 5x105 viable cells/ml and, in order to induce differentiation into a macrophage-like state, THP-1 cells were placed into fresh medium containing 100 ng/ml phorbol 12-myristate 13-acetate (PMA; Sigma-Aldrich, St. Louis, MO) and 1 ml of THP-1 cells were added to each well of 24-well cell culture plates. After 48 hrs of incubation, the cell culture medium was replaced by antibiotic-free medium, and cells were used in challenge studies.
Galleria mellonella: G. mellonella larvae were purchased from SWorm Ltd., South Korea, and were used within five days of receipt. For the G. mellonella killing assays, insects in the final instar larval stage were purchased from Vanderhorst, Inc. (St. Marys, OH), stored at 4°C in the dark.

extract_protocol:
RNA Extraction. Total RNA was extracted from those samples using the mirVana RNA Isolation Kit (Life Technologies, Grand Island, NY). Samples were bead-beaten for 1 min at maximum speed with 300 μl of 0.1-mm zirconia-silica beads (BioSpec Products, Bartlesville, Okla.) in the mirVana lysis buffer. Bacterial ribosomal RNA was depleted using Ribo-Zero rRNA Removal Kits (Bacteria) (Epicentre, Madison, WI) following the manufacturer's protocol. For RNA processing for eukaryotic analysis, we used Dynabeads mRNA Purification Kit to isolate eukaryotic mRNA for transcriptome analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols. For RNA sequencing, Illumina adapter-specific primers were used to amplify and selectively enrich for the cDNA generated from enriched mRNA. Quantified libraries were pooled and sequenced using a HiSeq 2500 machine, 2x100 Flow-cell (Illumina). The Nextera XT kit was used to generate libraries from amplified DNA.

treatment_protocol:
Bacterial infection experiments. P. gingivalis wild-type and Δcas3 mutant were harvested from the broth culture by centrifugation, bacteria were washed 3x in RPMI-1640 medium and adjusted to OD660 1.0 (approximately 1x109 CFU/ml) and added to PMA-activated THP-1 cells at a multiplicity of infection of 100, in the antibiotic-free medium, and after 2h of infection, THP-1 cells were washed to remove non-adherent bacteria. After 2hr incubation, THP-1 cells were treated for 1 hr with metronidazole (200 μg/ml)/gentamicin (300 μg/ml) to kill extracellular bacteria (94), were washed to remove antibiotics, then were lysed with sterile water, followed by addition of an equal volume of 2x PBS, and serial 10-fold dilutions of each lysate were plated on blood agar plates. CFU/ml of P. gingivalis was calculated. In separate experiments, THP-1 cells were cultured with P. gingivalis wild-type or the mutant, and both cell culture supernatant fluids, and RNA were harvested for measurement of cytokine expression and dual transcription, respectively.
Galleria mellonella infection model. Seven groups of 15 larvae, ranging from 200 to 300 mg, and with no signs of melanization, were randomly chosen and used for subsequent infection. A 25-μl Hamilton syringe was used to inject 5-μl aliquots of bacterial inoculum into each larva's hemocoel via the last left proleg (96). Two groups received wild-type P.gingivalis (7.7x108, and 7.7x107 CFUs per larvae), two groups received the cas3 mutant (4.3x108 and 4.3x107 CFUs per larvae). Three control groups included THSB medium alone, THSB + P. gingivalis wild-type heat-killed (10 min at 75oC), and THSB + Δcas3 mutant heat-killed (10 min at 75oC). After injection, larvae were incubated at 37°C, and the appearance of melanization and survival were recorded at 0.5, 1, 1.5, 2, 3, 3.75, 4.25, 6.25, 22, 24, 28 and 42 hours. After injection, larvae were incubated at 37°C, and appearance (signs of melanization) and survival were recorded at selected intervals. Larvae were scored as dead when they displayed no movement in response to touch. Kaplan-Meier killing curves were plotted, and estimations of differences in survival were compared using a log-rank test. A P value of ≤0.05 was considered significant. All data were analyzed with GraphPad Prism,

value: Cas3 KO


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A12_ad006


title: TfR KI + vehicle, astrocytes_9

description:
DRN-16971
TfR KI + vehicle, astrocytes
processed data file: dst133_processed_data.xlsx

value: TfR KI

value: Astrocytes

value: Male

value: Vehicle

value: Group 4, mouse 9

value: 88 pg/uL

value: TRUE


title: Porphyromonas gingivalis Cas3 KO in human serum KO2


title: Porphyromonas gingivalis Cas3 KO in human serum KO1


title: caMNK D4m.3a rep2

city: Montreal

first: Sonia

middle: V

last: del Rincon

state: Quebec

address: 3755 cote Sainte Catherine Road

country: Canada

institute: Lady Davis Institute

data_processing:
FastQ sequences were trimmed and filtered with Trimmomatic v0.32, removing adapters and other Illumina-specific sequences, trimming bases with Phred Quality lower than 30 and discarding short reads (less than 30 nucleotides) after trimming. In addition, the first 3 bases of each read were clipped and trimming by sliding window was applied, removing reads where the average quality of a 4nt window fell below 30.
Quality control of raw and processed reads was performed with FASTQC v0.11.2. The resulting high quality reads were aligned to the reference mouse genome (mm10) using STAR v2.5.3. Samtools v0.1.19, using mpileup, bcftools and varFilter commands were used to call variants.
Aligned reads were summarized through featureCounts v1.5.3
DESeq2 was used for normalization and gene expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files raw counts of aligned reads

source_name: Dartmouth murine mutant malignant melanoma-3A

extract_protocol:
Total RNA from D4M.3A pBABE and caMNK1 was prepared using RNeasy Plus Mini Kit (Qiagen, Hilden, Germany).
RNA-seq libraries were prepared using Illumina's TruSeq Stranded Total RNA LT kit following the manufacturer's protocol.

tag: cell line

value: Murine melanoma cell line

tag: passages

tag: mouse strain

value: constitutive activation of MNK


title: TfR KI + vehicle, neurons_9

description:
DRN-16969
TfR KI + vehicle, neurons
processed data file: dst133_processed_data.xlsx

tag: strain/background

tag: genotype/variation

value: Neurons

value: 3 months

value: 10 mg/kg

value: 4 weeks

tag: group

value: day 2

value: 48 pg/uL

value: FALSE


title: Porphyromonas gingivalis WT in Human serum WT3

description: Matrix_genes_counts_Pg_planktonic_growth_WT.csv

value: WT


title: Porphyromonas gingivalis WT in Human serum WT2


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A12_ad002

value: DG

value: male


title: Muscle_Al_06mo_rep1

source_name: gastrocnemius, aluminum, 6 months, replicate 1

value: Male

value: Sprague-Dawley

tag: tissue

value: Skeletal Muscle

value: Al


title: caMNK D4m.3a rep1

tag: cell type


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A11_ad006

tag: strain


title: Muscle_Al_03mo_rep1

source_name: gastrocnemius, aluminum, 3 months, replicate 1

tag: treatment


title: TfR KI + vehicle, microglia_9

description:
DRN-16973
TfR KI + vehicle, microglia
processed data file: dst133_processed_data.xlsx

value: TfR KI

value: Microglia

value: Vehicle

value: Group 4, mouse 9

tag: batch

value: 340 pg/uL

value: TRUE


title: Muscle_Al_01mo_rep1

source_name: gastrocnemius, aluminum, 1 month, replicate 1


title: TfR KI + vehicle, input_9

description:
DRN-16967
TfR KI + vehicle, input
processed data file: dst133_processed_data.xlsx

value: Input

tag: Sex

value: 3 months

value: 10 mg/kg

value: 4 weeks

value: 144 pg/uL


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A12_ad001

tag: brain region

value: DG

tag: age


title: pBABE D4m.3a rep2

value: Murine melanoma cell line

tag: genotype

value: control


title: caMNK D4m.3a rep3

value: constitutive activation of MNK


title: Porphyromonas gingivalis Cas3 KO inside THP-1 cells KO7

description: Matrix_genes_counts_Pg_intracellular_in_THP-1_cells_KO.csv

value: Cas3 KO


title: pBABE D4m.3a rep1


title: Porphyromonas gingivalis Cas3 KO inside THP-1 cells KO8


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A11_ad002

value: male


title: IDS KO/Tfr KI + ETV:IDS, astrocytes_8

description:
DRN-16963
IDS KO/Tfr KI + ETV:IDS, astrocytes
processed data file: dst133_processed_data.xlsx

value: IDS KO/Tfr KI

value: Astrocytes

value: Male

value: Group 3, mouse 8

value: day 1

value: 94 pg/uL


title: IDS KO/Tfr KI + ETV:IDS, microglia_8

description:
DRN-16965
IDS KO/Tfr KI + ETV:IDS, microglia
processed data file: dst133_processed_data.xlsx

value: Microglia

value: 216 pg/uL

value: TRUE


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A11_ad004


title: Porphyromonas gingivalis WT in Human serum WT1

value: WT


title: IDS KO/Tfr KI + ETV:IDS, neurons_8

description:
DRN-16961
IDS KO/Tfr KI + ETV:IDS, neurons
processed data file: dst133_processed_data.xlsx

value: Neurons

value: 3 months

value: 10 mg/kg

value: 4 weeks

value: 39 pg/uL

value: FALSE


title: IDS KO/Tfr KI + ETV:IDS, input_8

description:
DRN-16959
IDS KO/Tfr KI + ETV:IDS, input
processed data file: dst133_processed_data.xlsx

value: Input

value: 83 pg/uL


title: 0713cL

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
The submitted raw data have been transformed from the original read data. Read 1 contains the barcode and UMI. Read 2 is the biological read. The submitted format is compatible with the software st-pipeline: https://github.com/SpatialTranscriptomicsResearch/st_pipeline
The image reformed.png illustrates the raw data transformation.
The processed read was trimmed, mapped against the mouse genome (GRCh38), demultiplexed and annotated (Gencode release M11) using the ST pipeline v1.7.2.
The file barcodes.merge.sort.txt includes the barcode for each position. Column 1 = barcode, Column 2 = X coordinate, Column 3 = Y coordinate.
Genome_build: GRCh38
Supplementary_files_format_and_content: *tsv: Tab-delimited text files include counts for each pixels for each Sample.

value: Embryo

tag: developmental stage

value: Embryonic day 10

value: 25 micron


title: 0719cL

tag: resolution

value: 10 micron


title: IDS KO/TfR KI + vehicle, microglia_5

description:
DRN-16957
IDS KO/TfR KI + vehicle, microglia
processed data file: dst133_processed_data.xlsx

value: IDS KO/TfR KI

value: Male

value: Vehicle

value: Group 2, mouse 5

value: day 1

value: 281 pg/uL


title: Porphyromonas gingivalis Cas3 KO inside THP-1 cells KO4

value: Cas3 KO


title: 0702cL

value: 50 micron


title: 0628cL

source_name: mouse embryo, day 12

value: Embryonic day 12


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A11_ad001

value: DG

value: male


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A10_ad006


title: Porphyromonas gingivalis Cas3 KO inside THP-1 cells KO3


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A10_ad002


title: 50t


title: IDS KO/TfR KI + vehicle, astrocytes_5

description:
DRN-16955
IDS KO/TfR KI + vehicle, astrocytes
processed data file: dst133_processed_data.xlsx

value: Astrocytes

value: 3 months

value: 10 mg/kg

value: 4 weeks

value: 25 pg/uL

value: FALSE


title: Porphyromonas gingivalis WT inside THP-1 cells WT6

description: Matrix_genes_counts_Pg_intracellular_in_THP-1_cells_WT.csv

value: WT


title: IDS KO/TfR KI + vehicle, neurons_5

description:
DRN-16953
IDS KO/TfR KI + vehicle, neurons
processed data file: dst133_processed_data.xlsx

value: IDS KO/TfR KI

value: Neurons

value: Male

value: 19 pg/uL


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A1_ad012


title: Porphyromonas gingivalis WT inside THP-1 cells WT2


title: neurons_5

description:
DRN-9851
neurons, animal 5
processed data file: dst69_processed_data.xlsx

data_processing:
UMIs were extracted from raw sequencing reads using umi2index (Lexogen) and sequencing adapters were trimmed with skewer. Reads were aligned to the mouse genome version GRCm38_p6. A STAR index (version 2.5.3a) was built with the –sjdbOverhang=50 argument. Splice junctions from Gencode gene models (release M17) were provided via the –sjdbGTFfile argument. STAR alignments were generated with the following parameters: –outFilterType BySJout, –quantMode TranscriptomeSAM, –outFilterIntronMotifs RemoveNoncanonicalUnannotated, –outSAMstrandField intronMotif, –outSAMattributes NH HI AS nM MD XS and –outSAMunmapped Within. Alignments were obtained with the following parameters: –readFilesCommand zcat –outFilterType BySJout –outFilterMultimapNmax 20 –alignSJoverhangMin 8 –alignSJDBoverhangMin 1 –outFilterMismatchNmax 999 –outFilterMismatchNoverLmax 0.6 –alignIntronMin 20 –alignIntronMax 1000000 –alignMatesGapMax 1000000 –quantMode GeneCounts –outSAMunmapped Within –outSAMattributes NH HI AS nM MD XS –outSAMstrandField intronMotif –outSAMtype BAM SortedByCoordinate –outBAMcompression 6. Alignments mapped to the same genomic location that shared the same UMI were collapsed using the collapse_UMI_bam tool (Lexogen). Gene level counts were obtained using feature Counts from the subread package (version 1.6.2). Gene symbols and biotype information were extracted from the Gencode GTF file.
To calculate normalized counts per million (CPM) TMM normalization was applied across all genes annotated as protein_coding with the edgeR R package.
Genome_build: GRCm38
Supplementary_files_format_and_content: dst69_processed_data.xlsx: Excel (XLSX) file with sample annotations, raw counts and TMM-normalized counts per million (CPM).

source_name: whole brain

extract_protocol:
Live cells were sorted directly in 350uL RLT-plus buffer (Qiagen, Hilden, Germany) with 1:100 beta-mercaptoethanol. RNA was extracted using the RNeasy Plus Micro Kit (Qiagen, 74034) and resuspended in 14μL nuclease-free water. RNA quantity and quality were assessed with a RNA 6000 Pico chip (Agilent 5067-1513) on a 2100 Bioanalyzer (Agilent).
For QuantSeq library prep, RNA was processed using the QuantSeq 3' mRNAseq Library Prep Kit FWD for Illumina (Lexogen) with the UMI second strand synthesis module in order to identify and remove PCR duplicates, following the ‘low-input’ protocol defined by the manufacturer. Barcoded samples were quantified using the NEBNext Library Quant Kit for Illumina (NEB, E7630S). All samples were pooled in equimolar ratios into one sequencing library, which was quantified on a Bioanalyzer with a High Sensitivity DNA chip (Agilent, 5067-4626). 65 bp single end reads were generated on an Illumina HiSeq 4000 lane at the UCSF Center for Advanced Technology.

value: Wildtype

value: TRUE


title: IDS KO/TfR KI + vehicle, input_5

description:
DRN-16951
IDS KO/TfR KI + vehicle, input
processed data file: dst133_processed_data.xlsx

value: Input

value: Vehicle

value: Group 2, mouse 5

value: day 1

value: 217 pg/uL


title: neurons_4

description:
DRN-9850
neurons, animal 4
processed data file: dst69_processed_data.xlsx


title: IDS KO/Tfr KI + ETV:IDS, microglia_7

description:
DRN-16949
IDS KO/Tfr KI + ETV:IDS, microglia
processed data file: dst133_processed_data.xlsx

value: IDS KO/Tfr KI

value: Microglia

value: 3 months

value: Group 3, mouse 7

value: 459 pg/uL


title: neurons_3

description:
DRN-9849
neurons, animal 3
processed data file: dst69_processed_data.xlsx


title: Porphyromonas gingivalis Cas3 KO from injected G.mellonela Wax32

description: Matrix_genes_counts_Pg_in_G.mellonella_KO.csv

value: Cas3 KO


title: Porphyromonas gingivalis WT inside THP-1 cells WT1

value: WT


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A1_ad010

value: DG

value: male


title: neurons_2

description:
DRN-9848
neurons, animal 2
processed data file: dst69_processed_data.xlsx

value: Neurons

value: Male


title: IDS KO/Tfr KI + ETV:IDS, astrocytes_7

description:
DRN-16947
IDS KO/Tfr KI + ETV:IDS, astrocytes
processed data file: dst133_processed_data.xlsx

value: Astrocytes

value: 10 mg/kg

value: 4 weeks

value: 161 pg/uL

value: TRUE


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A1_ad007


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A1_ad008


title: IDS KO/Tfr KI + ETV:IDS, neurons_7

description:
DRN-16945
IDS KO/Tfr KI + ETV:IDS, neurons
processed data file: dst133_processed_data.xlsx

value: day 1

value: 34 pg/uL

value: FALSE


title: Porphyromonas gingivalis Cas3 KO from injected G.mellonela Wax31


title: Porphyromonas gingivalis WT inside THP-1 cells WT5


title: pooled_5

description:
DRN-9846
pooled, animal 5
processed data file: dst69_processed_data.xlsx

value: Wildtype

value: Input


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A1_ad006


title: pooled_4

description:
DRN-9845
pooled, animal 4
processed data file: dst69_processed_data.xlsx


title: Porphyromonas gingivalis Cas3 KO from injected G.mellonela Wax30


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A1_ad004


title: IDS KO/Tfr KI + ETV:IDS, input_7

description:
DRN-16943
IDS KO/Tfr KI + ETV:IDS, input
processed data file: dst133_processed_data.xlsx

value: IDS KO/Tfr KI

value: 3 months

value: Group 3, mouse 7

value: 283 pg/uL


title: IDS KO/TfR KI + vehicle, microglia_4

description:
DRN-16941
IDS KO/TfR KI + vehicle, microglia
processed data file: dst133_processed_data.xlsx

value: IDS KO/TfR KI

value: Microglia

value: Vehicle

value: Group 2, mouse 4

value: 182 pg/uL


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A1_ad002

value: DG

value: male


title: IDS KO/TfR KI + vehicle, astrocytes_4

description:
DRN-16939
IDS KO/TfR KI + vehicle, astrocytes
processed data file: dst133_processed_data.xlsx

value: Astrocytes

value: Male

value: 10 mg/kg

value: 4 weeks

value: 111 pg/uL

value: TRUE


title: pooled_3

description:
DRN-9844
pooled, animal 3
processed data file: dst69_processed_data.xlsx

value: Wildtype

value: Input


title: Porphyromonas gingivalis Cas3 KO from injected G.mellonela Wax28

value: Cas3 KO


title: Porphyromonas gingivalis Cas3 KO from injected G.mellonela Wax29


title: IDS KO/TfR KI + vehicle, input_4

description:
DRN-16935
IDS KO/TfR KI + vehicle, input
processed data file: dst133_processed_data.xlsx

value: 3 months

value: day 1

value: 376 pg/uL


title: astrocytes_5

description:
DRN-9841
astrocytes, animal 5
processed data file: dst69_processed_data.xlsx


title: CEMBA190625_10F_1_CEMBA190625_10F_2_A1_ad001


title: Porphyromonas gingivalis WT from injected G.mellonela Wax24

description: Matrix_genes_counts_Pg_in_G.mellonella_WT.csv

value: WT


title: TfR KI + vehicle, astrocytes_2

description:
DRN-16931
TfR KI + vehicle, astrocytes
processed data file: dst133_processed_data.xlsx

value: TfR KI

value: Vehicle

value: Group 1, mouse 2

value: 156 pg/uL


title: IDS KO/TfR KI + vehicle, neurons_4

description:
DRN-16937
IDS KO/TfR KI + vehicle, neurons
processed data file: dst133_processed_data.xlsx

value: IDS KO/TfR KI

value: Neurons

value: Group 2, mouse 4

value: 43 pg/uL

value: FALSE


title: Porphyromonas gingivalis Cas3 KO from injected G.mellonela Wax27


title: NASH liver-tomato positive

city: Minato ku

first: Satotaka

last: Omori

state: tokyo

address: shirokanedai, 4-6-1

country: Japan

institute: the university of Tokyo

description:
scRNA-derived cDNA library
Sacrificed two weeks after daily i.p. injection with TAM for 5 days
NASH 7m liver.h5ad
Merge for Kup and LSEC.h5ad

data_processing:
CellRanger v3.0.2 software used for base-calling, UMI recognization, and sequence alignment to mm10 reference.
Low quality single cell transcriptomes were filtered out with low gene content (genes<200), low UMI counts (UMI<800), doublet (genes>7000), and high mitochondial gene content (<10% for liver, <40% for kidney) through scanpy 1.4.5.post1
The UMI counts were normalized and log transformed by scanpy
After UMAP visualization and leiden clustering (n_neighbors=10), the cluster-dependent ranking genes were calculated by log-regression method, which were used in the marker gene defined cell type identification.
Genome_build: mm10
Supplementary_files_format_and_content: h5ad file for anndata structure

source_name: Hepatic non-parenchymal cells

extract_protocol:
The sorted cells were suspended in PBS, and then the single cell cDNA libraries were generated through following the protocol of Chromium Single Cell 3’GEM, Library & Gel Bead Kit v3.
scRNA libraries were prepared for sequencing using standard 10X Genomic protocols

treatment_protocol: All the mice were sacrificed two weeks after the daily i.p. injection with 80 mg/kgBW tamoxifen for 5 days at designated age. For NASH induction, the mice were maintained on rodent diet with 45% kcal% fat without added choline (CDHFD) for 6 months.

value: Hepatic non-parenchymal cells

value: C57BL/6 p16-CREERT2  ROS26-CMV-lsl-tdTomato

value: Fed with CDHFD for 6 months, 7m mouse

tag: disease state

value: NASH


title: TfR KI + vehicle, neurons_2

description:
DRN-16929
TfR KI + vehicle, neurons
processed data file: dst133_processed_data.xlsx

value: Male

value: 3 months

value: 10 mg/kg

value: 4 weeks

value: 44 pg/uL


title: astrocytes_3

description:
DRN-9839
astrocytes, animal 3
processed data file: dst69_processed_data.xlsx

value: Wildtype

value: Astrocytes

value: TRUE


title: Porphyromonas gingivalis WT from injected G.mellonela Wax23

value: WT


title: microglia_5

description:
DRN-9836
microglia, animal 5
processed data file: dst69_processed_data.xlsx

value: Microglia


title: Normal kidney-whole

description:
scRNA-derived cDNA library
Sacrificed two weeks after daily i.p. injection with TAM for 5 days
Normal 5m kidney.h5ad

source_name: Renal cells

value: Renal cells

value: Untreated, 5m mouse

value: normal


title: IDS KO/Tfr KI + ETV:IDS, microglia_6

description:
DRN-16925
IDS KO/Tfr KI + ETV:IDS, microglia
processed data file: dst133_processed_data.xlsx

value: IDS KO/Tfr KI

value: Group 3, mouse 6

value: day 1

value: 310 pg/uL


title: Normal liver-whole

description:
scRNA-derived cDNA library
Sacrificed two weeks after daily i.p. injection with TAM for 5 days
Normal 7m liver.h5ad
Merge for Kup and LSEC.h5ad

value: Hepatic non-parenchymal cells

value: C57BL/6 p16-CREERT2  ROS26-CMV-lsl-tdTomato

value: Untreated, 7m mouse


title: Porphyromonas gingivalis WT from injected G.mellonela Wax21


title: TfR KI + vehicle, microglia_2

description:
DRN-16933
TfR KI + vehicle, microglia
processed data file: dst133_processed_data.xlsx

value: TfR KI

value: Male

value: 3 months

value: Vehicle

value: 10 mg/kg

value: 4 weeks

value: Group 1, mouse 2

value: 301 pg/uL


title: Porphyromonas gingivalis Cas3 KO from injected G.mellonela Wax26

description: Matrix_genes_counts_Pg_in_G.mellonella_KO.csv

value: Cas3 KO


title: astrocytes_4

description:
DRN-9840
astrocytes, animal 4
processed data file: dst69_processed_data.xlsx

value: Wildtype

value: Astrocytes

value: TRUE


title: Porphyromonas gingivalis Cas3 KO from injected G.mellonela Wax25


title: NASH liver-whole

value: Fed with CDHFD for 6 months, 7m mouse

value: NASH


title: microglia_4

description:
DRN-9835
microglia, animal 4
processed data file: dst69_processed_data.xlsx

value: Microglia


title: astrocytes_2

description:
DRN-9838
astrocytes, animal 2
processed data file: dst69_processed_data.xlsx


title: IDS KO/Tfr KI + ETV:IDS, astrocytes_6

description:
DRN-16923
IDS KO/Tfr KI + ETV:IDS, astrocytes
processed data file: dst133_processed_data.xlsx

value: IDS KO/Tfr KI

value: Group 3, mouse 6

value: day 1

value: 166 pg/uL


title: Normal liver-tomato positive

value: Hepatic non-parenchymal cells

value: C57BL/6 p16-CREERT2  ROS26-CMV-lsl-tdTomato

value: Untreated, 7m mouse

value: normal


title: TfR KI + vehicle, input_2

description:
DRN-16927
TfR KI + vehicle, input
processed data file: dst133_processed_data.xlsx

value: TfR KI

value: Input

value: Male

value: 3 months

value: Vehicle

value: 10 mg/kg

value: 4 weeks

value: Group 1, mouse 2

value: 528 pg/uL


title: pooled_2

description:
DRN-9843
pooled, animal 2
processed data file: dst69_processed_data.xlsx

value: Wildtype

value: TRUE


title: IDS KO/Tfr KI + ETV:IDS, input_6

description:
DRN-16919
IDS KO/Tfr KI + ETV:IDS, input
processed data file: dst133_processed_data.xlsx

value: IDS KO/Tfr KI

value: Group 3, mouse 6

value: day 1

value: 308 pg/uL


title: Porphyromonas gingivalis WT from injected G.mellonela Wax22

description: Matrix_genes_counts_Pg_in_G.mellonella_WT.csv

value: WT


title: Normal kidney-tomato positive

value: Renal cells

value: C57BL/6 p16-CREERT2  ROS26-CMV-lsl-tdTomato

value: Untreated, 5m mouse

value: normal


title: 10t

value: Embryo

value: Embryonic day 10

value: 10 micron


title: IDS KO/Tfr KI + ETV:IDS, neurons_6

description:
DRN-16921
IDS KO/Tfr KI + ETV:IDS, neurons
processed data file: dst133_processed_data.xlsx

value: Neurons

value: Male

value: 3 months

value: 10 mg/kg

value: 4 weeks

value: 50 pg/uL

value: FALSE


title: Porphyromonas gingivalis WT from injected G.mellonela Wax20


title: Porphyromonas gingivalis WT from injected G.mellonela Wax19


title: ML005_clean_raw_counts_matrix_lateral_lobe

city: New York

first: Luis

last: Aparicio

state: NY

address: 390 Fort Washington Avenue  9E

institute: Columbia University

description: Mouse Prostate Sample 6 (Lateral lobe)

data_processing:
Reads were aligned either to the mouse GRCm38/mm10 reference genome or to the human GRCh38 reference genome, and quantified with the Cell Ranger Single-Cell Software Suite (v.2.1.1, 10x Genomics).
Genome_build: Mouse: GRCm38/mm10; Human: GRCh38
Supplementary_files_format_and_content: counts_matrix.txt

source_name: Prostate (Lateral Lobe)

extract_protocol:
Prostate tissue was minced with scissors, and incubated in Papain (20 units/ml) /DNaseI (200 units/ml) solution (Worthington, LK003150) at 37°C with gentle agitation. After 45 minutes, tissue fragments were gently triturated by manual pipetting, and incubated for further 45 minutes. Upon addition of an equal volume Ovomucoid (1 mg/ml)/Bovine Serum Albumin (1 mg/ml) solution (Worthington, LK003150) to inactivate papain, samples were passed through a 70 mm cell strainer (PluriSelect, 43-10070-70), followed by centrifugation at 150g for 5 minutes. Afterwards, samples were incubated in TrypLE Express (Gibco 12605-010)/DNaseI (200 units/ml) solution for 4 minutes at 37°C with gentle agitation. Upon addition of Fetal Bovine Serum (final conc. 10% v/v) to inactivate TrypLE, samples were gently resuspended by manual pipetting, passed through a 40 mm cell strainer (PluriSelect, 43-10040-70), washed in PBS/EDTA (1mM) solution, and spun down. Samples were resuspended in PBS/Bovine Serum Albumin (BSA, 0.04% w/v), passed through a 20 mm cell strainer (PluriSelect, 43-10020-70), automatically counted and spun down. At this point, samples were resuspended at 1 x 10E6 cells per ml, approximately, in PBS/BSA and were ready for single-cell RNAseq library preparation.
Before preparing single-cell RNA-seq libraries, samples were assessed for viability using the Countess™ II FL Automated Cell Counter (Thermo Fisher). Only samples with >85% single, live cells were used. We targeted 5000 cells for single-cell sequencing using a Chromium Controller (10x Genomics). Single-cell RNA-Seq libraries were generated using the Chromium Single Cell 3’ Reagent Kits v2 (10x Genomics) according to manufacturer’s instructions. We used 12 cycles for cDNA amplification and 12 cycles for library construction. Sequencing was performed on a NovaSeq 6000 (r1 = 26, i1 = 8, r2 = 91).
Single-cell RNA-seq (10x Genomics)

value: 8-10 weeks

value: Prostate (Lateral Lobe)

tag: pathology

value: Benign


title: microglia_3

description:
DRN-9834
microglia, animal 3
processed data file: dst69_processed_data.xlsx

value: Wildtype

value: Microglia

value: TRUE


title: IDS KO/TfR KI + vehicle, microglia_3

description:
DRN-16917
IDS KO/TfR KI + vehicle, microglia
processed data file: dst133_processed_data.xlsx

value: IDS KO/TfR KI

value: Vehicle

value: Group 2, mouse 3

value: day 1

value: 333 pg/uL


title: ML002_clean_raw_counts_matrix_anterior_lobe

description: Mouse Prostate Sample 3 (Anterior lobe)

source_name: Prostate (Anterior Lobe)

value: Prostate (Anterior Lobe)


title: Porphyromonas gingivalis WT from injected G.mellonela Wax17

value: WT


title: microglia_2

description:
DRN-9833
microglia, animal 2
processed data file: dst69_processed_data.xlsx

value: Male


title: IDS KO/TfR KI + vehicle, astrocytes_3

description:
DRN-16915
IDS KO/TfR KI + vehicle, astrocytes
processed data file: dst133_processed_data.xlsx

value: Astrocytes

value: 3 months

value: 10 mg/kg

value: 4 weeks

value: 184 pg/uL


title: IDS KO/TfR KI + vehicle, neurons_3

description:
DRN-16913
IDS KO/TfR KI + vehicle, neurons
processed data file: dst133_processed_data.xlsx

value: Neurons

value: 51 pg/uL

value: FALSE


title: MM013_clean_raw_counts_matrix_whole_prostate

description: Mouse Prostate Sample 2 (all lobes)

source_name: Prostate (All lobes)

value: 8-10 weeks

value: Prostate (All lobes)

value: Benign


title: ML001_clean_raw_counts_matrix_whole_prostate

description: Mouse  Prostate Sample 1 (all lobes)


title: SK-N-BE(2)-C_ctrl

city: Heidelberg

first: Carl

last: Herrmann

address: INF 267

department: Medical Faculty

country: Germany

institute: University Heidelberg

data_processing:
Pseudoalignment and generation of the transcript count matrix was performed using kallisto and bustools (kb-python) using pre-built transcriptome index for humans.
Low quality cells were removed through standard knee plot visualization, followed by keeping only those with (1) genes detected per cell > 1000, (2) total RNA count per cell > 3000 and (3) percentage of mitochondrial expressed genes < 20% were kept.
Doublets were removed using scDblFinder
Supplementary_files_format_and_content: Monocle3 cell_data_set object as a RDS R file

source_name: Neuroblastoma cell lines

growth_protocol: Cells were cultured in DMEM high glucose supplemented with 10% FCS, Glutamin and 1% non-essential amino acids at 37°C and 5% CO2 and subcultured every 3-4 days.

extract_protocol:
Cells were harvested using versene.
Libraries were prepared according to the 10x Genomics Chromium Single Cell 3' v3.1 protocol.
single-cell RNA-seq

treatment_protocol: Cells were treated with 100 ng/ml doxycycline or left untreated for 13 days.

tag: type

value: cell line

tag: cell line


title: IDS KO/TfR KI + vehicle, input_3

description:
DRN-16911
IDS KO/TfR KI + vehicle, input
processed data file: dst133_processed_data.xlsx

tag: strain/background

tag: genotype/variation

value: IDS KO/TfR KI

value: Input

value: Vehicle

value: Group 2, mouse 3

value: day 1

value: 354 pg/uL

value: TRUE


title: MM030_clean_raw_counts_matrix_ventral_lobe

description: Mouse Prostate Sample 5 (Ventral lobe)

source_name: Prostate (Ventral Lobe)

tag: tissue

value: Prostate (Ventral Lobe)

value: Beniign


title: MM037_clean_raw_counts_matrix

description: Human Prostate Sample 3

source_name: Prostate

value: Prostate


title: SK-N-BE(2)-C_HRAS

description: 10x Genomics Chromium Single Cell 3' v3.1

value: 100 ng/ml doxycycline


title: ML004_clean_raw_counts_matrix_dorsal_lobe

description: Mouse Prostate Sample 4 (Dorsal lobe)

source_name: Prostate (Dorsal Lobe)

value: Prostate (Dorsal Lobe)


title: 0725e10cL

source_name: mouse embryo, day 10

value: Embryo

value: Embryonic day 10

value: 50 micron


title: Porphyromonas gingivalis WT from injected G.mellonela Wax18

value: WT


title: MM033_human_clean_raw_counts_matrix

description: Human Prostate Sample 2

value: Benign


title: TfR KI + vehicle, microglia_1

description:
DRN-16909
TfR KI + vehicle, microglia
processed data file: dst133_processed_data.xlsx

source_name: brain

value: TfR KI

value: Microglia

value: Male

value: 3 months

value: 10 mg/kg

value: 4 weeks

tag: group

value: Group 1, mouse 1

value: 462 pg/uL


title: MF002_human_cleanraw_counts_matrix

description: Human Prostate Sample 1


title: TfR KI + vehicle, astrocytes_1

description:
DRN-16907
TfR KI + vehicle, astrocytes
processed data file: dst133_processed_data.xlsx

value: Astrocytes

value: Vehicle

value: day 1

value: 74 pg/uL

value: TRUE


title: TfR KI + vehicle, neurons_1

description:
DRN-16905
TfR KI + vehicle, neurons
processed data file: dst133_processed_data.xlsx

value: Neurons

value: 68 pg/uL

value: FALSE


title: EXOMEseq.GPX4KO.mouse2.786O.right_FR2dR

city: Hangzhou

first: Yilong

last: Zou

state: Zhejiang

address: Shilongshan Road #18, Cloud Town, Xihu District

department: School of Life Sciences

country: China

institute: Westlake University

data_processing:
library strategy: Exome-Seq
For RNA-seq data analysis, raw paired-end 150 bp/150 bp sequencing reads were mapped to human genome build hg38 (Dec 2013) using Bowtie2 (v2.3.1) with standard settings. On average 67% of read pairs were uniquely mapped to the hg38 genome. Mapped reads were counted to gene features by the htseq-count function from HTSeq (version 0.9.1) with standard settings, normalized to library size and analyzed for differentially expressed genes with DESeq2 (Bioconductor).
For Exome-seq data analysis, raw paired-end sequencing reads were mapped to human genome build hg38 (Dec 2013) using Bowtie2 (v2.3.1) with standard settings. The SAM files containing mapped reads were sorted and indexed into BAM files using Samtools (v1.10). Sorted BAM files were processed using the PICARD (2.22.2-0) tools and GATK (4.1.6.0) Exome-seq variant calling best practices pipeline. The following commands were sequentially used to pre-process the sample datasets, all with standard settings: MarkDuplicates, Samtools (sort+index), AddOrReplaceReadGroups, BaseRecalibrator, Apply Recalibration. GATK Mutect2 tool was used for variant calling, using GPX4 wildtype samples as normal control, while GPX4 KO ferroptosis resistant cells were treated as "tumor" samples. For variant filtering, the following GATK commands were used sequencially: GetPileupSummaries, CalculateContamination, FilterMutectCalls. Final variants that passed all thresholds in all ferroptosis-resistant samples were exported as "common variants" and in the "ExomeSeq.786O.FR2.common.variants.xlsx" file.
Genome_build: hg38
Supplementary_files_format_and_content: For RNA-seq, the normalized read count table in txt format is presented as a processed data file. For Exome-seq, the VCF file containing the chromosome positions and variant information is presented in xlsx format.

growth_protocol: 786-O cells were cultured with RPMI 1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin, and 5uM of ferrostatin-1 in a humidified incubator at 37 °C with 5% CO2.

extract_protocol:
Total RNA samples were extracted using the Rneasy Mini Kit (Qiagen) following manufacturer's instructions. Genomic DNA samples were extracted using the QIAamp Blood Mini DNA isolation kit (Qiagen) from manufacturer's instructions.
RNA sequencing library was prepared using NEB-Next Ultra RNA Library Prep Kit following the manufacturer’s recommendations. Briefly, total RNA samples were quantified and tested for contamination and degradation. After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo (dT) beads. For prokaryotic organisms or eukaryotic organisms' long-non-coding libraries, rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment. The qualified libraries are fed into Illumina Novaseq6000 sequencers after pooling according to its effective concentration and expected data volume using a 2x150 bp paired-end configuration.  Image analysis and base calling were conducted by the HiSeq Control Software. Raw sequence data generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.   To make Exome-sequencing library, DNA degradation and contamination were monitored on 1% agarose gels, and DNA concentration was measured using Qubit® DNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA). A total amount of 1.0 μg genomic DNA per sample was used as input material for the DNA library preparation. Sequencing libraries were generated using Agilent SureSelect Human All Exon kit (Agilent Technologies, CA, USA) following manufacturer's recommendations and index codes were added to each sample. Briefly, fragmentation was carried out by a hydrodynamic shearing system (Covaris, Massachusetts, USA) to generate 180-280bp fragments. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and enzymes were removed. After adenylation of 3’ ends of DNA fragments, adapter oligonucleotides were ligated. DNA fragments with ligated adapter molecules on both ends were selectively enriched in a PCR reaction. After PCR reaction, library hybridize with Liquid phase with biotin labeled probe, then use magnetic beads with streptomycin to capture the exons. Captured libraries were enriched in a PCR reaction to add index tags to prepare for hybridization. Products were purified using AMPure XP system (Beckman Coulter, Beverly, USA) and quantified using the Agilent high sensitivity DNA assay on the Agilent Bioanalyzer 2100 system. Sequencing libraries that passed quality threshold were sequenced on an Illumina Novaseq6000 platform according to effective concentration and data volume.

treatment_protocol: 786-O cells were splitted at 200,000 cells per well in 6-well plates one day before RNA and genomic DNA extraction. No special treatment was administered to these cells.

tag: cell line source

tag: gpx4 status

value: GPX4 knockout

tag: category

value: ferroptosis-resistant


title: TfR KI + vehicle, input_1

description:
DRN-16903
TfR KI + vehicle, input
processed data file: dst133_processed_data.xlsx

value: TfR KI

value: Input

tag: Sex

tag: treatment

tag: batch

value: 337 pg/uL


title: EXOMEseq.GPX4KO.mouse2.786O.left_FR2dL


title: STRAP Embryo eCLIP-1

city: Birmingham

first: Pran

middle: K

last: Datta

state: AL

address: 1824 6th Ave South, WTI 520C

department: Medicine

institute: University of Alabama at Birmingham

data_processing:
Library strategy: eCLIP-seq
Basecalls performed using Illumina's bcl2fastq version 2.18.0.12
Cutadapt version was used to trim primer adapters from raw FASTQ files using parameters: -f fastq --match-read-wildcards --times 1 -e 0.1 -O 1 --quality-cutoff 6 -m 18 -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT
To remove repetive elements, STAR version 2.5.2b was used on the trimmed FASTQ files using paramters: --outSAMunmapped Within --outFilterMultimapNmax 30 --outFilterMultimapScoreRange 1 --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted --outFilterType BySJout --outReadsUnmapped Fastx --outFilterScoreMin 10 --outSAMattrRGline $RG --alignEndsType EndToEnd
The unmapped reads from the first STAR alignments were then mapped to mm10 using STAR version 2.5.2b using parameters: --outSAMunmapped Within --outFilterMultimapNmax 30 --outFilterMultimapScoreRange 1 --outSAMattributes All  --outStd BAM_Unsorted --outSAMtype BAM Unsorted --outFilterType BySJout --outReadsUnmapped Fastx --outFilterScoreMin 10 --alignEndsType EndToEnd
Peaks were called on mm10 alignments using MACS version 1.4.2 using parameters: -t -c --name --format="BAM" -g mm --tsize=75
Genome_build: GRCm38 p4 Release M11
Supplementary_files_format_and_content: Tab-delimited Excel file containing the peaks identified for each sample by MACS

source_name: embryo

growth_protocol: EB cells were cultured in ES medium without LIF and then cultured in N2B27 medium supplemented with  10ng/ml bFGF  for additional 5 days.

extract_protocol:
UV-crosslinked EBs or embryos were lysed in CLIP lysis buffer followed by sonication and STRAP-RNA complexes were isolated with anti-STRAP antibody.
eCLIP libraries were prepared for sequencing using eCLIP-seq protocols.

value: embryo

tag: strain

tag: age

value: prenatal day 9.5

tag: genotype

value: wild type


title: STRAP EB eCLIP-1

source_name: ESCs derived embryoid body

value: ESCs derived embryoid body


title: STRAP EB eCLIP-2


title: EXOMEseq.GPX4KO.mouse1.786O.left_FR2aL


title: EXOMEseq.GPX4KO.mouse1.786O.right_FR2aR


title: HBEC-6KT-ABCF1-Ctrl-VACV-70-rep2

city: Waterloo

first: Jennifer

middle: A.

last: Aguiar

state: ON

address: 200 University Avenue East

department: Biology

institute: University of Waterloo

hyb_protocol: Labeled cDNA was hybridized to GeneChip™ Clariom_S_Human arrays according to ThermoFisher Scientific instructions.

scan_protocol: Arrays were scanned GeneChip Scanner 3000 7G using AGCC software.

data_processing: Raw intensity values from the microarray experiment using the Affymetrix Clariom S Human chip-type were imported into the R statistical language environment (version 3.6.1). Probe definition files were obtained from the Brainarray database (version 24). The Single Channel Array Normalization (SCAN) method was used to obtain log2-transformed normalised expression values with the SCAN.UPC R package (version 2.26.0), with annotation data from the Bioconductor project (version 3.9). Determination of statistically significant differential gene expression was performed using the empirical Bayes method via the eBayes function from the limma R package (version 3.40.0). P values were adjusted using the Benjamini & Hochberg method, with a significance cutoff of 0.05.

label: Biotin

source_name: Human airway epithelial cell line HBEC-6KT culture exposed to ABCF1 siRNA + VACV-70

label_protocol: cDNA was amplified using GeneChip™ WT PLUS Reagent Kit, from ThermoFisher Scientific following manufacturers instructions.

growth_protocol: An immortalized human airway epithelial cell line (HBEC-6KT) over expressing human telomerase reverse transcriptase (hTERT) and cyclin-dependent kinase 4 (Cdk4) was cultured as a submerged monolayer. HBEC-6KT were grown in keratinocyte serum free medium supplemented with 0.8 ng/mL epithelial growth factor, 50 μg/mL bovine pituitary extract and 1X penicillin/streptomycin. All cells were grown at 37℃ at 5% CO2  and all experiments were performed within 5 passages.

extract_protocol: Cells were harvested directly in culture plates using the Buffer RLT mixed with 2-ME. Following harvest, total RNA was extracted as instructed by the RNeasy Mini Kit manual.

treatment_protocol: All in vitro knockdown experiments in HBEC-6KT were done using siRNA transfected with DharmaFECT Transfection Reagent according to the manufacturer’s instructions. Cells were transfected with siABCF1 or siCTRL for 24 hours. After knockdown, cells were transfected with an immunostimulatory ligand for 24h followed by outcome measurements of cell viability (LDH and cell morphology), function (CXCL10 secretion), protein expression (immunoblot), or gene transcription (microarray). For  VACV-70 stimulation experiments, a concentration-response study was performed using  0.1-3.16 mg/ml (VACV-70) followed by incubation for 24h.


title: HBEC-6KT-ABCF1-Ctrl-VACV-70-rep1


title: HBEC-6KT-ABCF1-Ctrl-control-VACV-70-rep3

source_name: Human airway epithelial cell line HBEC-6KT culture exposed to ABCF1 siRNA + control VACV-70


title: HBEC-6KT-ABCF1-Ctrl-control-VACV-70-rep1


title: HBEC-6KT-ABCF1-Ctrl-control-VACV-70-rep2


title: HBEC-6KT-ABCF1-Ctrl-VACV-70-rep3


title: HBEC-6KT-siCtrl-VACV-70-rep3

source_name: Human airway epithelial cell line HBEC-6KT culture exposed to siCtrl + VACV-70


title: EXOMEseq.GPX4WT.786O.right_WTR

value: GPX4 wildtype

value: ferroptosis-sensitive


title: HBEC-6KT-siCtrl-VACV-70-rep2


title: EXOMEseq.GPX4WT.786O.left_WTL


title: STRAP EB eCLIP Input


title: STRAP Embryo eCLIP Input


title: STRAP Embryo eCLIP-2


title: Muscle_Al_12mo_rep1

data_processing: Raw signal intensity data was background corrected, log2 transformed and normalized with robust multi-array average (RMA) from the Affymetrix data bank using the “oligo” package in R v4.0.1 (8). Each Affymetrix chip contains 25,117 probesets, including 2163 control and unmapped probesets.

source_name: gastrocnemius, aluminum, 12 months, replicate 1

extract_protocol: Total RNA was isolated from gastrocnemius muscle using TRIzol® reagent (Invitrogen, Carlsbad, CA) following manufacturer’s protocol. For each metal and time point, three Affymetrix chips (Clariom S Rats) were used with 250 ng of total RNA derived from a pooled sample from 2-3 animals.

tag: gender

value: Male

value: Sprague-Dawley

value: Skeletal Muscle

value: Al

tag: time


title: RNAseq.GPX4KO.mouse2.786O.right.rep1_FR2dR

data_processing:
For RNA-seq data analysis, raw paired-end 150 bp/150 bp sequencing reads were mapped to human genome build hg38 (Dec 2013) using Bowtie2 (v2.3.1) with standard settings. On average 67% of read pairs were uniquely mapped to the hg38 genome. Mapped reads were counted to gene features by the htseq-count function from HTSeq (version 0.9.1) with standard settings, normalized to library size and analyzed for differentially expressed genes with DESeq2 (Bioconductor).
For Exome-seq data analysis, raw paired-end sequencing reads were mapped to human genome build hg38 (Dec 2013) using Bowtie2 (v2.3.1) with standard settings. The SAM files containing mapped reads were sorted and indexed into BAM files using Samtools (v1.10). Sorted BAM files were processed using the PICARD (2.22.2-0) tools and GATK (4.1.6.0) Exome-seq variant calling best practices pipeline. The following commands were sequentially used to pre-process the sample datasets, all with standard settings: MarkDuplicates, Samtools (sort+index), AddOrReplaceReadGroups, BaseRecalibrator, Apply Recalibration. GATK Mutect2 tool was used for variant calling, using GPX4 wildtype samples as normal control, while GPX4 KO ferroptosis resistant cells were treated as "tumor" samples. For variant filtering, the following GATK commands were used sequencially: GetPileupSummaries, CalculateContamination, FilterMutectCalls. Final variants that passed all thresholds in all ferroptosis-resistant samples were exported as "common variants" and in the "ExomeSeq.786O.FR2.common.variants.xlsx" file.
Genome_build: hg38
Supplementary_files_format_and_content: For RNA-seq, the normalized read count table in txt format is presented as a processed data file. For Exome-seq, the VCF file containing the chromosome positions and variant information is presented in xlsx format.


title: HBEC-6KT-siCtrl-VACV-70-rep1


title: HBEC-6KT-siCtrl-control-VACV-70-rep2

source_name: Human airway epithelial cell line HBEC-6KT culture exposed to siCtrl + control VACV-70


title: Embryo 8.0-2

data_processing:
Basecalls performed using Illumina's bcl2fastq version 2.18.0.12
FASTQ files were aligned with STAR version 2.5.2b with parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Cufflinks version 2.2.1 was used on the STAR BAM files with parameters --library-type fr-firststrand -G -L
rMATS version 3.2.5 was used on the STAR BAM files with parameters -b1 -b2 -gtf -t paired -len 74 -novelSS1
Genome_build: GRCm38 p4 Release M11
Supplementary_files_format_and_content: Tab-delimited Excel file containing FPKM values for each sample

growth_protocol: ESCs were routinely cultured in ES medium. EB cells were cultured in ES medium without LIF and then cultured in N2B27 medium supplemented with  10ng/ml bFGF  for additional 5 days.

extract_protocol:
Samples were directly lysed using Trizol (ThermoFisher Scientific), treated with DNase (QIAGEN) and purified using RNeasy Minielute Cleanup Kit (QIAGEN). Ribosomal RNA was removed from each RNA extraction using NEBNext rRNA depletion kit (NEB).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: prenatal day 8.0


title: RNAseq.GPX4KO.mouse2.786O.left.rep2_FR2dL


title: HBEC-6KT-transfection-reagent-ABCF1-siRNA-rep2

source_name: Human airway epithelial cell line HBEC-6KT culture exposed to transfection reagent and ABCF1 siRNA


title: HBEC-6KT-siCtrl-control-VACV-70-rep3


title: HBEC-6KT-transfection-reagent-ABCF1-siRNA-rep3


title: RNAseq.GPX4KO.mouse2.786O.right.rep2_FR2dR


title: RNAseq.GPX4KO.mouse1.786O.right.rep1_FR2aR


title: RNAseq.GPX4KO.mouse1.786O.right.rep2_FR2aR


title: EB KO-1

source_name: ESC-derived embryoid body

value: ESC-derived embryoid body

value: Strap-/-


title: Apc min/+;Sirt7KO_3

city: Shanghai

first: Xiyang

last: Liu

state: Shanghai

address: 320 Yueyang Road, Shanghai, 20025 P.R. China

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

data_processing:
RNA-seq libraries were pooled for deep sequencing by using Illumina Hiseq Xten (2 × 150) platforms at the CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China
Raw read qualities were evaluated with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, v0.11.5)
Adaptor sequences and read sequences on both ends with Phred quality scores below 30 were trimmed
Trimmed reads were mapped with the Tophat algorithm (TopHat v2.1.1) to target sequences
Gene expression levels were quantified by the software package HTSeq (v0.6.1p1)
The list of differentially expressed genes were generated by DESeq2 with P<0.05
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normarllized counts for each Sample

source_name: intestine

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA-seq libraries were prepared according to the Illumina TruSeq protocol

value: intestine

value: 5 months

value: APC min/+ ; Sirt7 -/-


title: EB WT-1


title: Apc min/+;Sirt7KO_2


title: Embryo 9.0-2

value: prenatal day 9.0


title: Embryo 9.0-1

value: embryo


title: RNAseq.GPX4KO.mouse1.786O.left.rep2_FR2aL

value: GPX4 knockout

value: ferroptosis-resistant


title: Embryo 8.0-1

value: wild type


title: Apc min/+;Sirt7KO_1


title: EB WT-2


title: RNAseq.GPX4KO.mouse2.786O.left.rep1_FR2dL


title: RNAseq.GPX4WT.786O.right.rep2_WTR

value: GPX4 wildtype


title: APC min/+_3

value: Apc min/+


title: RNAseq.GPX4WT.786O.right.rep1_WTR

value: ferroptosis-sensitive


title: EB KO-2


title: HBEC-6KT-siCtrl-control-VACV-70-rep1


title: HBEC-6KT-transfection-reagent-control-siRNA-rep2

source_name: Human airway epithelial cell line HBEC-6KT culture exposed to transfection reagent and control siRNA


title: HBEC-6KT-transfection-reagent-control-siRNA-rep3


title: HBEC-6KT-transfection-reagent-only-rep2

source_name: Human airway epithelial cell line HBEC-6KT culture exposed to transfection reagent only


title: HBEC-6KT-transfection-reagent-only-rep3


title: Hereford semitendinosus muscle_Cy3 vs Holstein-Friesian semitendinosus muscle_Cy5_2

city: Warsaw

first: Tomasz

last: Sadkowski

address: Nowoursynowska 159

department: Department of Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences - SGGW

description: Biological replicate 2 of 4. Hereford semitendinosus muscle_Cy3 vs Holstein-Friesian semitendinosus muscle_Cy5_DYE SWAPPED to make Holstein-Friesian a reference sample_rep 2

hyb_protocol: Probe were hybridized using Gene Expression Hybridization Kit (Agilent Technologies, USA) according to the manufacturers protocol. RNA Spike In Kit (Agilent Technologies, USA) was used as an internal control.

scan_protocol: Acquisition and analysis of hybridization intensities were performed using the Agilent DNA microarray scanner and Agilent Feature Extraction software 10.7.3.1. according to the standard manufacturer’s procedures and LOWESS normalization.

data_processing: Linear Lowess normalized. The statistical analysis was performed using Gene Spring 13 software default protocol (Agilent Technologies, USA). The statistical significance of the differences was evaluated using student test (p<0.05) and fold change FC>1.3.

organism: Bos taurus

source_name: Hereford muscle_Cy3

label_protocol: Low Input Quick Amp Labeling Kit (Agilent Technologies, USA) was used to amplify and label target RNA to generate complementary RNA (cRNA).

extract_protocol: Total RNA was isolated by using a total RNA kit (A&A BIOTECHNOLOGY, Poland). RNA quantity was measured spectrophotometrically using NanoDrop (NanoDrop Technologies, USA). The analysis of final RNA quality and integrity was performed with BioAnalyzer 2100 (Agilent Technologies, USA). To ensure optimal data quality only RNA samples with RIN number ≥ 9 were included into the analysis.

tag: breed

value: Hereford

value: 15 month old

value: m. semitendinosus

source_name: Holstein-Friesian muscle_Cy5

tag: brred

value: Holstein-Friesian


title: HBEC-6KT-transfection-reagent-control-siRNA-rep1

tag: cell line


title: HBEC-6KT-transfection-reagent-only-rep1


title: APC min/+_2

tag: genotype/variation


title: Hereford semitendinosus muscle_Cy3 vs Holstein-Friesian semitendinosus muscle_Cy5_3

description: Biological replicate 3 of 4. Hereford semitendinosus muscle_Cy3 vs Holstein-Friesian semitendinosus muscle_Cy5_DYE SWAPPED to make Holstein-Friesian a reference sample_rep 3

tag: tissue


title: HBEC-6KT-transfection-reagent-ABCF1-siRNA-rep1


title: RNAseq.GPX4WT.786O.left.rep2_WTL


title: Hereford semitendinosus muscle_Cy3 vs Holstein-Friesian semitendinosus muscle_Cy5_4

description: Biological replicate 4 of 4. Hereford semitendinosus muscle_Cy3 vs Holstein-Friesian semitendinosus muscle_Cy5_DYE SWAPPED to make Holstein-Friesian a reference sample_rep 4


title: RNAseq.GPX4KO.mouse1.786O.left.rep1_FR2aL


title: Hereford semitendinosus muscle_Cy3 vs Holstein-Friesian semitendinosus muscle_Cy5_1

description: Biological replicate 1 of 4. Hereford semitendinosus muscle_Cy3 vs Holstein-Friesian semitendinosus muscle_Cy5_DYE SWAPPED to make Holstein-Friesian a reference sample_rep 1


title: ES KO

source_name: embryonic stem cell (ESC)

value: embryonic stem cell (ESC)


title: RNAseq.GPX4WT.786O.left.rep1_WTL


title: APC min/+_1


title: ES WT