title: [nCATS] Revertant dermis nCATS

city: Sapporo

first: Yoshikazu

last: Furuta

state: Hokkaido

address: North 20 West 10, Kita-ku

department: International Institute for Zoonosis Control

institute: Hokkaido University

description:
DNA-seq
4_nCATS_counts.txt

data_processing:
Basecalls were performed using Guppy 5.0.11 using dna_r9.4.1_450bps_sup.cfg as a DNA model.
Mapping to the genomic sequence of COL7A1 (RefSeq Accession # NC_000003.12:c48595302-48564073) using minimap2 2.16-r922.
Information of reads mapped to both loci of the mutations (19630th base of the reference for c.5932C>T, 27712th base for c.8029G>A) was extracted using samtools.
Supplementary_files_format_and_content: Count of haplotype of each read.

source_name: Human dermis

growth_protocol: A 4 or 5 mm punch biopsy was performed on a patient's clinically revertant skin spots that did not show any skin fragility via manual rubbing. Adjacent non-revertant skin samples were also obtained.

extract_protocol:
gDNA was extracted from the epidermis, dermis, or peripheral blood by the Puregene Blood Core Kit (Qiagen, Valencia, CA, USA).
Libraries were constructed using Ligation Sequencing Kit SQK-LSK109 and Native Barcoding Expansion kit EXP-NBD104 and EXP-NBD114 (Oxford Nanopore Technologies). gDNA was treated with Quick Calf Intestinal Phosphatase and Cas9 before library construction for Nanopore Cas9-targeted sequencing (nCATS).

treatment_protocol: Not applicable.

tag: diagnosis

value: Epidermolysis bullosa

value: Revertant dermis


title: [nCATS] Non-revertant dermis nCATS

status: Public on Jan 13 2022

type: SRA

country: Japan

description:
DNA-seq
4_nCATS_counts.txt

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: tissue

value: Non-revertant dermis


title: [nCATS] Revertant epidermis nCATS

description:
DNA-seq
4_nCATS_counts.txt

source_name: Human epidermis

value: Revertant epidermis


title: [nCATS] Non-revertant epidermis nCATS

description:
DNA-seq
4_nCATS_counts.txt

value: Non-revertant epidermis


title: A10.1 (wild type) inflorescence_10DAS_rep1

city: St. Louis

first: Elizabeth

middle: A.

last: Kellogg

state: MO

address: 975 North Warson Rd.

country: USA

institute: Donald Danforth Plant Science Center

library_source: transcriptomic

data_processing:
Adaptors and low-quality reads were trimmed using Trimmomatic (Bolger et al., 2014) and reads were quality-checked using fastqc after trimming.
The S. viridis reference genome (v1) was indexed using bowtie 2 (Langmead and Salzberg, 2012) from Sviridis_311_v1.0.fa.gz file at PhytozomeV11 (phytozome.jgi.doe.gov). Reads were mapped to the reference genome using tophat2 and differentially expressed genes were identified using cuffdiff (Trapnell et al., 2012).
Expression levels quantified in Fragments Per Kilobase of transcript per Million (FPKM) were extracted for 35,214 S. viridis primary transcripts (Tables S5, S6). Gene annotation and grass homolog identification followed Zhu et al. ((2018)).
Genome_build: Genome_build: Sviridis_311_v1
Supplementary_files_format_and_content: Processed data files are MS Excel spreadsheets.  Table S5. RNA-seq library sequencing and mapping statistics.  Table S6.  Expression of all S. viridis genes from each replicate (R1-R4) of the developmental stages (10, 12, 14 DAS) in A10.1 and spp1. Table S7. Expression of differentially expressed genes between A10.1 and spp1 at each developmental stage (10, 12, 14 DAS).

molecule: total RNA

organism: Setaria viridis

growth_protocol: Mutants in the sparse panicle1 locus (spp1) were used in this study. Seeds were planted in MetroMix 360 soil (Sun Gro Horticulture company) and grown in a controlled growth chamber with the following conditions: temperature of 31°C/23°C (day/night), light intensity of 200 µmol/sq.meter/sec for 12 hours (6am-6pm) and 50% relative humidity, at the Donald Danforth Plant Science Center’s Integrated Plant Growth Facility. Plants were fertilized with Jack’s 15-16-17 (Hummert International) twice a week.

extract_protocol:
Inflorescences were hand-dissected into fresh 100% acetone on dry ice from wildtype (A10.1) and mutant (sparse panicle1) S. viridis seedlings at 10, 12, and 14DAS. Depending on the representative size at a given stage, 10-30 individual inflorescence primordia were pooled per biological replicate; three to four biological replicates were collected for each stage. All sampling was performed within a two-hour window in the morning to control for circadian effects. Acetone was removed and samples were flash-frozen in liquid nitrogen and ground into a fine powder using 3mm tungsten-carbide beads (Qiagen) in a Tissue Lyser-II. Total RNA was isolated using the PicoPure RNA Isolation Kit (Thermo Fisher Scientific) with in-column DNase I treatment following manufacturer's protocols.
RNA-seq libraries were generated from 1µg total RNA using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs Inc.) and size-selected for 200 bp inserts. Libraries were quantified on a bioanalyzer (Agilent 2100) using a DNA 1000 chip to confirm the insert size and quantified again on a Qubit 3.0 Fluorometer (Life Technologies) to ensure different libraries were equally loaded
Libraries were sequenced using standard Illumina protocols (Illumina, Inc.) for either paired-end (PE) sequencing at 100bp on the Illumina HiSeq 2500 platform at the University of Illinois at Urbana-Champaign W.M. Keck Center.

tag: genotype/variation

value: A10.1 (wild type)

tag: developmental stage


title: [Peripheral blood PCR] RDEB PB, 35 cycles #3

description:
DNA-seq
3_blood_PCR_counts.txt

source_name: Human peripheral blood

value: Recessive Dystrophic Epidermolysis Bullosa (RDEB)

value: Peripheral blood


title: LN_Saline_36

city: Los Angeles

first: Roberto

last: Spreafico

state: CA

address: UCLA

department: Institute for Quantitative and Computational Biosciences

institute: University of Califonia Los Angeles

data_processing:
Reads were quality-controlled using FastQC.
Illumina adapters were removed using cutadapt.
Trimmed reads were mapped to the mouse transcriptome (GRCm38) based on Ensembl annotations using Kallisto
Transcript counts were imported and aggregated to gene counts using tximport
Gene counts were analyzed using the R package DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: rlog function from DESeq2 package

organism: Mus musculus

source_name: Lymph Node

extract_protocol:
RNA was isolated from TRI Reagent samples using phenol-chloroform extraction or column-based extraction systems (Direct-zol RNA Microprep and Miniprep, Zymo Research) according to the manufacturer’s protocol. RNA concentration and purity (260/280 and 260/230 ratios) were measured by NanoDrop (Thermo Fisher Scientific).
RNA samples were quantified using Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and RNA integrity was checked with RNA Screen Tape on Agilent 2200 TapeStation (Agilent Technologies). RNA sequencing library preparation was prepared using TruSeq Stranded mRNA library Prep kit following manufacturer’s protocol (Illumina, Cat# RS-122-2101). Briefly, mRNAs were first enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 8 minutes at 94°C. First strand and second strand cDNA were subsequently synthesized. The second strand of cDNA was marked by incorporating dUTP during the synthesis. cDNA fragments were adenylated at 3’ends, and indexed adapter was ligated to cDNA fragments. Limited cycle PCR was used for library enrichment. The incorporated dUTP in second strand cDNA quenched the amplification of second strand, which helped to preserve the strand specificity. Sequencing libraries were validated using DNA Analysis Screen Tape on the Agilent 2200 TapeStation (Agilent Technologies), and quantified by using Qubit 2.0 Fluorometer (Thermo Fisher Scientific) as well as by quantitative PCR (Applied Biosystems). The sequencing libraries were multiplexed and clustered on 1 lane of flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) High Output configuration.

value: Lymph Node

tag: treatment

value: Saline

tag: time point

value: 24 hr

tag: batch


title: LN_Saline_35


title: LN_Saline_34


title: [Peripheral blood PCR] RDEB PB, 35 cycles #2

description:
DNA-seq
3_blood_PCR_counts.txt


title: LN_Mannan_33

value: Mannan


title: LN_Mannan_32


title: [Peripheral blood PCR] RDEB PB, 35 cycles #1

description:
DNA-seq
3_blood_PCR_counts.txt


title: LN_Glucan_30

value: Beta-glucan


title: [Peripheral blood PCR] RDEB PB, 30 cycles #2

description:
DNA-seq
3_blood_PCR_counts.txt


title: [Peripheral blood PCR] RDEB PB, 30 cycles #1

description:
DNA-seq
3_blood_PCR_counts.txt


title: LN_Glucan_28


title: [Peripheral blood PCR] RDEB PB, 25 cycles #3

description:
DNA-seq
3_blood_PCR_counts.txt


title: LN_Saline_27

value: 6 hr


title: LN_Mannan_31


title: LN_Saline_26


title: [Peripheral blood PCR] RDEB PB, 25 cycles #1

description:
DNA-seq
3_blood_PCR_counts.txt


title: LN_Saline_25


title: [Peripheral blood PCR] Normal human PB, 25 cycles #3

description:
DNA-seq
3_blood_PCR_counts.txt

value: Healthy


title: [Peripheral blood PCR] Normal human PB, 25 cycles #2

description:
DNA-seq
3_blood_PCR_counts.txt


title: [Peripheral blood PCR] Normal human PB, 25 cycles #1

description:
DNA-seq
3_blood_PCR_counts.txt


title: LN_Mannan_24


title: [skin PCR] Revertant epidermis PCR #3

description:
DNA-seq
2_skin_PCR_counts.txt


title: [skin PCR] Revertant epidermis PCR #1

description:
DNA-seq
2_skin_PCR_counts.txt


title: [nCATS] Normal human epidermis nCATS

description:
DNA-seq
4_nCATS_counts.txt

value: Normal epidermis


title: [skin PCR] Revertant dermis PCR #3

description:
DNA-seq
2_skin_PCR_counts.txt


title: LN_Glucan_20


title: [skin PCR] Revertant dermis PCR #2

description:
DNA-seq
2_skin_PCR_counts.txt


title: LN_Mannan_23


title: Skin_Saline_9

source_name: Skin

value: Skin


title: Skin_Saline_7


title: [Peripheral blood PCR] RDEB PB, 30 cycles #3

description:
DNA-seq
3_blood_PCR_counts.txt


title: Skin_Saline_8


title: [skin PCR] Revertant dermis PCR #1

description:
DNA-seq
2_skin_PCR_counts.txt

value: Epidermolysis bullosa


title: Skin_Mannan_6


title: [skin PCR] Non-revertant epidermis PCR #2

description:
DNA-seq
2_skin_PCR_counts.txt


title: [skin PCR] Non-revertant epidermis PCR #3

description:
DNA-seq
2_skin_PCR_counts.txt


title: Skin_Mannan_5


title: Skin_Glucan_3


title: [skin PCR] Non-revertant epidermis PCR #1

description:
DNA-seq
2_skin_PCR_counts.txt


title: [skin PCR] Non-revertant dermis PCR #3

description:
DNA-seq
2_skin_PCR_counts.txt


title: [Peripheral blood PCR] RDEB PB, 25 cycles #2

description:
DNA-seq
3_blood_PCR_counts.txt


title: Skin_Glucan_2


title: [skin PCR] Non-revertant dermis PCR #2

description:
DNA-seq
2_skin_PCR_counts.txt


title: [skin PCR] Non-revertant dermis PCR #1

description:
DNA-seq
2_skin_PCR_counts.txt


title: Skin_Mannan_4


title: Skin_Glucan_1


title: LN_Glucan_21


title: [skin PCR] Revertant epidermis PCR #2

description:
DNA-seq
2_skin_PCR_counts.txt


title: LN_Mannan_22


title: 11DAF-3 resequenced

city: East Lasing

first: Erich

last: Grotewold

state: MI

address: 603 Wilson Rd.

department: Biochemistry and Molecular Biology

institute: Michigan State University

data_processing:
Base calling was done by Illumina Real Time Analysis (RTA) v2.7.7 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.
Sample quality control was performed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, V0.11.5). Adapters and low quality reads were trimmed with Trimmomatic (Bolger et al., 2014) using the following parameters: ILLUMINACLIP:Adapter.fastq:2:40:15 SLIDINGWINDOW:4:20 MINLEN:30
Cleaned reads were mapped to the reference genome (V2.0, http://camelinadb.ca) using (nuclear chromosomes only) using bowtie2 v2.3.4.1 (Langmead and Salzberg, 2012)
Peaks were called using GEM v3.4
RNA-seq: Cleaned reads were mapped to the reference genome (V2.0, http://camelinadb.ca) using HISAT2 (2.0.4)
RNA-seq: Reads aligned to genes were counted with the R package Rsubread v1.32.2
Genome_build: V2.0, http://camelinadb.ca
Supplementary_files_format_and_content: narrowPeak; raw counts

organism: Camelina sativa

source_name: Seed

growth_protocol: Camelina sativa cultivar Suneson was grown in the plant biology greenhouse at Michigan State University. RNA-seq and DAP-seq experiments were performed on plants grown for one month at 22 °C and under 16:8 -h light/dark cycles. For RNA-seq of seed, total RNA was extracted from seedpods harvested at 5, 8, and 11 DPAs. For DAP-seq, a pool of ten leaves from six mature (two-month-old) plants were collected

extract_protocol:
DAP-seq: Camelina sativa genomic DNA were extracted using urea buffer (7M urea, 350mM NaCl, 50mM Tris-HCl pH8, 20mM EDTA, 1% N-lauroyl sarcosine) and mixed with phenol:chloroform:isoamyl alcohol 25:24:1. The supernatants containing DNA were further precipitated using 3M NaOAc (pH 5.2) and isopropanol followed by 70% ethanol wash. The DNA pellet was resuspended in UltraPure™ DNase/RNase-Free Distilled Water (Invitrogen) followed by RNase A (Roche) treatment and ethanol precipitation.
RNA-seq: Total RNA from fresh seed was extracted using Spectrum Plant Total RNA Kit (Sigma-Aldrich) according to the manufacturer’s protocol. The total RNA was prepared with three biological replicates, each with ~100 mg seeds. The quality of total RNA was determined by TapeStation4200 (Agilent), and cDNA library was generated with 1 μg of total RNA using TruSeq stranded mRNA (Illumina)
DAP-seq: gDNA libraries were constructed following the protocol of Bartlett et al., 2017 with minor modifications. Extracted gDNA were fragmented to the size range between 200-400 bp using Diagenode’s Bioruptor® 300 for 40 cycles with 30 seconds on/off at high energy. The fragmented DNA was further used for end repair and adapter ligation. To create modification free DNA, additional 11 cycles of PCR amplifications were performed using the adapter ligated libraries, followed by ethanol precipitation. Finally, the amplified gDNA libraries (ampDAP) were used for all protein-DNA interaction procedures. All the buffers and procedures for DNA-protein interaction were as published (Bartlett et al., 2017). except that the input gDNA library amount and the final step of library size selection. About 200 ng of ampDAP gDNA library were added as an input to mix with each pIX-HALO-TF protein. Finally, to perform double-size selection targeting 300-400 bp fragments, 0.7 volume of Agencourt AMPure XP beads (35 µl) to 1 volume of sample (50 µl) were mixed for 5 minutes and the bead was discarded to remove fragments with size larger than 400 bp. Next, the supernatant (85 µl) containing < 400 bp fragments were added to 0.2 volume of Agencourt AMPure XP beads (10 µl) and mixed for 15 minutes. The bound fragments were eluted from the beads by adding 18 ml UltraPure™ DNase/RNase-Free Distilled Water (Invitrogen). The concentrations of eluted DNA were measured using the Qubit HS dsDNA assay kit, and approximate 5-20 ng/µl final concentrations were obtained. The fragment size and binding capacity to the flow cell were further examined on the agarose gel by six cycles of PCR using 2 µl of eluted ampDAP-seq library with Illumina P5 and P7 primers. Twelve libraries were pooled in one lane and sequenced by Illumina HiSeq 4000 SE50 at RTSF Genomics core at Michigan State University.
RNA-seq : Total RNA from fresh seed was extracted using Spectrum Plant Total RNA Kit (Sigma-Aldrich) according to the manufacturer’s protocol. The total RNA was prepared with three biological replicates, each with ~100 mg seeds. The quality of total RNA was determined by TapeStation4200 (Agilent), and cDNA library was generated with 1 μg of total RNA using TruSeq stranded mRNA (Illumina). The pooled libraries were sequenced with a paired-end read length of 150 bp by Illumina HiSeq 4000 at the Research Technology Support Facility Genomics Core at Michigan State University.

tag: cultivar

value: Suneson

value: seeds 11 days post-anthesis

value: WT


title: 11DAF-2


title: 11DAF-2 resequenced


title: 11DAF-1 resequenced


title: 11DAF-1


title: 8DAF-3 resequenced

value: seeds 8 days post-anthesis


title: 5x2 Gy_Irradiated_APTK_Conditioned_Media_Treated Fibroblasts_II

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20.0.422
STAR version 2.5.2a was used to align the reads to the mm10 genome using 2 mismatches within 50 bases
featureCounts version 1.5.0-p1 was used to quantify reads for genes in mm10 version 84
Genome_build: mm10 version 84
Supplementary_files_format_and_content: Tab-delimited gene counts

molecule: polyA RNA

source_name: Radiated APTK Supernatant Treated Fibroblasts

growth_protocol: Tissue Culture Plates (2D Fibroblasts Culture) in 10% FBS Advanced DMEM F12

extract_protocol: Qiagen RNeasy mini Kit

treatment_protocol: Stimulation for 24 hours with organoids conditioned media

tag: cell type

value: Colon Fibroblasts

tag: strain


title: 5x2 Gy_Irradiated_APTKA_Conditioned_Media_Treated Fibroblasts_III

source_name: Radiated APTKA Supernatant Treated Fibroblasts


title: 5x2 Gy_Irradiated_APTKA_Conditioned_Media_Treated Fibroblasts_IV


title: APTK_Conditioned_Media_Treated Fibroblasts_IV

source_name: APTK Supernatant Treated Fibroblasts


title: 11DAF-3


title: 8DAF-3


title: 5x2 Gy_Irradiated_APTK_Conditioned_Media_Treated Fibroblasts_I


title: 5x2 Gy_Irradiated_APTKA_Conditioned_Media_Treated Fibroblasts_I


title: 5x2 Gy_Irradiated_APTK_Conditioned_Media_Treated Fibroblasts_III


title: 8DAF-2 resequenced


title: 8DAF-2


title: APTK_Conditioned_Media_Treated Fibroblasts_III


title: 8DAF-1 resequenced


title: APTK_Conditioned_Media_Treated Fibroblasts_I


title: APTKA_Conditioned_Media_Treated Fibroblasts_IV

source_name: APTKA Supernatant Treated Fibroblasts


title: 8DAF-1


title: 5DAF-3 resequenced

value: seeds 5 days post-anthesis


title: 5DAF-3


title: APTKA_Conditioned_Media_Treated Fibroblasts_II


title: 5x2 Gy_Irradiated_APTK_Conditioned_Media_Treated Fibroblasts_IV


title: 5DAF-1 resequenced


title: 5x2 Gy_Irradiated_APTKA_Conditioned_Media_Treated Fibroblasts_II


title: Wild-Type Fibroblasts IV

source_name: Untreated Fibroblasts


title: Csa19g036630_deM

source_name: DNA-binding

value: Mature plants

value: deMethylated


title: 5DAF-2 resequenced


title: 5DAF-2


title: Wild-Type Fibroblasts I


title: 5DAF-1


title: APTKA_Conditioned_Media_Treated Fibroblasts_I


title: Wild-Type Fibroblasts II


title: Csa19g005080_deM


title: Halo_deM


title: APTKA_Conditioned_Media_Treated_Fibroblasts IV

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20.0.422
STAR version 2.5.2a was used to align the reads to the mm10 genome using 2 mismatches within 50 bases
featureCounts version 1.5.0-p1 was used to quantify reads for genes in mm10 version 97
Genome_build: mm10 version 97
Supplementary_files_format_and_content: Tab-delimited gene counts

source_name: Non-radiated APTKA Fibroblast

extract_protocol: Qiagen Rneasy mini kit

treatment_protocol: APTKA_conditioned_media treated fibroblats were either non-irradiated or (3 x 2 Gy) irradiated with samples collected 72 hours post first dose irradiation

tag: tag


title: 3X2Gy_APTKA_Conditioned_Media_Treated_Fibroblasts III

source_name: 3x2 Gy Radiated APTKA Fibroblast


title: 3X2Gy_APTKA_Conditioned_Media_Treated_Fibroblasts II


title: Csa13g021450_deM


title: APTKA_Conditioned_Media_Treated_Fibroblasts III


title: Wild-Type Fibroblasts III


title: Csa13g019570_deM


title: 3X2Gy_APTKA_Conditioned_Media_Treated_Fibroblasts I


title: Csa17g034220_deM


title: Csa13g011780_deM


title: Csa18g003140_deM


title: APTK_Conditioned_Media_Treated Fibroblasts_II


title: APTKA_Conditioned_Media_Treated_Fibroblasts II


title: Csa11g072230_deM


title: APTKA_Conditioned_Media_Treated Fibroblasts_III


title: APTKA_Conditioned_Media_Treated_Fibroblasts I


title: Csa11g037200_deM


title: Csa11g015700_deM


title: 3X2Gy_APTKA_Conditioned_Media_Treated_Fibroblasts IV


title: Csa06g051300_deM


title: Csa08g011090_deM


title: Csa09g088620_deM


title: Ms10_sham_DG

city: Columbus

middle: Diana

last: Kirby

state: OH

address: 1835 Neil Ave, 55 Psycholgy

department: Psychology

institute: The Ohio State University

data_processing:
Basecalls performed using Casava 1.8.2
Reads were trimmed using AdapterRemoval v2.2.0 to remove sequencing adapters
Reads were aligned against the human decontaminome using HISAT2 v2.0.6 using default parameters
Unaligned deconaminome reads were aligned against the human genome using HISAT2 v2.0.6 using default parameters
Reads were quantified using Subread FeatureCounts using GENCODE release M14
Genome_build: GRCh38
Supplementary_files_format_and_content: TSV Counts tables generated using Subread FeatureCounts, Unfiltered

source_name: Whole DG

extract_protocol:
To isolate DGs for subsequent fluorescence activated cell sorting (FACS), adult mice (6-9 wk old) were anesthetized and perfused with HBSS as described above. Following perfusion, brains were removed and placed in cold HBSS on ice. To expose the hippocampus, brains were bisected along the midsagittal line and the cerebellum and diencephalic structures were removed. Under a dissection microscope (Zeiss), the DG was excised using a beveled syringe needle and placed in ice cold HBSS without calcium or magnesium. DGs were then mechanically dissociated with sterile scalpel blades before enzymatic dissociation with a pre-warmed papain (Roche 10108014001)/dispase (Stem Cell Technologies 07913)/DNase (Stem Cell Technologies NC9007308) (PDD) cocktail at 37°C for 20 min. Afterwards, the tissue was again mechanically disrupted by trituration for 1 min. Dissociated cells were collected by centrifugation at 500g for 5 min before resuspending in HBSS without calcium/magnesium. Cells were then filtered through a 35µm nylon filter before staining with fluorescent antibodies (Supplementary Table 5) on ice for 30 minutes. During the last 10 minutes of staining, Hoechst dye was added for live/dead discrimination. All cells were washed twice following staining and immediately sorted as NSC or IPC populations based on fluorescent markers with the FACSAria III (BD Biosciences, Franklin Lakes, NJ). CD31, CD45, O1, and O4 negative live cells were designated as NSCs if double positive for GLAST and GFP or IPCs if GFP positive and GLAST negative.
Libraries were generated with the Clontech SMART-Seq HT kit . Purified library products were then used in HiSeq 4000 paired-end sequencing (Illumina) to a depth of 15 - 20 million 2x150 bp clusters.

treatment_protocol: none or lateral fluid percussion injury/sham

value: NestinGFP mouse dentate gyrus

tag: age

value: 6-9 weeks

value: sham

value: Whole DG


title: Ms4_sham_NSC

source_name: Neural stem cell

value: Neural stem cell


title: Ms9_TBI_DG

value: TBI


title: Ms6_sham_NSC


title: Ms7_TBI_DG


title: Ms12_sham_DG


title: Ms8_TBI_DG


title: Ms3_TBI_NSC


title: Csa04g050690_deM


title: Csa04g023980_deM


title: Ms11_sham_DG


title: Ms1_TBI_NSC


title: Ms6_sham_IPC

source_name: Intermediate neural progenitor

value: Intermediate neural progenitor


title: Ms5_sham_IPC


title: Csa02g060070_deM


title: Csa01g013850_deM


title: Ms4_sham_IPC


title: Pooled_Input

first: Kalpana

last: Ghoshal

address: 420 W 12th Ave

data_processing:
Peak locations were determined using the MACS algorithm (v1.4.2) with a cutoff of p-value = 1e-7
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program
Reads were aligned to the human genome  (hg38) using the BWA algorithm (default settings)
Genome_build: hg38
Supplementary_files_format_and_content: The resulting histograms (genomic “signal maps”) were stored in bigWig files

source_name: hepatocellular carcinoma

growth_protocol: HCCLM3 cells were maintained in DMEM supplemented with L-glutamine (2 mM), 10% FBS, sodium pyruvate (1 mM) and penicillin/ streptomycin/amphotericin (Thermo Fisher Scientific, Pittsburg, PA) at 37°C with 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and chromatins were isolated with antibodies
For ChIP-sequencing experiment, Illumina sequencing libraries were prepared from the ChIP and input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end). Reads were aligned to the human genome  (hg38) using the BWA algorithm (default settings). Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome.

treatment_protocol: HCCLM3 cells were treated with AZD (10 uM) or DMSO for 12 hours

tag: cell line

value: hepatocellular carcinoma

tag: chip antibody

value: None (input)


title: AZD5153_BRD4

value: BRD4 (Bethyl Labs, A301-985A1)


title: Csa06g004330_deM

value: Suneson


title: Csa04g012470_deM


title: DMSO_BRD4

value: DMSO


title: AZD5153_H3K27Ac

value: H3K27Ac (Active Motif)


title: Ms3_TBI_IPC


title: DMSO_H3K27Ac


title: MS6_DG


title: Csa05g079950_deM


title: MS5_DG.2


title: Ms2_TBI_IPC


title: Csa10g008930_deM


title: Ms2_TBI_NSC


title: Ms1_TBI_IPC


title: MS5_DG.1


title: MS4_DG


title: L3_S9_R1_001

city: Taipei

first: Liang‑Chuan

last: Lai

state: Not Listed

address: No.1 Jen Ai road section 1

department: Graduate Institute of Physiology

country: Taiwan

institute: National Taiwan University

data_processing:
Raw Illumina FASTQ sequencing reads were mapped to the miRbase mature miRNA reference (http://www.mirbase.org/) using Partek Flow™ v5.0 (Partek Inc., St. Louis, MO, USA) with default alignment options. The remaining reads were aligned to human genome reference (RefSeq Hg19). Quantitation of normalized miRNA reads were obtained through Reads per Kilo-base per Million (RPKM) calculation within the Partek Flow pipeline. In the comparison of miRNA expression profile differences, the statistical significance was determined by using a two-sided student t-test.
Genome_build: Hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: breast cancer cell line

growth_protocol: The MCF7 cell line was purchased from Bioresource Collection and Research Center (Hsinchu, Taiwan). MCF7 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) (Gibco, Thermo Fisher, CA) with 1% penicillin-streptomycin (GIBCO) and 10% fetal bovine serum (HyClone, Logan, UT, USA). The cultured plates were maintained at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was extracted using TRIZOL reagent (Invitrogen). RNA concentration and quality were determined using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA), which calculates an RNA integrity number (RIN). Total RNA with A260/A280 = 1.8-2.0 and RIN >8.0 were selected. Intact RNA samples were normalized to 200 ng/μl with DEPC-treated H2O. Total 2μg RNA was used in microRNA library preparation.
The first step of microRNA library preparation involves 3’end ligation using a 5’ adenylated DNA adapter with a blocked 3’end. Using a truncated version of T4 RNA Ligase 2, the ATP-less reaction is driven by the adenylated group on the adapter, resulting in ligation to molecules with a 3’hydroxy group.  The second step of microRNA library preparation involves a 5’RNA adapter which is ligated to the 5’phosphate end of microRNA by T4 RNA Ligase 1. RNA molecules with a 5’phosphate are the only substrates for this ligation reaction.  The third step of microRNA library preparation involves annealing a reverse transcription primer to the 3’ligated adapter and extension. Then followed by PCR amplification using a pair of primers that add on Illumina flow cell binding sequences and barcodes. The final amplified small RNA library consists of approximately 120 bases of adapter sequence plus an insert of between 22 - 30 bases. Higher molecular weight products are removed by PAGE purification.  Single-read 75 nucleotide reads from each microRNA library were obtained using NextSeq500 (Illumina Inc., CIC bioGUNE, Bilbao, Spain).

treatment_protocol: MCF7 cells were incubated at 37°C in 5% CO2 and grown to 80-90% confluence before treatment. MCF7 were treated respectively with 4 mM lidocaine, 1 mM bupivacaine, or left untreated for 6 hours.

value: epithelial

value: treated with 4 mM lidocaine for 6 hours


title: MS3_NSC_1


title: MS2_NSC_3


title: B3_S6_R1_001

value: treated with 1 mM bupivacaine for 6 hours


title: C3_S3_R1_001

value: untreated


title: C2_S2_R1_001


title: MS2_NSC_2

value: NestinGFP mouse dentate gyrus


title: B1_S4_R1_001


title: Shank3_LSD1

city: Buffalo

first: Zhen

last: Yan

state: NY

address: 955 Main St

institute: SUNY Buffalo

description:
Neuronal nuclei
Shank3 +/∆C

data_processing:
For mapping, we used Bowtie2 method with default setting to map reads against the reference genome of mm10. Peak Calling was performed with MACS2 to generate the peak calling file for ChIP BAM and input BAM, with P value = 0.01 and extension of 140 bp. GO analysis was performed as described in RNA-seq section. To generate a bigWig database, we used bamCompare deepTools (https://deeptools.readthedocs.io/en/develop/index.html). This was performed on BAM alignment files using default settings. Bigwig files were visualized in IGV for further examination. These data were then analyzed with additional functions in deepTools packages, in which bigWig files were prepared in computeMatrix and plotted using plotHeatmap to generate the heatmap and plotprofile to TSS range, revealing peak enrichment around TSS regions in the mouse genome associated with H3K4me2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files

source_name: PFC

extract_protocol:
Cortical neuronal nuclei sorting and H3K4me2 ChIPseq were performed as previously described (Jiang et al., 2017; Kundakovic et al., 2017). Each sample was the cortex pooled from three mice in the same group. In brief, frozen brain tissue was placed in a douncer containing a hypotonic lysis solution and homogenized, followed by ultracentrifugation and resuspension of the nuclei pellet in 1 ml Dulbecco’s phosphate buffered saline (DPBS) containing 0.1% bovine serum albumin (BSA) and 1:1,000 anti-NeuN antibody (Alexa Fluor 488 conjugated, Millipore MAB377X). The nuclei were incubated for 45 minutes at 4°C, shielded from light. DAPI (1:1,000 dilution) was added to the nuclei prior to sorting. Nuclei were sorted into DPBS to separate NeuN+ and NeuN- populations, followed by pelleting for ChIP experiments. All sorting was done at the Flow Cytometry Center at Mount Sinai.
Immediately following nuclei sorting, NeuN+ and NeuN- populations were digested with MNase primarily into mononucleosomes. MNase digestion was stopped with 0.5M EDTA, and the sample was either placed on ice for further processing or frozen at -80C for further use. Next, the sample was treated with a hypotonic solution and mild detergent, and H3K4me2 antibody (Cat#ab7766, Abcam) was added for overnight incubation. H3K4me2 enriched genomic DNA was captured with Protein A/G magnetic beads (88803, Thermo Fisher Scientific), followed by a wash step, elution, and treatment with RNase A and Proteinase K. DNA was purified via phenol-chloroform extraction followed by ethanol precipitation.
Following ChIP, library preparation was done to prepare the enriched DNA for sequencing. The steps include: blunting DNA fragments, adding a 3' poly-A tail, ligation of barcoded adaptors, and PCR amplification of ligated DNA. The libraries were then run on an Agilent 2100 Bioanalyzer to check for fragment size. A successful library preparation consisted of a sharp 275bp fragment (150bp for the mononucleosome fragment length + 125bp for adaptor length). The sequencing was performed at the Genomics and Bioinformatics Core of State University of New York at Buffalo.

value: Prefrontal cortex

tag: genotype

value: Shank3 +/<delta>C

value: 6 weeks

value: H3K4me2 (Abcam ab7766)


title: L1_S7_R1_001


title: C1_S1_R1_001


title: MS2_NSC_1.2

value: 6-9 weeks

value: Neural stem cell


title: MS2_NSC_1.1


title: L2_S8_R1_001


title: MS1_NSC_3


title: MS3_NSC_2.2


title: MS1_NSC_2


title: Shank3_LSD1_1_PFC

description:
Total cell lysate (bulk)
Shank3 +/∆C

data_processing:
Sequencing was carried out with the HiSeq 2500 platform (Illumina).
Reads were first trimmed using Cutadapt to remove the 3’ end adapters and trailing sequences.
RNA-seq tags reads were aligned to the mouse RefSeq mRNAs using TopHat2 with default parameters. Alignments with a mapping score <10 were discarded using SAMtools.
FeatureCounts was used to generate a matrix of mapped fragments per USCS RefSeq known annotated gene, from which genes annotated by RefSeq as rRNA were discarded.
Analysis for differential gene expression was performed using the edgeR package with the default setting.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_featureCounts.txt: Tab-delimited text files include counts.

extract_protocol:
RNA extraction from PFC samples of biological duplicates in each group used the RNeasy Mini kit (Qiagen), coupled to an RNase-free DNase step (Qiagen). The strand-specific RNA sequencing libraries were generated from 1 μg purified RNA.
The RNA sequencing libraries were constructed by TruSeq stranded total RNA plus Ribo-zero kits (Illumina). Sequencing was carried out with the HiSeq 2500 platform (Illumina) at the Genomics and Bioinformatics Core of State University of New York at Buffalo.

value: 6-8 weeks


title: MS3_NSC_3


title: Shank3

description:
Neuronal nuclei
Shank3 +/∆C

value: Vehicle


title: WT

description: Neuronal nuclei

value: WT (C57BL/6 x C3H)


title: Csa02g073390_deM

value: Suneson

value: Mature plants

value: deMethylated


title: Shank3_veh_1_PFC

description:
Total cell lysate (bulk)
Shank3 +/∆C


title: MS3_IPC_3

value: Intermediate neural progenitor


title: B2_S5_R1_001

value: epithelial


title: Shank3_veh_2_PFC

description:
Total cell lysate (bulk)
Shank3 +/∆C


title: MS3_IPC_1.2


title: MS3_NSC_2.1


title: WT_veh_2_PFC

description: Total cell lysate (bulk)


title: MS2_IPC_3.1


title: MS3_IPC_1.1


title: MS2_IPC_3.2


title: WT_veh_1_PFC

description: Total cell lysate (bulk)


title: MS1_NSC_1


title: MS2_IPC_2.1


title: MS1_IPC_3.1


title: MS1_IPC_3.2


title: MS1_IPC_2


title: MS2_IPC_1


title: MS2_IPC_2.2


title: SARAF KO rep#2

city: Rehovot

first: Eitan

last: Reuveny

state: Please Select

address: Dept. Biomolecular Sciences, 234 Hertzl St.

country: Israel

institute: Weizmann Inst. of Science

data_processing:
Sequenced reads were mapped to the Mus musculus genome version GRCm38, using TopHat v2.0.10.
Genes were identified using a gtf obtained from Ensembl release 82. Per gene, reads were counted using HTSeq.
Normalization of read counts and P-values for differentially expressed genes were computed using DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: DE2output

source_name: Embryonic fibroblasts

growth_protocol: E14.5 embryos were dissected, and their trunks were extracted into cold PBS. Trunks were finely minced using a razor until they were pipettable. Cells were suspended in 3ml trypsin-EDTA 0.05%, at 37C for 10 min. Cells were flushed through 21g (3ml) syringe three times, and double serum levels blocked trypsin. Next, cells were centrifuged at 1800rpm for 5 min, and the pellet re-suspended in 8ml of MEF media, containing 10% fetal calf serum, 2% Penstrep, 1% L-glutamine, and 1% sodium pyruvate. Cells from each embryo were plated on a 100mm dish coated with 0.1% gelatin. Cells were split 1:4 and frozen when they reached confluence.

extract_protocol:
Total RNA was extracted from the indicated cell cultures using the RNeasy kit (QIAGEN). Then, RNA integrity was evaluated on Bioanalyzer (Agilent 2100 Bioanalyzer), requiring a minimal RNA integrity number (RIN) of 8.5.
Libraries were prepared according to Illumina’s instructions accompanying the TruSeq RNA Sample Preparation Kit v2 (cat # RS-122–2001).

tag: strain background

value: SARAF KO

value: Embryonic fibroblasts


title: SARAF KO rep#3


title: SARAF KO rep#1


title: MS1_IPC_1

value: NestinGFP mouse dentate gyrus


title: AA_6

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

data_processing:
The Illumina base call raw data were converted in fastq files through the bcl2fastq software (version v2.20.0.422, Illumina). The sequence reads were trimmed using the Cutadapt software to reduce the reads length from 600 bp to 350 bp. The custom reference sequence was built by predicting the NHEJ-mediated integration in the locus of interest. The cleaved donor DNA sequence was inserted between the -3 and -4 bases of the gRNA sequence. All sequencing reads were aligned with their respective reference sequence using the BWA-SW(MIT, Boston, MA, USA).
Genome_build: HITI_alb_RHO_reference
Supplementary_files_format_and_content: compressed binary allignment results (bam)

growth_protocol: Mice were housed at TIGEM animal house (Pozzuoli, Italy) and maintained under a 12 hours light/dark cycle. Animals were raised in accordance with the Institutional Animal Care and Use Committee (IACUC) guidelines for the care and use of animals in research.

extract_protocol:
Conventional lysis buffer [400mM NaCl, 1% SDS, 20mM TRIS-CL pH 8.0, 5mM EDTA (pH 8.0)] was used for DNA extraction from temporal retina and liver. Lysis buffers were supplemented with proteinase K, which was inactivated after lysis for 15 minutes at 80℃. DNA extracted from one retina or one liver was used for PCR amplification of HITI junctions. Both 5’and 3’ junctions of integration were amplified. The following primers were used:  mRho HITI 5’ junction Fwd: 5'-TTGGTCTCTGTCTACGAAGAGCC-3'  mRho HITI 5’ junction Rev: 5'-GGCTTGATGACGTTCTCAGTGC-3'  mRho HITI 3’ junction Fwd: 5'-CGACCTGCAGAAGCTTGGATCT-3'  mRho HITI 3’ junction Rev: 5'-GGGCCCAAAGACGAAGTAGCC-3'  mAlb HITI 5’ junction Fwd: 5’-GCCTGCTCGACCATGCTATACT-3’  mAlb HITI 5’ junction Rev: 5’-CCTTGGAGCCGTACTGGAACTG-3’  mAlb HITI 3’ junction Fwd: 5’-CGACCTGCAGAAGCTTGGATCT-3’  mAlb HITI 3’ junction Rev: 5’-TCTCTGGCTGCCACATTGCT-3’  PCR products were cloned into PCR-Blunt II-TOPO (Invitrogen) and single clones were sequenced to confirm the identity of the PCR products before next-generation sequencing (NGS) analysis.
For NGS library preparation, 10 ng of DNA from the PCR products were used as input for the NEBNext® UltraTM II DNA Library Prep Kit for Illumina (New England Biolabs).
The libraries were sequenced on a MiSeq sequencing system using a v3, 600 cycles flow cell (Illumina, San Diego, USA). The Illumina base call raw data were converted in fastq files through the bcl2fastq software (version v2.20.0.422, Illumina).

treatment_protocol: For the retina, surgery was performed under general anesthesia, and all efforts were made to minimize animal suffering. C57BL/6J mice were anesthetized with an intraperitoneal injection of 10 μL/gr of body weight of ketamine (10 mg/Kg) combined with medetomidine (1mg/Kg), then AAV8 vectors were delivered subretinally via a trans-scleral transchoroidal approach, as described by Liang et al [82]. Eyes were injected with 0,7-1 μL of vector solution. For the liver, the injections were performed under general anesthesia, as described above. C57BL/6J mice were injected at post-natal (p)1-p2 through the temporal vein following the protocol published by Gombash Lampe et al. The total volume of injection was 40 µl.

value: retina


title: MS3_IPC_2


title: AA_5


title: Shank3_LSD1_2_PFC

description:
Total cell lysate (bulk)
Shank3 +/∆C

value: Prefrontal cortex

value: Shank3 +/<delta>C


title: H2O2_single-cells

data_processing:
10X single-cell reads were demultiplexed using cellranger (v3.1.0) mkfastq using default parameters
Demultiplexed fastq files were then grouped by cellbarcode, UMI collapsed, aligned, and analyzed using cellranger (v3.1.0) count using default parameters
Basecalls performed using Casava 1.8.2
Reads were trimmed using AdapterRemoval v2.2.0 to remove sequencing adapters
Reads were aligned against the human decontaminome using HISAT2 v2.0.6 using default parameters
Unaligned deconaminome reads were aligned against the human genome using HISAT2 v2.0.6 using default parameters
Reads were quantified using Subread FeatureCounts using GENCODE release M14
Genome_build: GRCh38
Supplementary_files_format_and_content: TSV Counts (vehicle and H2O2 treated) tables generated using Subread FeatureCounts, Unfiltered; Seurat v3.1.0 was used to post-process 10X generated counts table using default workflow: Transcripts present in less than 5 cells were filtered out; Cells with less than 200 or greater than 2500 transcripts were filtered out; Cells with more than 5% mitochondrial counts were filtered out; The resulting counts table was log-normalized; Cells in resulting counts table were ordered by cluster according to Seurat's default clustering algorithm with parameters reduction = 'pca', dims=1:10, and resolution = 0.5

source_name: Cultured adult dentate gryus NSCs

growth_protocol: Grown on poly-d-lysine laminin coated plates in neurobasal A media with 1x B27 (without vitamin A), 1 x glutaMAX, 20 ng/ml recombinant epidermal growth factor and 20 ng/ml basic fibroblast grwoth factor. Mice were all housed in standard vivarium ventillated cages with ad libitum food and water, 12h light cycle

extract_protocol:
Cells from two female and one male adult NSPC cultures were harvested with accutase and resuspended and washed in HBSS before making a mixed sample with equal numbers from culture for input to 10x genomics chip as per manufacturer instructions.
10X Genomics 3’ RNA-seq library was sequenced using paired-end 150bp approach on an Illumina HiSeq 4000 sequencer. CellRanger v3.0.2 (Zheng et al., 2017) was used to demultiplex, align, and deduplicate sequencing reads in BCL files. Single-cell data in feature-barcode matrices were then processed using Seurat v3.0.1’s default pipeline (Butler et al., 2018) to identify unsupervised cell clusters and generate a t-Distributed Stochastic Neighbor Embedding (t-SNE) plot. Seurat’s feature expression analysis was used to visualize genes markers known to be expressed in cell populations displayed in the t-SNE plot.

treatment_protocol: 24h with 500 uM H2O2

tag: passage


title: AA_2

value: liver


title: AA_1


title: GO_3c: MZ-54 STAT3-KO#3c

city: Leipzig

first: Knut

last: Krohn

address: Philipp-Rosenthal-Straße 55

department: Medizinische Fakultät

institute: University Leipzig

data_processing:
Basecalls and Demultiplexing was performed using bcl2fastq v2.20.0.422 (Illumina)
Raw read were adapter trimmed with cutadapt version 1.9.1.
RNA seq reads were aligned to the GRCm38/GRCh38 genome assembly using Bowtie2 version 2.2.7 allowing 1 mismatch and alignment to multiple targets
Further processing was done using Tophat and Cufflinks
Genome_build: GRCh38
Supplementary_files_format_and_content: text (cufflinks-output)
Supplementary_files_format_and_content: Processed data files contain raw counts, DESeq and EdgeR normalised counts als labelled

source_name: Human glioblastoma cell line

growth_protocol: cells were grown until they reached sufficient confluency and were subjected to RNA isolation

extract_protocol:
Total RNA extraction was performed based on TRIZOL according to the Manufacturer`s standard protocol.
Libraries were prepared using the Ovation Human FFPE RNA-Seq Library Systems (Nugen) according to the instructions of the manufacturer. Purification and quantification of barcoded libraries were performed using the Library quantification kit - Illumina/Universal.

treatment_protocol: untreated

value: glioblastoma


title: GO_3a: MZ-54 STAT3-KO#3a


title: GO_3b: MZ-54 STAT3-KO#3b


title: 10pgH2O2-2

growth_protocol: Grown on poly-d-lysine laminin coated plates in neurobasal A media with 1x B27 (without vitamin A), 1 x glutaMAX, 20 ng/ml recombinant epidermal growth factor and 20 ng/ml basic fibroblast growth factor. Mice were all housed in standard vivarium ventillated cages with ad libitum food and water, 12h light cycle

extract_protocol:
Approximately 30,000 cells from two female and two male adult NSPCs cultures were harvested with accutase and washed with HBSS before RNA was isolated from pelleted cells with the Clontech Nucleospin RNA XS Plus isolation kit (Takara 740990.10) per manufacturer protocol. RNA quality and quantity was assessed with a Qubit RNA HS assay kit (Invitrogen). All cultured samples used had a RIN value of 10.
Libraries were generated with the Clontech HT kit . Purified library products were then used in HiSeq 4000 paired-end sequencing (Illumina) to a depth of 15 - 20 million 2x150 bp clusters.

treatment_protocol: 24h with veh (water) or 500 uM H2O2

value: Cultured adult dentate gryus NSCs

value: 6-9 weeks

tag: rna input


title: 10pgCon-1

value: veh


title: 10pgCon-3


title: GO_2c: MZ-54 STAT3-KO#1c


title: GO_2b: MZ-54 STAT3-KO#1b


title: 10pgCon-2


title: 100pgH2O2-3


title: Rag2-/-_MC57-SIY_CD45+_day 7

city: Cambridge

first: Ellen

last: Duong

state: MA

address: 500 Main Street, 76-401

department: Koch Institute for Integrative Cancer Research; Biology Department

institute: Massachusetts Institute of Technology

data_processing:
Demultiplexing, mapping to the mm10 genome, and barcode and UMI counting were performed with 10X Genomics Cell Ranger v3.0.1. The resultant raw counts matrix was loaded into Seurat v2.3.4 for further processing. Cells expressing less than 200 genes or more than 6000 genes, as well as cells expressing more than 25% mitochondrial transcripts were excluded. The data was normalized using the Seurat LogNormalize function with the default scale factor of 10^4. Reported normalized counts were extracted from the data slot of the Seurat object.
Genome_build: mm10
Supplementary_files_format_and_content: CSV file with normalized, log-transformed matrix from Seurat v2.3.4
Supplementary_files_format_and_content: CSV file with raw counts matrix from CellRanger v3.0.1 mat2csv

source_name: live CD45+ immune cells from subcutaneous MC57-SIY tumors from Rag2-/- hosts

growth_protocol: MC57-SIY tumor cells were passaged under sterile, standard cell culture conditions.

extract_protocol:
At day 7, tumors were harvested and enzymatically dissociated into a single cell suspension. Live CD45+ cells were FACS-sorted from the dissociated tumor cell suspension.
cDNA libraries were prepared using the 10X Genomics Chromium Single Cell 3' Reagent Kits v2 following manufacturer's instructions.  The libraries were sequenced with an Illumina HiSeq2000.
scRNA-seq (10X Genomics)

treatment_protocol: All mice were housed in specific-pathogen free cages and given free access to food and water ad libitum. MC57-SIY tumor cells were implanted s.c. into flanks of Rag2-/- C57BL/6 mice and grown for 7 days.


title: 100pgH2O2-2


title: GO_1c: MZ-54 Wtc


title: GO_2a: MZ-54 STAT3-KO#1a


title: 100pgH2O2-1


title: Input_1963

city: Chicago

first: Lu

last: Wang

state: Illinois

address: 303 E. Superior Street Simpson Querrey 7-414

department: Biochemistry and Molecular Genetics

institute: Northwestern University

description: normal cells

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
ChIP-seq ATAC-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9 and STAR version 2.5.2.  Only uniquely mapping reads with at most two mismatches were retained.
ATAC-seq reads were aligned to UCSC hg19 using BWA version 0.7.12. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

growth_protocol: cells were maintained with DMEM (Gibco, Gaithersburg, MD) or ATCC-formulated RPMI-1640 medium  containing 10% FBS (Sigma)

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit. For ATAC-seq, frozen cells were thawed and washed once with PBS and then resuspended in 500 uL of cold ATAC lysis buffer. The cell number was assessed by Cellometer Auto 2000 (Nexcelom Bioscience). 50K to 100K nuclei were then centrifuge (pre-chilled) at 500 g for 10 min. Supernatant was then removed and the nuclei were resuspended in 50 uL of tagmentated DNA by pipetting up and down six times. The reactions were incubated at 37 °C for 30 min in a thermomixer shaking at 1,000 rpm, and then cleaned up by the MiniElute reaction clean up kit (Qiagen).
ChIP-seq: ChIP-sequencing libraries were prepared using KAPA HyperPrep Kit (Kapa Biosystems) following manufacturer’s recommendation. In brief, 500ng of input DNA sheared by Covaris LE220 ultrasonicator or 10 ng of immunoprecipitated DNA was end-repaired and 3'-dA tailed. Adapter was then ligated to the DNA, and ligated product was PCR amplified and cleaned up using SPRIselect Reagent (Beckman Coulter). for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit
RNA-seq: Paramagnetic beads coupled with oligo d(T) are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual. Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendation (NEBNext® Ultra™ II RNA Nondirectional Library Prep Kit for Illumina®). The first strand is synthesized with the Protoscript II Reverse Transcriptase with an longer extension period (40 minutes for 42◦C). All remaining steps for library construction were used according to the NEBNext® Ultra™ II RNA Nondirectional Library Prep Kit for Illumina®. Illumina 8-nt dual-indices were used. Samples were pooled and sequencing on a HiSeq with a read length configuration of 150 PE.
ATAC-seq: Tagmentated DNA was amplified with barcode primers. Library quality and quantity were assessed with Qubit 2.0 DNA HS Assay (ThermoFisher, Massachusetts, USA), Tapestation High Sensitivity D1000 Assay (Agilent Technologies, California, USA), and QuantStudio® 5 System (Applied Biosystems, California, USA). Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® HiSeq (Illumina, California, USA) with a read length configuration of 150 PE for 50M PE reads (25M in each direction) per sample.

treatment_protocol: Cells were treated with either DMSO or HDAC1/2 inhibitor MERCK60 or EZH2 inhibitior GSK126 for 24 to 96 hours.

value: small cell lung cancer

tag: passages

value: Low passages (6-10)

value: wild type


title: 100pgCon-3


title: GO_1b: MZ-54 Wtb


title: 100pgCon-2


title: GO_1a: MZ-54 Wta


title: 10pgH2O2-3


title: YMR_30d_2

city: Shenyang

first: Hongyan

last: Qi

state: Liaoning

address: No.120 Dongling Road, Shenhe District

department: College of Horticulture

country: China

institute: Shenyang Agricultural University

data_processing:
The high-quality pair-end reads of melon for each sample were mapped to the melon reference genome by HISAT2, then used HTseq-count to get the raw gene expression readcount.
Genome_build: Cucumis_melo.Melonv4.49
Supplementary_files_format_and_content: TXT, Gene expression raw read count number

organism: Cucumis melo

source_name: oriental melon

extract_protocol:
The samples of two cultivars oriental melon fruits were collected and frozen in liquid nitrogen. The tatal RNA was extracted using Trizol reagent and checked its integrity. The qualified RNA was used to construct cDNA libraries.
cDNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: fruit

value: anthesis after 30 days

value: YMR-WF


title: YMR_30d_1

tag: developmental stage


title: YMR_35d_2

value: anthesis after 35 days


title: YMR_25d_3

value: anthesis after 25 days


title: YMR_35d_3


title: YMR_35d_1


title: 10pgH2O2-1

tag: treatment


title: Aged_PGE2_Rep_3

city: Stanford

first: Helen

last: Blau

address: 269 Campus Dr.

institute: Stanford University

data_processing:
Illumina Casava1.7 software used for basecalling.
STAR read mapping
RSEM
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files raw counts values for each Sample

source_name: Muscle stem cell

growth_protocol:
CD45-Sca1-CD31-CD11b-alpha7Integrin+CD34+ stem cells were isolated by FACS from hindlimb muscles of 2-4 mo or 24 mo old C57BL6 mice
20% FBS/40% Low Glucose DMD/40% F-10

extract_protocol:
Qiagen RNAeasy Micro Kit
NuGEN Ovation v2 cDNA amplification, Illumina RNASeq v2 Library construction

treatment_protocol: Prostaglandin E2 treatment (10 ng/ml) in culture for 24 hr

value: muscle

value: 24 month old


title: YMR_25d_1


title: YMR_15d_3

value: anthesis after 15 days


title: Aged_PGE2_Rep_2


title: YMR_15d_2


title: YMR_15d_1


title: 100pgCon-1


title: 1ngH2O2-3


title: Aged_PGE2_Rep_1


title: 1ngH2O2-2


title: Young_PGE2_Rep_3

value: 2-4 month old


title: YMR_5d_3

value: anthesis after 5 days


title: YMR_5d_2


title: YMR_5d_1


title: 1ngH2O2-1


title: YMR_30d_3


title: Young_PGE2_Rep_2


title: HDB_35d_2

value: HDB-OF


title: 1ngCon-3

value: Cultured adult dentate gryus NSCs


title: HDB_30d_3


title: 1ngCon-2

value: 6-9 weeks


title: Young_PGE2_Rep_1


title: YMR_25d_2


title: HDB_25d_3


title: 1ngCon-1

value: veh


title: HDB_30d_2


title: HDB_25d_2


title: NAM B2

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

data_processing:
Basecalling (bcl2fastq v2.20.0.422)
QC (FASTQC v0.11.8, Picard v2.21.1, Samtools v1.9, Preseq v2.0.3, RseQC v3.0.1, edgeR v3.26.5, Qualimap v2.2.2-dev)
Trimming and alignment (Cutadapt v2.5, STAR v2.6.1.d)
Counting hit counts and transcripts (featureCounts v1.6.4, StringTie v2.0)
Differential gene expression (DESeq2 v1.22.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited file (txt) for raw hit counts

source_name: Non Alveolar Mac Nb D14

growth_protocol: Alveolar macrophages were prepared from whole lung lysates from Cx3cR1-CreER x Rosa26-tandem dimer Tomato(TdT) control and infected mice were sort-purified on live CD45+CD64+F4/80+CD11c+SiglecF+ and then sorted based on expression of TdT

extract_protocol:
RNA was extracted using the RNeasy Plus Micro Kit (catalog no. 74034; QIAGEN)
Illumina-compatible libraries were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (catalog no. E7645S; New England BioLabs) and sequenced using an Illumina NextSeq 550 in a single-end 75-base pair (bp) read configuration.

treatment_protocol: All mice were administered tamoxifen (75mg/kg) on days -1 and +1 day after Nb inoculation.


title: NAM B5


title: HDB_30d_1


title: HDB_15d_3


title: NAM B1


title: GPx2KD

city: Bronx

first: Rachel

last: Hazan

address: 1300 Morris Park Avenue

department: Pathology

institute: Albert Einstein College of Medicine

data_processing:
The unfiltered gene-barcode matrix for each sample were imported into R 3.6.1 and were converted into SingleCellExperiment (SCE) objects
Cells passing QC were proceeded to normalization using the SCTransform pipeline in Seurat 3.1.1.
Seurat 3.1.1 was used for further quality control and preprocessing of the exported SCE objects
using the integration pipeline in Seurat with the genes commonly retained between control and GPx2sh tumors serving as integration anchors
Principal component analysis was performed to enable unsupervised clustering on the integrated data from control and GPx2sh tumors, and clustered cells were projected in two dimension using Uniform Manifold Approximation and Projection (UMAP) for cluster visualization
Genome_build: mm9
Supplementary_files_format_and_content: cluster data and Cell Ranger output

source_name: Mammary gland tumor cells

growth_protocol: We labeled mammary gland tumor cells with GFP in vitro and then injected into mammary fat pad for incubating 45 days. We then generated single cell suspension by FACS sorting.

extract_protocol:
The cells were pre-labelled with eGFP in vitro before injection into mammary fat pad. The suspension cells were then sorted using a FACSAria II (BD Biosciences). Chromium Single Cell 3ʹ protocol was used for generating Single Cell 3ʹ Gene Expression libraries from single cells.
Library preparation for 10X Genomics v3 chemistry was performed following the Chromium Single Cell 3ʹ protocol  for generating Single Cell 3ʹ Gene Expression libraries from single cells.

treatment_protocol: Use GPx2 shRNA to knock down GPx2 expression in cells

value: Mouse derived Mammary gland tumor cells

value: a mixed Bl6/129S/FVB/N background

value: GPx2 shRNA


title: HDB_25d_1

value: fruit


title: NTtumor

value: Untreated


title: HDB_15d_2


title: TdT PlusB4

source_name: Monocyte derived Alveolar Mac Nb D14

value: Tdt+ Alveolar macrophages (CD45+CD64+F4/80+CD11c+SiglecF+)


title: HDB_15d_1


title: HDB_5d_3


title: HDB_5d_2


title: HDB_35d_3

value: anthesis after 35 days


title: [Standard curve] Input WT 100% #3

city: Sapporo

first: Yoshikazu

last: Furuta

address: North 20 West 10, Kita-ku

institute: Hokkaido University

description:
DNA-seq
plasmid DNA
1_standard_curve_counts.txt

data_processing:
Basecalls were performed using Guppy 5.0.11 using dna_r9.4.1_450bps_sup.cfg as a DNA model.
Mapping to the genomic sequence of COL7A1 (RefSeq Accession # NC_000003.12:c48595302-48564073) using minimap2 2.16-r922.
Information of reads mapped to both loci of the mutations (19630th base of the reference for c.5932C>T, 27712th base for c.8029G>A) was extracted using samtools.
Supplementary_files_format_and_content: Count of haplotype of each read.

organism: Escherichia coli

source_name: Plasmid PCR fragment

extract_protocol:
gDNA was extracted from the epidermis, dermis, or peripheral blood by the Puregene Blood Core Kit (Qiagen, Valencia, CA, USA).
Libraries were constructed using Ligation Sequencing Kit SQK-LSK109 and Native Barcoding Expansion kit EXP-NBD104 and EXP-NBD114 (Oxford Nanopore Technologies). gDNA was treated with Quick Calf Intestinal Phosphatase and Cas9 before library construction for Nanopore Cas9-targeted sequencing (nCATS).

tag: sample type

value: Plasmid


title: TdT PlusB2


title: TdT PlusB3


title: [Standard curve] Input WT 100% #1


title: HDB_5d_1


title: HDB_35d_1


title: TdT B3

source_name: Tissue Resident Alveolar Mac Nb D14

value: Tdt- Alveolar macrophages (CD45+CD64+F4/80+CD11c+SiglecF+)


title: TdT B2


title: [Standard curve] Input WT 75% #2


title: [Standard curve] Input WT 75% #3


title: [Standard curve] Input WT 50% #3


title: TdT B1


title: RSC2

first: Ken

last: Kadoya

address: Kita-15, Nishi-7, Sapporo

data_processing:
Total RNA integrity was checked using an Agilent Technologies 2100 Bioanalyzer with an RNA Integrity Number (RIN) value greater than or equal to 7.
Read quality was checked for each sample using FastQC v0.11.2.
High-quality reads were then imported into TopHat v2.1.0 for alignment into BAM files.
BAM files were imported into the Cufflinks v2.2.1, and FPKM counts were calculated.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Rattus norvegicus

source_name: Repair Schwann cell from adult rat

extract_protocol:
SCPs were prepared from bilateral sciatic nerves and brachial plexus of E14 embryos which were harvested from time-mated pregnant females. RSCs were prepared from distal segments of transected sciatic nerves of 10 week old rats. After enzymatic dissociation, RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: LEWIS

value: Sciatic nerve

value: 10 weeks old

value: 1 week after nerve cut

value: wild type


title: RSC3


title: SCP3

source_name: Schwann cell precursor from E14 rat

value: Sciatic nerve and brachial plexus

value: Embryonic day 14


title: [Standard curve] Input WT 75% #1


title: SCP2


title: RSC1


title: SCP1


title: [Standard curve] Input WT 50% #2


title: [Standard curve] Input WT 50% #1


title: [Standard curve] Input WT 100% #2


title: NAM A4

source_name: Non Alveolar Mac Nb D7


title: NAM A3


title: ahl13 DC3000 rep2

city: 福州市

first: baomin

last: Feng

state: 福建省

address: 福建农林大学, 上下店路15号， 诚智楼C4层

institute: 福建农林大学

data_processing:
Adapters filtered with fastp parameters：-q 10 -u 50 -y -g -Y 10 -e 20 -l 100 -b 150 -B 150
Filter rRNA，mRNA: 0.1, use soap comparison：soap -a 1.fq.gz -b 2.fq.gz -D
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Use TopHat2 to map reads to Arabidopsis genome, and Cufflinks to splice transcripts and expression quantitation.
Gene anotation was done by comparing with annotated Arabidopsis genome and BLAST with other databases.
Differential gene expression was analyzed by using DESeq
Supplementary_files_format_and_content: Excel table include FPKM and count values for each sample

organism: Arabidopsis thaliana

source_name: leaf (4-week)

growth_protocol: Plants were germinated on 1/2 MS plates and grown under short-day conditions (8 hrs light/16hours dark, 75 uE/m-2s-1). For DC3000 inoculation, plants were grown in soil for 4 weeks under short-day conditions too.

extract_protocol:
Seedlings or leaves were flash-frozen in liquid nitrogen and total RNA extracted with Trizol reagent. VAHTS mRNA-seq V3 Library Prep Kit for Illumina was used with  1ug of total RNA to construct sequencing libraries.
RNA libraries were constructed using standard Illumina protocols

treatment_protocol: The PstDC3000 (OD600=0.0005) was used to inoculate leaves of 4-week-old Arabidopsis plants, and samples were collected after 3 days post inoculation. 10-day-old seedlings on 1/2 MS plates were treated with 100nm flg22 for 1 hour before harvesting for RNA extraction.

tag: ecotype

value: pstDC3000, 3dpi


title: [Standard curve] Input WT 25% #3

growth_protocol: A 4 or 5 mm punch biopsy was performed on a patient's clinically revertant skin spots that did not show any skin fragility via manual rubbing. Adjacent non-revertant skin samples were also obtained.


title: ahl13 DC3000 rep1

address: 福建农林大学, 上下店路15号， 诚智楼C4层


title: [Standard curve] Input WT 25% #1


title: NAM A2


title: [Standard curve] Input WT 10% #3


title: [Standard curve] Input WT 10% #2


title: Col-0 DC3000 rep2

address: 福建农林大学, 上下店路15号， 诚智楼C4层

value: WT


title: [Standard curve] Input WT 1% #3


title: Col-0 DC3000 rep1

address: 福建农林大学, 上下店路15号， 诚智楼C4层


title: [Standard curve] Input WT 10% #1


title: TdT PlusA4

source_name: Monocyte derived Alveolar Mac Nb D7


title: ahl13 flg22 rep1

address: 福建农林大学, 上下店路15号， 诚智楼C4层

source_name: Seedling (10-day)


title: TdT PlusA5


title: [Standard curve] Input WT 0.1% #3


title: [Standard curve] Input WT 1% #2


title: ahl13 rep1

address: 福建农林大学, 上下店路15号， 诚智楼C4层


title: [Standard curve] Input WT 0.1% #2


title: TdT A5

source_name: Tissue Resident Alveolar Mac Nb D7


title: Col-0 flg22 rep2

address: 福建农林大学, 上下店路15号， 诚智楼C4层


title: [Standard curve] Input WT 1% #1


title: TdT PlusA2


title: TdT A1


title: [Standard curve] Input WT 0% #1


title: [Standard curve] Input WT 0% #2


title: [Standard curve] Input WT 0% #3


title: Col-0 flg22 rep1

address: 福建农林大学, 上下店路15号， 诚智楼C4层


title: [Standard curve] Input WT 0.1% #1


title: [Standard curve] Input WT 25% #2


title: AMS N5

source_name: Naive Alveolar Mac


title: Col-0 rep2

address: 福建农林大学, 上下店路15号， 诚智楼C4层


title: Col-0 rep1

address: 福建农林大学, 上下店路15号， 诚智楼C4层


title: C2 PBL

city: Houston

first: John

middle: William

last: Lindsey

state: TX

address: 6431 Fannin St, Ste 7.044 MSB, Neurology Dept

institute: University of Texas Health Science Center At Houston

description: healthy control, peripheral blood leukocytes

data_processing: FPKM

source_name: peripheral blood leukocytes

growth_protocol: stimulate with antigen for 6 days

extract_protocol:
Takara NucleoSpin RNA XS
Takara SMARTer Stranded Total RNA-Seq kit v2-Pico Input Mammalian

treatment_protocol: either brain antigens or influenza used for stimulation

tag: condition

value: healthy


title: C1 PBL


title: C3 PBL


title: M5 PBL

description: MS patient, peripheral blood leukocytes

value: MS


title: AMS N4

tag: cell type


title: M4 PBL

description: MS patient, peripheral blood leukocytes


title: M3 PBL

description: MS patient, peripheral blood leukocytes


title: AMS N2


title: LP 39, ruxolitinib

city: Rochester

first: Chantal

last: McCabe

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

data_processing:
Illumina Casava software used for basecalling.
We aligned the reads to the NCBI Build 38 reference genome (hg38) using MAPRSeq 3.0. Gene expression levels were obtained for 39,436 genes/transcripts annotated in the RefSeq database.
Genome_build: NCBI Build 38 reference genome (hg38)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: #2 L ANTER THIGH RESPONSIVE

growth_protocol: Patient samples

extract_protocol:
The Frozen samples are treated with Qiazol which is for RNA extraction through Qiagen Kit processing.  The Kit that is used is Qiagen miRNeasy Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Fresh frozen tissue

value: skin

tag: disease state

value: cutaneous lichen planus (LP)

value: ruxolitinib

tag: time

value: Week 4

tag: phenotype

value: R


title: M2 PBL

description: MS patient, peripheral blood leukocytes


title: LP 35, ruxolitinib

source_name: #2 L FOREARM RESPONSIVE


title: WT_MC57-SIY_ISG+ DC_day 7_r2

data_processing:
Paired-ended 38mer RNA-seq reads were pre-processed to trim five low-quality read positions from the second read (R2) of each pair, using the FASTX-Toolkit (Hannon Lab, CSHL). Reads were then mapped to the USCC mm9 mouse genome build (genome.ucsc.edu) using Bowtie v1.2.3 (Langmead, Trapnell, Pop, & Salzberg, 2009) and gene counts were quantified using RSEM v1.3.1 (Li & Dewey, 2011).
Genome_build: mm9
Supplementary_files_format_and_content: Estimated_counts_from_rsem.csv: CSV file with raw estimated read counts per gene per sample from RSEM v1.3.1.

source_name: sorted ISG+ DC from subcutaneous MC57-SIY tumors from WT hosts

extract_protocol:
At day 7, tumors were harvested and enzymatically dissociated into a single cell suspension. Live CD103+ DC1 and ISG+ DC were FACS-sorted from the dissociated tumor cell suspension.
cDNA libraries were prepared using the Clontech SMARTer Stranded Total RNAseq Kit - Pico Input (Clontech ZapR). The libraries were sequenced with an Illumina NextSeq 500.

treatment_protocol: All mice were housed in specific-pathogen free cages and given free access to food and water ad libitum. MC57-SIY tumor cells were implanted s.c. into flanks of WT or Rag2-/- C57BL/6 mice and grown for 7 days. Two independent replicate experiments were performed for each sample.

value: sorted ISG+ DC

value: from d7 tumor


title: C3 flu

description: healthy control, T cells specific for influenza

source_name: cultured T lymphocytes


title: C2 flu


title: LP 34, ruxolitinib

source_name: #1 R THIGH RESPONSIVE


title: WT_MC57-SIY_ISG+ DC_day 7_r1


title: C1 flu


title: LP 31, ruxolitinib

source_name: #2 L SHIN RESPONSIVE


title: TdT A3

value: Tdt- Alveolar macrophages (CD45+CD64+F4/80+CD11c+SiglecF+)


title: Rag2-/-_MC57-SIY_ISG+ DC_day 7_r3

source_name: sorted ISG+ DC from subcutaneous MC57-SIY tumors from Rag2-/- hosts


title: M3 flu

description: MS patient, T cells specific for influenza


title: Rag2-/-_MC57-SIY_ISG+ DC_day 7_r2


title: M2 flu


title: LP 27, ruxolitinib

source_name: #1 L LOWER ABD RESPONSIVE


title: M1 flu


title: Rag2-/-_MC57-SIY_CD103+ DC1_day 7_r3

source_name: sorted CD103+ DC1 from subcutaneous MC57-SIY tumors from Rag2-/- hosts

value: sorted CD103+ DC1


title: LP 22, ruxolitinib

source_name: # 2L WRIST RESPONSIVE


title: Vitamin C, replicate 2

city: Vilnius

first: Kotryna

last: Kvederaviciute

address: Sauletekio av. 7

department: Life Sciences Center

country: Lithuania

institute: Vilnius University

data_processing:
Reads quality was checked using FASTQC and reads were trimmed using BBDUK from BBMAP packages according to manufacturers recommendations (parameters: ktrim=r k=23 mink=11 hdist=1 minlength=50 maxns=1 tpe tbo qtrim=r trimq=15).
Data was mapped using hisat2 (parameters :—no-unal --no-mixed --no-discordant --rna-strandness FR —dta), deduplicated using samtools. StringTie2 was used to evaluate gene expression and get TPM counts (parameters -e -B -A)
Genome_build: V2
Supplementary_files_format_and_content: tab-delimited text files include geneID, gene name, reference ID, gene strand, start, end, coverage, FPKM and TPM values.

organism: Laccaria bicolor

source_name: Mycelium

growth_protocol: Mycelium culture was maintained at 25°C in the dark on solid (2% agar) modified Pachlewski medium (10 g/L glucose, 3 g/L malt extract, 0.25 g/L (NH4)2SO4, 0.5 g/L KH2PO4, 0.15 g/L MgSO4·7H2O, 0.05 g/L CaCl2, 0.025 g/L NaCl, 0.0012% FeCl3, 100 mg/L thiamine, 2.3 mg/L ZnSO4·7H2O, 8.5 mg/L H3BO3, 0.5 mg MnCl2·4H2O, 0.6 mg/L CuSO4·5H2O, 0.4 mg/L (NH4)2MoO4). For nucleic acid extraction, mycelium was collected after 8 weeks from a liquid medium inoculated with a small amount of mycelium from agar plates.

extract_protocol:
RNA was extracted using RNAzol® RT Reagent (MRC) according to recommendations of the vendor, treated with DnaseI (Thermo Scientific) as recommended by the vendor and >200 nt fraction was purified using RNA clean and concentrator-5 kit (Zymo research). Then, ribosomal RNAs were depleted using Ribo-Zero Gold rRNA Removal Kit (Yeast, Illumina) according to recommendations of the vendor, and >200 nt fraction was purified using RNA clean and concentrator-5 kit (Zymo research).
Collibri Stranded RNA Library Prep Kit (Invitrogen™) for Illumina was used to prepare the libraries.

treatment_protocol: For vitC treatment, mycelium was incubated with 5 mM vitC for 2 days.

tag: strain

value: Orton S238N-H82

value: vitamin C


title: Rag2-/-_MC57-SIY_CD103+ DC1_day 7_r2


title: Vitamin C, replicate 1


title: LP 21, ruxolitinib

source_name: #1 R WRIST RESPONSIVE


title: C2 brain

description: healthy control, T cells specific for brain


title: LP 16, ruxolitinib

source_name: #1 L BUTTOCK RESPONSIVE


title: C1 brain


title: Untreated, replicate 2

value: untreated


title: Young IFTKO 2

first: Peter

middle: K

last: Jackson

address: 279 Campus Dr., CCSR 3230

data_processing:
bcbio-nextgen framework (https://bcbio-nextgen.readthedocs.io/) was used (version: 1.1.8-b): RNA sequences were aligned against the Mus musculus genome (mm10) using STAR
Salmon was used for calling transcripts and calculating transcripts per million (TPM) values as well as total counts
Differential expression was analysed in R using DESeq2 library
Genome_build: mm10
Supplementary_files_format_and_content: Salmon output (*.sf files) containing TPM and count values, and DESeq output contining LFC and p-values.

source_name: Muscle stem cell

growth_protocol:
CD45-Sca1-CD31-CD11b-alpha7Integrin+CD34+ stem cells were isolated by FACS from hindlimb muscles of 2-4 mo Pax7-CreERT2;IFT88 f/f or control mice, or from 24 mo wt C57BL6 mice
20% FBS/40% Low Glucose DMD/40% F-10

treatment_protocol: Aged MuSCs were grown on hydrogels and treated for 24hr with vehicle or 5µM SAG (Smo agonist)

value: muscle


title: LP 15, ruxolitinib


title: M5 brain

description: MS patient, T cells specific for brain


title: LP 14, ruxolitinib

source_name: #2 Abdomen, responsive


title: Untreated, replicate 1


title: M1 PBL

description: MS patient, peripheral blood leukocytes


title: Young control 2


title: M4 brain

description: MS patient, T cells specific for brain


title: Young control 1


title: L. bicolor 5fC fC-Seal control

data_processing:
For fo/hm-TOP-seq: select reads with length >= 80 nt, for fC/hmC select reads with length >= 15 and trim if quality <20
For fo/hm-TOP-seq: Select reads with 5' adapter and trim 3' adapter from the remaining reads
Align reads to a reference genome
Remove PCR duplicates (used an in house script); subsample (for hMe/fC-Seal)
Remove background signal and calculate coverage per CG (used an in house script)
Genome_build: V2 for L. bicolor (JGI) and V1 for C. cinerea (JGI)
Supplementary_files_format_and_content: Tab-delimited text files contain CG (or bin) coverage for each sample

growth_protocol: Laccaria bicolor (Maire) Orton S238N-H82 haploid monokaryotic strain (Taxonomy ID: 486041, NCBI:txid486041) mycelium culture was maintained at 25°C in the dark on a solid (2% agar) modified Pachlewski medium (10 g/L glucose, 3 g/L malt extract, 0.25 g/L (NH4)2SO4, 0.5 g/L KH2PO4, 0.15 g/L MgSO4·7H2O, 0.05 g/L CaCl2, 0.025 g/L NaCl, 0.0012% FeCl3, 100 mg/L thiamine, 2.3 mg/L ZnSO4·7H2O, 8.5 mg/L H3BO3, 0.5 mg MnCl2·4H2O, 0.6 mg/L CuSO4·5H2O, 0.4 mg/L (NH4)2MoO4). For nucleic acid extraction, mycelium was collected after 8 weeks from a liquid medium inoculated with a small amount of mycelium from agar plates. Mycelium of Coprinopsis cinerea haploid monokaryotic strain Okayama 7 (Taxonomy ID: 240176, NCBI: txid240176) was maintained on solid (1% agar) YMG medium (Rao and Niederpruem, 1969). For nucleic acid extraction, 300 ml of liquid medium in a 1 L flask was inoculated with a small amount of mycelium and grown without shaking at 30°C for 14 days in the dark.

extract_protocol:
Mycelium was crushed to a powder with a pinch of polyvinylpyrrolidone (PVP, K25) using a mortar, pestle and liquid nitrogen. Powder (~1ml) was incubated at 55˚C for 90 min in 4.5 ml of lysis buffer (100 mM Tris-HCl pH 8.0, 20 mM EDTA, 2 M NaCl, 2% hexadecyltrimethylammonium bromide (CTAB), 2% PVP) with Proteinase K (Thermo Scientific, TS). Then, DNA was extracted using chloroform and precipitated for 30 min at 4˚C using 1.5 volumes of isopropanol and 0.4 volumes of 3 M sodium acetate pH 5.2. DNA was dissolved in 10 mM Tris-HCl and treated with RNase A/T1 (TS) for 1.5 h at 37˚C and then purified by chloroform extraction and ethanol precipitation. DNA quality was checked by agarose electrophoresis, concentration determined with Qubit™ dsDNA HS Assay Kit (Invitrogen™).
For the hMe-Seal and fC-Seal libraries genomic DNA was sonicated on a Bioruptor UCD-200 (Diagenode) instrument in 10 mM Tris-HCl (pH 8.5) to on average 200-250 bp fragments and purified using DNA clean and concentrator kit (Zymo research, ZR).   5hmC protection and 5fC reduction to 5hmC was performed as in (Ličytė et al., 2020). To achieve similar processing of 5fC and 5hmC samples, the same purification steps were performed with both samples, but omitting glycosylation with unmodified UDP-glucose and reduction with NaBH4 for 5hmC. 2.6-2.7 μg of DNA was labeled using UDP-6-azide-glucose and T4 BGT (Thermo Scientific, TS) as described above (see Evaluation of 5hmC and 5fC enrichment). Two control DNA samples were prepared: for 5hmC control samples, BGT was omitted in the labeling step; for controlling 5hmC protection in 5fC samples, glucosylated DNA without the reduction step was used.   The biotinylation step was performed in a 130 μl reaction (as described in Evaluation of 5hmC and 5fC enrichment), and then, DNA was end-filled using a DNA End Repair Kit (TS) according to the vendor’s recommendations and purified using DNA clean and concentrator kit (ZR). Biotinylated DNA was then enriched as described above in 40 μl using 0.1 mg of Dynabeads MyOne Streptavidin C1 (TS) and recovered by resuspending beads in 20 μl of 50 mM DTT, 60 mM Tris (pH 7.8), followed by a 1 h incubation on a roller. Released DNA was separated from the beads.  DNA was ligated overnight at 22 °C to 4.2 pmol of Ion Torrent™ barcoded adapters (Kapa Biosystems) in a 30 μl reaction containing 0.5 mM ATP, 10 mM MgCl2, 5% PEG 4000 and 7.5 U of T4 Ligase (TS). Adapter removal was then performed using MagJet NGS Cleanup and Size-selection kit (TS). Then, adaptor-ligated DNA was incubated with 10 mM 2-mercaptoethanol for 10 min at room temperature (to preclude inadvertent formation of inter-nucleotide disulphide cross-links), followed by PCR in 50 μl in Taq Buffer with (NH4)2SO4 supplemented with 0.2 mM dNTP, 2 mM MgCl2, 1 μM primers and 2.5 U of Taq DNA Polymerase (TS). PCR cycling conditions were: 1 min 50°C, 5 min 72°C, 4 min 94°C, 1 min 65°C, 5 min 72°C, 15 cycles of 1 min 94°C, 1 min 65°C, 1 min 72°C and the final extension step is at 72°C for 5 min. The libraries were size-selected for 300 bp fragments (MagJet NGS Cleanup and Size-selection kit, TS) and subjected to Ion Proton (TS) sequencing.  For hmTOP-seq and foTOP-seq libraries DNA was sonicated to yield ~200-250 bp fragments with Covaris M220 instrument and purified using DNA clean and concentrator kit (ZR). 5fC reduction to 5hmC, 5hmC protection, and azide-labeling of 5hmC (5.8 μg of DNA in this step) were performed as described above for the hMe-Seal and fC-Seal libraries. Then, DNA was end-filled for 15 min at 20°C using a DNA End Repair Kit (TS) according to the vendor’s recommendations and purified using DNA clean and purified using the GeneJet Purification Kit. DNA was then dA-tailed in 120 μl with 30 u of Klenow exo- polymerase in its buffer (TS) in the presence of 0.5 mM dATP at 37°C for 45 min, enzyme inactivated at 75°C for 15 min followed by purification through GeneJet (TS) columns. Partially complementary annealed adaptors A1/A2 (2.25 μM, A1 5’ P-GATTGGAAGAGTGGTTCAGCAGGAATGCTGAG and A2 5’ ACACTCTTTCCCTACATGACACTCTTCCAATCT) were ligated in 120 µl by incubating the DNA with 30 u of T4 DNA Ligase (TS) in its buffer at 22°C overnight, followed by thermal inactivation at 65°C for 10 min and column purification (DNA Clean and Concentrator, ZR).  TOP-seq library enrichment and preparation was then done as in (Ličytė et al., 2020) and libraries were subjected to Ion Proton (TS) sequencing.

treatment_protocol: For the enhancement of TET activity, C.cinerea mycelium was grown for 7 days and then treated with 5 mM vitC for 2 days, untreated control was grown for the same time period.  For L. bicolor mycelium was also incubated with 5 mM vitC for 2 days.

tag: method

value: fC-Seal


title: Aged SAG 3


title: LP 7, ruxolitinib

source_name: #2 FOREARM Responsive TREATMENT


title: M5 flu


title: M3 brain

description: MS patient, T cells specific for brain


title: M2 brain

description: MS patient, T cells specific for brain


title: L. bicolor 5fC fC-Seal, replicate 1


title: L. bicolor 5fC fC-Seal, replicate 2


title: M4 flu


title: LP 30, ruxolitinib

source_name: #1 L KNEE RESPONSIVE


title: C3 brain


title: M1 brain

description: MS patient, T cells specific for brain


title: L. bicolor 5hmC hMe-Seal, replicate 2

value: hMe-Seal


title: LP 24, ruxolitinib

source_name: #1 L Lateral Thigh, Refractory

value: NR


title: LP 38, ruxolitinib

source_name: #1 L CALF REFRACTORY


title: Aged veh 3


title: Aged SAG 2


title: L. bicolor 5hmC hMe-Seal control


title: LP 3, ruxolitinib

source_name: R ANKLE RESPONSIVE


title: LP 13, ruxolitinib

source_name: #1 R Elbow, refractory


title: L. bicolor 5hmC hMe-Seal, replicate 1


title: Aged veh 2


title: Young IFTKO 1


title: LP 10, ruxolitinib

source_name: #1 L wrist, refractory


title: L. bicolor 5fC + vitC TOP-seq background

value: foTOP-seq


title: Aged veh 1


title: LP 6, ruxolitinib

source_name: #1 R LEG REFRACT TREAT

value: skin


title: Aged_Rep_2

tag: age

value: 24 month old


title: CI-H_P8

city: Planegg-Martinsried

first: Eduardo

last: Beltrán

state: Bayern

address: Großhaderner Str. 9

department: Institute of Clinical Neuroimmunology

institute: University Hospital, LMU Munich

description: CITE-seq

data_processing:
Cell Ranger software (10x Genomics, v.6.1) was used to demultiplex samples, process raw data, align reads to the GRCh38 human reference genome and summarize unique molecular identifier (UMI) counts. Filtered gene-barcode and CSP-barcode matrices that contained only barcodes with UMI counts that passed the threshold for cell detection were used for further analysis
We processed the filtered UMI count matrices using the R package Seurat (version 4.0.3).
As a QC steps we filtered out cells that expressed fewer than 500 genes and/or >15% mitochondrial reads, and genes expressed in less than 3 cells were removed from the count matrix. After QC, only raw gene counts in high-quality singlets were submitted to: log-normalization; identification of high variable genes by using the vst method; scaling; and regression against the number of UMIs and mitochondrial RNA content per cell.
Integration was performed to remove bath effects and the integrated assay was used for principal component analysis and unsupervised clustering. After marker identification for each CD4+ T cell cluster, only cells where a TCR clonotype was detected, were used for upstream analysis of TCR repertoire. Single-cell TCR annotation was performed using the 10x cellranger vdj pipeline.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with filtered feature-barcode counts for every gene and every cell
Supplementary_files_format_and_content: Matrix table with filtered feature-barcode counts for every TotalSeq-C antibody and every cell
Supplementary_files_format_and_content: Seurat meta.data file

source_name: PBMCs

tag: cell type sorted

value: non-MS

tag: disease course

value: healthy

tag: Sex

value: f

tag: gex _ file-name-prefix

tag: csp _ file-name-prefix


title: CJ-H_P8

description: CITE-seq


title: L. bicolor 5fC TOP-seq background


title: LP 37, ruxolitinib

source_name: #2 L THIGH DISEASE

tag: tissue

value: cutaneous lichen planus (LP)

value: ruxolitinib

value: Week 0

value: D


title: Aged_Rep_1


title: L. bicolor 5fC + vitC TOP-seq, replicate 2

value: Orton S238N-H82

tag: treatment


title: L. bicolor 5fC + vitC TOP-seq, replicate 1

value: vitamin C


title: LP 36, ruxolitinib

source_name: #1 L LEG DISEASE


title: LP 32, ruxolitinib

source_name: #1 R POST FOREARM DISEASE


title: BW-H_P8

description: CITE-seq

value: m


title: Young_Rep_3

value: muscle

value: 2-4 month old


title: CE-MS_P8

description: CITE-seq

value: MS

value: RRMS


title: L. bicolor 5fC TOP-seq, replicate 2

source_name: Mycelium

value: foTOP-seq

value: untreated


title: Young_Rep_2


title: LP 29, ruxolitinib

value: skin


title: BW-MS_P8

description: CITE-seq


title: LP 28, ruxolitinib

source_name: #1 L FOREARM DISEASE


title: BU-H_P8

description: CITE-seq

value: non-MS


title: Young_Rep_1


title: CJ-MS_P8

description: CITE-seq

value: Dimethyl Fumarate


title: L. bicolor 5fC TOP-seq, replicate 1


title: L. bicolor 5hmC + vitC TOP-seq background

value: hmTOP-seq


title: Aged SAG 1


title: L. bicolor 5hmC TOP-seq background


title: LP 25, ruxolitinib

source_name: #1 L Back Disease

value: cutaneous lichen planus (LP)


title: A113678

city: Davis

first: Janine

last: LaSalle

address: Medical Microbiology and Immunology

institute: UC Davis

data_processing:
library strategy: WGS
Raw read files were mapped to human reference genome hg38 using Burrows-Wheeler Aligner (BWA) with the default setting. SAMtools was utilized to sort the bam files and Picard was used to merge bam files from the same sample identify duplicate reads. Single nucleotide polymorphisms (SNPs), small insertion, and deletions (InDels) were called using GATK and annotated variant using ANNOVAR. Copy number variations (CNVs), longer than 50 bp, were identified using control-FREEC and CREST. Structural variants (SVs) detection and genotyping, larger than 50 bp were performed using DELLY with the default settings.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files for SV, INDEL, CNV and variant call format VCF files for SNP at each sample

source_name: TD_Cord Blood

extract_protocol:
DNA was extracted from whole umbilical cord blood with the Gentra Puregene Blood kit (Qiagen, Hilden, Germany) and quantified with the Qubit dsDNA HS Assay kit (Thermo Fisher Scientific, Waltham, MA, USA).
Sequencing libraries were generated using NEBNest DNA library prep kit (NEB, Ipswich, MA, USA) with 150 bp paired-end reads in HiSeq X Ten (San Diego, CA, USA) by Novogene (Sacramento, CA, USA) with at least 30x coverage per sample.

tag: genotype

value: TD

value: Cord Blood


title: BD-H_P8

description: CITE-seq

value: healthy

value: f


title: LP 23, ruxolitinib

source_name: #1 R SHIN DISEASE

value: ruxolitinib

value: Week 0

value: D


title: L. bicolor 5hmC + vitC TOP-seq, replicate 2

value: Orton S238N-H82

value: vitamin C


title: LP 20, ruxolitinib

source_name: #3 L wrist, Disease


title: A113489

source_name: ASD_Cord Blood

value: ASD


title: CI-MS_P8

description: CITE-seq

value: MS

value: RRMS


title: A113359


title: AW-H_P8

description: CITE-seq


title: A113300


title: LP 19, ruxolitinib

source_name: #1 L Post Forearm, Disease

value: skin


title: AW-MS_P8

description: CITE-seq


title: CE-H_P8

description: CITE-seq

value: non-MS


title: A113276


title: AS-H_P8

description: CITE-seq

value: m


title: LP 17, ruxolitinib

source_name: #1R ARM DISEASE


title: A112591


title: LP 12, ruxolitinib

source_name: #3 R chest, disease


title: AI-H_P8

description: CITE-seq


title: L. bicolor 5hmC TOP-seq, replicate 2

value: hmTOP-seq

value: untreated


title: L. bicolor 5hmC TOP-seq, replicate 1


title: AS-MS_P8

description: CITE-seq

value: SPMS


title: L. bicolor 5hmC + vitC TOP-seq, replicate 1


title: C. Cinerea 5fC fC-Seal, replicate 2

organism: Coprinopsis cinerea

value: Okayama 7

value: fC-Seal


title: A111956

value: Cord Blood


title: LP 11, ruxolitinib

source_name: #1 R anterior medial thigh, disesae

value: cutaneous lichen planus (LP)

value: ruxolitinib


title: G-H_P8

description: CITE-seq

value: healthy

value: f


title: BU-MS_P8

description: CITE-seq


title: A111919


title: C. Cinerea 5hmC hMe-Seal control

value: hMe-Seal


title: CJ-H_P5

description: CITE-seq

tag: tr _ file-name-prefix


title: A111723

value: ASD


title: C. Cinerea 5hmC hMe-Seal, replicate 2


title: LP 9, ruxolitinib

source_name: #2 L WRIST DISEASE

value: Week 0

value: D


title: CJ-MS_P5

description: CITE-seq

value: MS

value: Dimethyl Fumarate

value: RRMS


title: LP 8, ruxolitinib

source_name: #1 L SHIN DISEASE

value: skin


title: LP 5, ruxolitinib

source_name: #2 R ARM Disease


title: A111212

value: TD


title: LP 18, ruxolitinib

source_name: #2R FLANK DISEASE


title: LP 4, ruxolitinib

source_name: #1 L LAT LEG Disease


title: A113062


title: C. Cinerea 5fC fC-Seal control

value: untreated


title: LP 2, ruxolitinib

source_name: #2 L FOREARM Disease


title: C. Cinerea 5hmC TOP-seq, replicate 2

source_name: Mycelium

value: Okayama 7

value: hmTOP-seq


title: C. Cinerea 5hmC TOP-seq, replicate 1


title: C. Cinerea 5hmC TOP-seq background


title: A110881

value: Cord Blood


title: LP 1, ruxolitinib

source_name: #1 R ANKLE Disease

value: cutaneous lichen planus (LP)


title: CI-H_P5

description: CITE-seq

source_name: PBMCs

value: non-MS


title: CE-H_P5

description: CITE-seq

value: healthy


title: C. Cinerea 5fC fC-Seal, replicate 1

value: fC-Seal


title: Lipopolysaccharides 24h induced DPSCs + Laser irradiated DPSCs replicate 2

type: RNA

city: São Paulo

first: Fabio

middle: Dupart

last: Nascimento

state: SP

address: Rua Doutor Gabriel Piza, 636 apto 23

department: Biochemistry

country: Brazil

institute: Federal University of Sao Paulo

description:
Group 2
SAMPLE 6

data_processing:
CT values were exported to an Excel file to create a table of CT values. This   table was then uploaded on to the data analysis web  portal at http://www.qiagen.com/geneglobe
Relative quantification was carried out using the ΔCt method. This method results in ratios between the target genes and the housekeeping reference gene, in this case, the enzyme β-2-microglobulin (positive control) for DSPCs. This assay is based on gene fold-Regulation approach, that represents in fold-change (fc) results of the evaluated genes. Fold-change values greater than one indicates a positive- or an upregulation in gene expression, while fold-change values less than one indicate a negative or down-regulation, of the evaluated gene.
The p-values were calculated based on a Student’s t-test of the replicate 2^(ΔCt) values for each gene in the experimental or control groups

label: SYBR Green

source_name: Human Dental Pulp Stem Cells

label_protocol: The Qiagen RT² Profiler PCR Arrays are highly reliable and sensitive gene expression profiling tools for analyzing focused panels of genes in  signal transduction, biological processes or disease research pathways using real-time PCR. Each cataloged RT² Profiler PCR  Array contains a list of the pathway-focused genes as well as five housekeeping (reference) genes on the array. In addition, each  array contains a panel of proprietary controls to monitor genomic DNA contamination (GDC) as well as the first strand synthesis  (RTC) and real-time PCR efficiency (PPC). The qPCR Assays used in PCR Arrays are laboratory-verified and optimized to work  under standard conditions enabling a large number of genes to be assayed simultaneously. Their specificity is guaranteed when  RT² SYBR Green qPCR Master Mixes are used as part of the complete PCR Array System protocol.

growth_protocol: The cells were seeded into culture flasks with α-MEM, supplemented with 10% FCS, 100 μML-ascorbic acid, 2mML-glutamine and penicillin (100 U/mL)/streptomycin (100 mg/ml) and incubated at 37°C with 5% CO2. In the initial stage, after adhering to culture flasks, cells grew slowly. Cell colonies were identified after 10–14 days, with their fibroblastoid appearance, which showed to be dependent on the cell density obtained in initial plating. After reach 70% of confluence, cells were considered ready to proceed with experiments.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

treatment_protocol: To promote in vitro cellular inflammatory response, 2 ×106 of DPSCs were seeded in six wells plates with α-MEM, supplemented with 10% FCS, 100 μML-ascorbic acid,  2mML-glutamine and penicillin (100U/mL)/streptomycin (100 mg/ml) and incubated from 24 h at 37°C with 5% CO2 for complete adhesion. Previous to the experiment cells were starved for 6hs in αMEM without FCS. After starvation period, 10 μg/ml of LPS were added in α-MEM, supplemented with 10% FCS, 100 μML-ascorbic acid, 2 mML-glutamine and penicillin (100 U/mL)/streptomycin (100 mg/ml), for 24 hs.Part of these cells was further irradiated  with a laser device in the infrared wavelength (808 nm) that delivered a total energy of 6 J (100mW× 60 s). (Group 1); while the other part remained not irradiated for subsequent analysis (Group 2).

value: Stem Cells

tag: protocol

value: Lipopolysaccharides 24h induced + Laser irradiated

value: pulp


title: LP Ctrl 10, pre-therapy

source_name: #2 R POST FOREARM NORMAL

value: Normal

value: pre-therapy

value: Week 0

value: C


title: BW-H_P5

description: CITE-seq

value: m


title: Lipopolysaccharides 24h induced DPSCs + Laser irradiated DPSCs replicate 1

description:
Group 2
SAMPLE 5

tag: cell type


title: BW-MS_P5

description: CITE-seq

tag: disease state

value: MS

value: RRMS


title: LP Ctrl 9 , pre-therapy

source_name: #3 L Thigh NORMAL

value: skin

tag: time


title: A110677

source_name: TD_Cord Blood

value: TD


title: Lipopolysaccharides 24h induced DPSCs replicate 2

description:
Group 1
SAMPLE 4

value: Lipopolysaccharides 24h induced


title: A110144

source_name: ASD_Cord Blood

value: ASD

value: Cord Blood


title: LP Ctrl 8, pre-therapy

source_name: #3 R HIP Normal

tag: phenotype


title: C. Cinerea 5hmC hMe-Seal, replicate 1

tag: strain

value: Okayama 7

value: hMe-Seal

value: untreated


title: Lipopolysaccharides 24h induced DPSCs replicate 1

description:
Group 1
SAMPLE 3

value: Stem Cells


title: A110028


title: BU-MS_P5

description: CITE-seq

value: f


title: A110911


title: LP Ctrl 7, pre-therapy

source_name: #2 R HIP NORMAL

value: Normal


title: Control replicate 2

description:
CTR
SAMPLE 2

value: Control

value: pulp


title: LP Ctrl 6, pre-therapy

source_name: #2 L Post Forearm, Normal

value: pre-therapy

value: Week 0

value: C


title: Control replicate 1

description:
CTR
SAMPLE 1


title: A109885


title: LP Ctrl 5, pre-therapy

source_name: #3R HIP NORMAL


title: BD-H_P5

description: CITE-seq

value: non-MS

value: healthy


title: AW-H_P5

description: CITE-seq


title: CI-MS_P5

description: CITE-seq

value: MS

value: RRMS


title: A109572

value: TD


title: A110843

value: Cord Blood


title: A109511

value: ASD


title: LP Ctrl 4, pre-therapy

source_name: #2 R anterior lateral thigh, normal

value: skin


title: CE-MS_P5

description: CITE-seq


title: PBMCs, YUTORY, BCR scVDJ-seq

first: Aaron

middle: M

last: Newman

state: California

address: 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine, Department of Biomedical Data Science

description: Sample was prepared using the Chromium Single Cell 5’ kit, sequenced on Illumina NovaSeq, and aligned using Cell Ranger v3.1.0

data_processing:
Raw scV(D)J-seq reads were mapped with Cell Ranger v3.1.0 or v5.0.1 to reference “refdata-cellranger-vdj-GRCh38-altsensembl-4.0.0”.
The resulting clonotype assemblies were downloaded from Loupe V(D)J browser v3.0.0 (10x Genomics, Pleasanton, CA).
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated values (CSV) files per patient, with separate files for TCR and BCR scVDJ-seq, including cell barcodes, TCR or immunoglobulin chain types, CDR3 amino acid sequences, CDR3 nucleotide sequences, and V, D, J and C genes.

source_name: Peripheral blood

extract_protocol:
Single-cell suspensions from PBMC samples were obtained and prepared to a concentration of 700-1,200 viable cells/μl using a hemacytometer (Thermo Fisher Scientific, Waltham, MA) or Coulter Counter (Beckman Coulter Life Sciences, Indianapolis, IN) for cell counting, per the manufacturers’ instructions.
Chromium Single Cell 5’ Library Construction Kit (10x Genomics, Pleasanton, CA) following the manufacturer’s protocol.
Single-cell suspensions underwent library preparation for scRNA-seq with paired single-cell V(D)J sequencing (scVDJ-seq) for T cell receptor (TCR) and B cell receptor (BCR) clonotypes using the 5’ transcriptome kit (10x Genomics, Pleasanton, CA) per the manufacturer’s instructions. Complementary DNA libraries were sequenced on a NovaSeq instrument (Illumina, San Diego, CA) with 2 x  92 bp paired-end reads targeting a mean of 20k reads per cell.

tag: patient

value: YUTORY

value: Blood

tag: diagnosis

value: Melanoma

value: Male

tag: immunotherapy type

value: Combination

tag: highest irae grade

tag: cohort

value: Single-cell discovery

tag: sequencing batch

value: A


title: PBMCs, YUVARDO, BCR scVDJ-seq

value: YUVARDO

tag: Sex

tag: age


title: LP Ctrl 3, pre-therapy

source_name: #3 L THIGH NORMAL

tag: tissue

value: Normal

tag: treatment

value: pre-therapy

value: Week 0

value: C


title: AS-H_P5

description: CITE-seq

tag: cell type sorted

value: non-MS

tag: disease course

value: healthy

value: m

tag: gex _ file-name-prefix

tag: csp _ file-name-prefix

tag: tr _ file-name-prefix


title: PBMCs, YUTHEA, BCR scVDJ-seq

value: YUTHEA


title: A110711

state: CA

tag: genotype

value: ASD

value: Cord Blood


title: A109410


title: A109486


title: LP Ctrl 2, pre-therapy

source_name: #3 R THIGH Normal

value: skin

tag: disease state

tag: time

tag: phenotype


title: AS-MS_P5

description: CITE-seq

value: MS

value: SPMS


title: BU-H_P5

description: CITE-seq

value: f


title: PBMCs, YUTAUR, BCR scVDJ-seq

tag: patient

value: YUTAUR

value: Blood

tag: diagnosis

value: Melanoma

value: Male

tag: immunotherapy type

value: Combination

value: Single-cell discovery


title: A109359


title: LP Ctrl 1, pre-therapy

value: Normal

value: pre-therapy

value: Week 0

value: C


title: AI-H_P5

description: CITE-seq

value: non-MS

value: healthy

value: m


title: AI-MS

description: CITE-seq

value: CD3+CD4+ and CD11c+


title: A108734

value: TD

value: Cord Blood