title: MSC_S1

description: AML06 MSC P3

value: AML patient


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B3_AD007

status: Public on May 02 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

source_name: brain

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.) or snmC-seq3 protocol described in (Liu, H. et al., Biorxiv. 2023:2023-04.). The libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x1012 to 1x1013 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

tag: tissue

value: brain

tag: source

value: SC

tag: target

value: P

tag: Sex

value: male


title: rep2, plate6, spaceA3

city: Stanford

first: Alan

last: Cheng

address: 240 Pasteur Drive

institute: Stanford University

library_source: transcriptomic

data_processing:
Raw reads were pre-processed using FASTQC, Cutadapt, and PRINSEQ, followed by sequence alignment with the Tuxedo suite (Bowtie, Bowtie2, TopHat) and SAMtools, using default settings.
Transcript counts were quantified as fragments per kilobase of transcript per million mapped reads (FPKM) generated by TopHat/Cufflinks.
Assembly: mm10

molecule: total RNA

source_name: otic vesicle and periotic tissue

extract_protocol:
Dissociated tdTomato+ cells were sorted into individual wells of 96-well plates using a FACSAria II instrument. Each well contained 5ul of lysis buffer from the Clontech SMARTer Ultra Low Input RNA kit V3, which was used for cDNA generation following manufacturer instructions.
Illumina libraries were constructed using the Nextera XT DNA Sample Preparation kit following manufacturer instructions.

value: otic vesicle and periotic tissue

tag: genotype

tag: developmental stage

tag: cell type

value: tdTomato+


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B3_AD006

value: THp

value: STR

value: female


title: rep2, plate5, spaceA3


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B3_AD002

value: THl


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B3_AD001


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B4_AD004


title: MDA231 IP 2

city: New York

first: Siting

last: Gan

state: NY

address: 417 East 68th Street

department: SKI

institute: MSKCC

data_processing:
Xenome classified the reads as either human or mouse genome
FASTQ raw sequences were mapped by STAR RNA-seq aligner using human genome reference GRCh38 and mouse genome reference GRCm38
Uniquely mapped reads were assigned to annotated genes by HTSeq to measure read counts
Counts were normalized by library size to be subject to differential gene expression analysis
Assembly: GRCh38 and GRCm38

molecule: polyA RNA

organism: Homo sapiens

source_name: Brain

extract_protocol:
Mice were injected with 250mg/kg 5-fluorocytosine and after 12 hours brains were harvested and homogenized. mRNA was extracted by 4 × 250 uL/brain Oligo (dT)25 magnetic beads and immunoprecipitated with 2.5 ug/brain anti-BrdU antibody
SMARTer PCR cDNA kit was used to construct libraries using the immunoprecipitated mRNA

value: Brain

tag: cell line

value: breast cancer cell line

value: brain metastatic derivative


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B2_AD010


title: rep2, plate4, spaceA3


title: FB after coculture 3

city: San Diego

first: Anna

last: Di Nardo

address: 9500 Gilman Drive

department: Dermatology ACTRI

institute: UCSD

description: SR75 run type

data_processing:
Partek software 10.0.22.0330
Sequence reads were trimmed for adaptor sequence/low-quality sequence (parameter- Quality limit: 0.05)
Alligment STAR 2.7.8a
Assembly: Assembly hg38 rel 105
Supplementary files format and content: tab-delimited text files include Attrbute values for each Sample: ADN_HMC+DF+Commensal+EXP2+triplicate_sample_attributes.txt
Supplementary files format and content: tab-delimited text files includeANOVA comparison s for each Sample: ANOVA.txt
Supplementary files format and content: tab-delimited text files include DESeq2 values for each Sample: DESeq2 Report.txt
Supplementary files format and content: tab-delimited text files include feature distribution normalized: feature_distribution_normalized.txt
Supplementary files format and content: tab-delimited text files include feature distribution for transcript: feature_distribution(transcripts).txt
Supplementary files format and content: Tab delimited text of Gene Set ANOVA report: Gene Set ANOVA report..txt
Supplementary files format and content: tab-delimited text files include gene level distribution: gene_level_feature_distribution.txt
Supplementary files format and content: tab-delimited text files include QuantificationSummary(gene counts): QuantificationSummary(gene counts).txt
Supplementary files format and content: tab-delimited text files include QuantificationSummary(transcripts): QuantificationSummary(transcripts).txt

source_name: human fibroblasts after coculture

growth_protocol: 1. hMCs 15 weeks from cord blood CD34+ cells, cultured in Stemline II Hematopoietic Stem Cell Expansion Medium from Sigma with 100 ng/ml SCF and IL-6.

extract_protocol:
5. Collect the cells, make the final concentration for each sample is 1000 cells/uL in PBS with 0.04% BSA. For FB collection, TrypLE Express Enzyme from Invitrogen was used to detach the FB from the 6-well plate.
mRNA stranded

treatment_protocol:
2. Primary Dermal Fibroblast Normal; Human, Neonatal (ATCC PCS-201-010), cultured in the same medium as hMC.3. When FB reached about 40% confluency in 6-well plate, 1x10^5 hMCs were added to the FB in the same well without transwell insert to mimic the interactions between MC and FB in dermis.
4. Coculture for 1 week. 5. Collect the cells, make the final concentration for each sample is 1000 cells/uL in PBS with 0.04% BSA. For FB collection, TrypLE Express Enzyme from Invitrogen was used to detach the FB from the 6-well plate.

value: dermis

value: primary cells

value: mesenchymal

value: WT

tag: treatment

value: in vitro expansion and co cultured with mast cells for 7 days


title: rep1, plate3, spaceA3


title: FB after coculture 2

description: SR75 run type


title: CD28 CAR, day 14, scRNAseq

city: St. Louis

first: Nathan

last: Singh

state: MO

institute: Washington University School of Medicine

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Downstream single-cell analysis was performed using Seurat package v4.0.5 within the R programming environment v4.1.2.16 Lower bound for the number of genes in individual cells was chosen based on binary logarithm distribution and was set to 9.8. Cells with more than 7,500 genes were filtered out.
The percentage of mitochondrial counts was calculated for every cell, and only cells with mitochondrial percentage less than 10% were used in further analysis. Filtered matrices were normalized using a scaling factor of 10,000 and centered.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Engineered T cells

extract_protocol:
CAR T cells from chronic stimulation cultures were isolated using flow-based sorting.
Cells were processed using the 10x Genomics Chromium Single Cell V(D)J Reagent Kits (10x Genomics, PN-1000006, PN-1000020, PN-120262) to generate single-cell emulsions for barcoding, reverse transcription and cDNA amplification. Immediately following these steps, 10x barcoded fragments were pooled and attached to standard Illumina adaptors to generate a barcoded single-cell RNA library.

value: CD19-directed human CAR T cells containing CD28

value: Co-culture with Nalm6 cells

tag: time

value: day 14


title: MSC_S8

type: RNA

city: Navi Mumbai

first: Jyoti

middle: Anand

last: Kode

state: Maharashtra

address: Kharghar

department: Kode Lab

country: India

institute: Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre

description: Bilineage Leukemia (ETP-ALL) 02 MSC P5

hyb_protocol: Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Scanned using Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX  : 75th percentile shift  method and gene based analysis was performed

source_name: MSC cultured from Bone Marrow

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). The total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Bone marrow (BM) from cancer patients (AML/ ETP-ALL/ Lymphoma) was divided in two parts. One part from BM (AML/ ETP-ALL) was processed using ficoll-hypaque (FH) density gradient centrifugation to obtain leukemic blast population. Leukemic cells obtained were stored in RNAlater at -20°C. Second part of BM (AML/ ETP-ALL/ Lymphoma) was treated with Stem Cell Enrichment cocktail and MSC were enriched by separation on FH gradient. Enriched cells were seeded in culture flasks with DMEM media supplemented with 10% FBS and 1% antibiotics and glutamine. Adherent fibroblastoid cells were expanded upto passage P5.

extract_protocol: RNA was extracted using Qiagen’s RNeasy minikit as per the manufacturer’s protocol

treatment_protocol: Leukemic cells were washed in PBS and pelleted. The cell pellet was suspended in RNA 200-500ul RNAlater and stored at -200C. AML cell line was cultured and store in RNAlater. MSC culture at 80% confluency was trypisinized, washed with PBS and cell pellet was stored in 200-500µl of RNAlater at -20°C.

value: Bone marrow

tag: donor

value: Bi-lineage leukemia patient

tag: cell details

value: Cultured Bi-lineage Leukemia MSC at passage P5


title: rep1, plate2, spaceA3

value: otic vesicle and periotic tissue

value: tdTomato+


title: FB after coculture 1

description: SR75 run type


title: MSC_S5

description: Lymphoma 02 Uninvolved BM MSC P4

value: Lymphoma patient

value: Cultured uninvolved BM MSC at passage P4


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B1_AD012

value: brain

value: SC

value: P

value: female


title: 41BB CAR, day 0, scRNAseq

value: CD19-directed human CAR T cells containing 41BB

value: day 0


title: rep2, plate6, spaceA2


title: FB only 3

description: SR75 run type

source_name: human fibroblasts only

value: dermis

value: primary cells

value: mesenchymal

value: WT

value: in vitro expansion


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B1_AD010


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B1_AD008

value: male


title: FB only 2

description: SR75 run type


title: rep1, plate1, spaceA3


title: rep2, plate4, spaceA2


title: rep1, plate3, spaceA2


title: CD28 CAR, day 0, scRNAseq

value: CD19-directed human CAR T cells containing CD28

value: Co-culture with Nalm6 cells


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B1_AD004

value: THp

value: STR


title: MFSE3

description: SR75 run type

source_name: human Mast cell after coculture + S epidermidis

value: CD34 positive cells

value: myeloid

value: these groups are hMCs cocultured with fibroblasts for 7 days, then the hMC treated with the same conditions above


title: FB only 1

description: SR75 run type


title: rep1, plate2, spaceA2

value: otic vesicle and periotic tissue

value: tdTomato+


title: MFSE2

description: SR75 run type


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B1_AD002

value: brain

value: THl

value: female


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B2_AD002


title: MFSE1

description: SR75 run type

value: primary cells


title: rep1, plate1, spaceA2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B12_AD012

value: SC

value: P


title: MFSA3

description: SR75 run type

source_name: human Mast cell after coculture + S aureus

value: WT


title: rep2, plate6, spaceA11


title: MFSA2

description: SR75 run type


title: rep2, plate5, spaceA11


title: MFT3

description: SR75 run type

source_name: human Mast cell after coculture + TSB (control)


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B1_AD007

value: male


title: MFSA1

description: SR75 run type


title: rep2, plate5, spaceA2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B12_AD008


title: rep1, plate3, spaceA11


title: MFT2

description: SR75 run type


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B12_AD004


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B12_AD007


title: rep2, plate4, spaceA11


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B12_AD006


title: MSC_S4

description: Bilineage Leukemia (ETP-ALL) 01 MSC P5

value: Bone marrow

value: Bi-lineage leukemia patient

value: Cultured Bi-lineage Leukemia MSC P5


title: MFT1

description: SR75 run type


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B12_AD002

value: STR


title: MSE3

description: SR75 run type

source_name: human Mast cell + S epidermidis

value: CD34 positive cells

value: hMC treated with sterile supernatant of bacteria Staphylococcus epidermidis 12228 strain


title: rep1, plate2, spaceA11


title: Cancer cells 2

description:
3189_SG-602_d27_inh_tumor_IGO_12437_196_sparse_counts_barcodes.csv
3189_SG-602_d27_inh_tumor_IGO_12437_196_sparse_counts_genes.csv
3189_SG-602_d27_inh_tumor_IGO_12437_196_sparse_molecule_counts.csv

data_processing:
GFP+ cancer cell and GFP- non cancer cell samples were mapped to hg38 and mm38 genome references, respectively.
The SEQC pipeline performed read alignment, multi-mapping read resolution, and cell barcode and UMI correction to generate a raw UMI-based (cell × gene) count matrix per sample.
An in-house method called SHARP (https://github.com/hisplan/sharp, version 0.2.1) assigned a cell as labeled by a particular Hashtag oligo and thereby belonging to the specific mouse (bearing either MDA231-BrM metastases or HCC1954-BrM metastases) barcoded with this oligo or as a doublet or low-quality droplet.
Assembly: hg38 and mm38
Supplementary files format and content: barcode gene counts
Supplementary files format and content: gene counts
Supplementary files format and content: molecule counts

extract_protocol:
4 weeks post innoculation with cancer cells, brains were harvested from euthanized mice and processed for enzymatic tissue dissociation with the Adult Brain Dissociation kit, removal of myelin with myelin removal beads II, and removal of debris and dead cells. Single cell suspensions of each sample were incubated with an anti-human Hashtag antibody and an anti-mouse Hashtag antibody, 1:100 TruStain FeX Fc receptor blocking solution, 1:100 TruStain FeX anti-mouse CD16/32 antibody, and 1:20 APC Annexin V. Calcein Violet positive and Annexin V negative cells of each sample were sorted into 3 groups, GFP positive mCherry positive, GFP negative mCherry positive, and GFP negative mCherry negative cells.
Single-cell RNA-Seq of FACS-sorted cell suspensions was performed on the Chromium instrument (10X genomics). Droplet encapsulation was performed on the cells after sorting and viability assessment. After reverse transcription and cell barcoding within droplets, emulsions were broken and cDNA purified using Dynabeads MyOne SILANE followed by PCR amplification per user manual instruction. Resulting libraries were sequenced on Illumina NovaSeq S4 platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles).

value: breast cancer cell line

value: brain metastatic derivative


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B12_AD001


title: Cancer cells 2 HTO


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B12_AD010


title: rep2, plate5, spaceA10

value: otic vesicle and periotic tissue

value: tdTomato+


title: Cancer cells 1 HTO

description:
2108_Cancer_cells_IGO_11324_13_sparse_counts_barcodes.csv
2108_Cancer_cells_IGO_11324_13_sparse_counts_genes.csv
2108_Cancer_cells_IGO_11324_13_sparse_molecule_counts.csv

value: brain


title: rep2, plate4, spaceA10


title: Cancer cells 1


title: MSE2

description: SR75 run type

value: myeloid


title: MSE1

description: SR75 run type

value: primary cells


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B11_AD010

value: SC

value: female


title: MSA3

description: SR75 run type

source_name: human Mast cell + S aureus

value: WT

value: hMC treated with sterile supernatant of bacteria Staphylococcus aureus SA113 strain


title: rep1, plate3, spaceA10


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B11_AD008

value: P

value: male


title: rep1, plate2, spaceA10


title: AML_148

city: Hong Kong

first: Margaret HL

last: Ng

address: Prince of Wales Hospital

department: Department of Anatomical and Cellular Pathology

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
Transcripts per million (TPM) were quantified by salmon (v1.5.2) with human transcriptome (ensembl annotation version GRCh37.75)
Data processing was performed using the Ubuntu 18.04.6 platform.
Assembly: GRCh37.75
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: bone marrow

extract_protocol:
RNA was extracted using QIAamp RNA Blood Mini Kit (Qiagen).
mRNA library preparation (poly A enrichment) done by Novogene.

value: bone marrow

value: leukemic blast cells

value: pretreatment diagnostic


title: AML_147


title: rep2, plate6, spaceA10


title: rep1, plate1, space A10


title: AML_146


title: MSA1

description: SR75 run type

value: CD34 positive cells


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B11_AD007


title: AML_137


title: rep2, plate6, spaceA1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B11_AD001

value: THl

value: STR


title: MT3

description: SR75 run type

source_name: human Mast cell + TSB (control)

value: hMC treated with 3% Tryptic Soy Broth (TSB) which is used for bacteria culture medium, so this is the control for bacteria supernatants treatments


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B11_AD012


title: rep1, plate3, spaceA4

value: otic vesicle and periotic tissue

value: tdTomato+


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B10_AD012

value: brain


title: AML_118


title: rep2, plate5, spaceA1


title: rep2, plate4, spaceA1


title: AML_115


title: MT2

description: SR75 run type

value: primary cells

value: myeloid


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B10_AD010

value: SC

value: female


title: MT1

description: SR75 run type

value: WT


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B10_AD008

value: P


title: rep1, plate3, spaceA1


title: AML_113


title: human Mast cell after coculture + S aureus

description: SR75 run type

data_processing:
Partek software 10.0.22.0330
Sequence reads were trimmed for adaptor sequence/low-quality sequence (parameter- Quality limit: 0.05)
Alligment STAR 2.7.8a
Assembly: Assembly hg38 rel 105
Supplementary files format and content: tab-delimited text files include Attrbute values for each Sample: sample_names and attributes_attributes.txt
Supplementary files format and content: tab-delimited text files include GSA for each Sample: gene_list_GSA_report.txt
Supplementary files format and content: tab-delimited text files include DESeq2 values for each Sample: DESeq2 Report.txt
Supplementary files format and content: tab-delimited text files include feature distribution normalized: feature_distribution_normalized_CPM.tx5
Supplementary files format and content: tab-delimited text files include feature distribution for transcript: feature_distribution of transcript-level.txt
Supplementary files format and content: tab-delimited text files include gene level distribution: gene_level_feature_distribution.txt
Supplementary files format and content: tab-delimited text files include QuantificationSummary(gene counts): QuantificationSummary(gene counts).txt
Supplementary files format and content: tab-delimited text files include QuantificationSummary(transcripts): QuantificationSummary of transcript levels.txt

source_name: CD34 positive cells

extract_protocol:
5. Collect the cells, make the final concentration for each sample is 1000 cells/uL in PBS with 0.04% BSA. For FB collection, TrypLE Express Enzyme from Invitrogen was used to detach the FB from the 6-well plate.
The protocol used was the Illumina Truseq stranded mRNA kit, with sequencing then done at 75 base pair, single reads, on a Hiseq 4000.

value: these groups are hMCs cocultured with fibroblasts for 7 days, then the hMC treated with sterile supernatant of bacteria Staphylococcus aureus SA113 strain


title: MSA2

description: SR75 run type

value: hMC treated with sterile supernatant of bacteria Staphylococcus aureus SA113 strain


title: human Mast cell after coculture + S epidermidis

description: SR75 run type

value: these groups are hMCs cocultured with fibroblasts for 7 days, then the hMC treated with Staphylococcus epidermidis 12228 strain


title: AML_105

value: bone marrow

value: leukemic blast cells

value: pretreatment diagnostic


title: MMTV-ErbB2-Par

description:
MMTV-Erbb2_NormalizedCounts.csv
MMTV-Erbb2_RawCounts.xlsx

data_processing:
FASTQ raw sequences were mapped by STAR RNA-seq aligner using human genome reference GRCh38 and mouse genome reference GRCm38
Uniquely mapped reads were assigned to annotated genes by HTSeq to measure read counts
Counts were normalized by library size to be subject to differential gene expression analysis
Assembly: GRCh38 and GRCm38
Supplementary files format and content: Processed data files are formated for normalized gene counts
Supplementary files format and content: Gene names are listed in the first column

growth_protocol: Cells were grown in either DMEM or RPMI based media supplemented with 10% FBS, 2mM L-glutamine, 100IU.mL Pen/strep, and 1 µg/mL amphotericin B to a confluence of 80%

extract_protocol:
Cells were extracted as a pellet and lysed using the QIAshredder columns in Buffer RLT from QIAgen supplemented with 1:100 β-Mercaptoethanol. RNA isolation was performed usng the QIAgen RNeasy mini kit.
cDNA libraries were constructed using either TruSeq RNA Sample Prep Kit v2 or NEBNext Ultra RNA Library Prep Kit and sequenced on a HiSeq 2500 system at a depth of 25-50 million reads per sample

value: breast cancer cell line

value: parental


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B10_AD007

value: male


title: MMTV-ErbB2-Par 2


title: AML_98


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B10_AD006

value: THp

value: STR


title: human Mast cell after coculture + TSB (control)

description: SR75 run type

value: CD34 positive cells

value: primary cells

value: these groups are hMCs cocultured with fibroblasts for 7 days, then the hMC treated with TSB


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B10_AD004

value: brain


title: human Mast cell after coculture + LTA

description: SR75 run type

value: myeloid

value: WT

value: these groups are hMCs cocultured with fibroblasts for 7 days, then the hMC treated with LTA in PBS


title: AML_97


title: MMTV-ErbB2-BrM 2a 2

value: brain metastatic derivative


title: MMTV-ErbB2-BrM 2a 1


title: human Mast cell after coculture + PBS (control)

description: SR75 run type

value: these groups are hMCs cocultured with fibroblasts for 7 days, then the hMC treated with PBS, control


title: human Mast cell + S aureus

description: SR75 run type

value: hMC treated with sterile supernatant of bacteria Staphylococcus aureus SA113 strain


title: AML_94

value: bone marrow

value: leukemic blast cells


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B10_AD002

value: THl

value: female


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_B10_AD001

value: male


title: AML_92

value: pretreatment diagnostic


title: AML_93


title: human Mast cell + S epidermidis

description: SR75 run type

value: hMC treated with sterile supernatant of bacteria Staphylococcus epidermidis 12228 strain


title: MMTV-ErbB2-BrM 2a

value: breast cancer cell line


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A9_AD012

value: SC

value: P


title: 41BB CAR, day 6, biol rep 3, ATACseq

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq2 software.
ATAC-seq reads were trimmed using attack (version 0.1.5, https://atactk.readthedocs.io/en/latest/index.html)
Trimmed ATAC-seq reads were aligned to the UCSC hg19 using Bowtie version 1.1.2.
Peaks were called uing MACS with the significance cut-off FDR <=0.05
narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg19
Supplementary files format and content: narrowPeak

extract_protocol:
Omni-ATAC protocol: Nuclei were isolated from 50,000 sorted CART19 cells, followed by the transposition reaction using Tn5 transposase (Illumina) for 30 minutes at 37°C with 1000rp mixing.Purification of transposed DNA was completed with DNA Clean and Concentrator (Zymo)
Omni-ATAC protocol: DNA fragments were barcoded with ATAC-seq indices.Final libraries were double size selected using AMPure beads prior to sequencing.

value: Primary

value: CD19-directed human CAR T cells containing 41BB

value: Co-culture with Nalm6 cells

value: Day 6


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A9_AD008

value: brain


title: 41BB CAR, day 13, biol rep 3, ATACseq

value: Day 13


title: 41BB CAR, day 0, biol rep 3, ATACseq

value: Day 0


title: human Mast cell + TSB (control)

description: SR75 run type

value: CD34 positive cells

value: primary cells

value: myeloid

value: WT

value: hMC treated with 3% Tryptic Soy Broth (TSB) which is used for bacteria culture medium, so this is the control for bacteria supernatants treatments


title: human Mast cell + LTA

description: SR75 run type

value: hMC treated with LTA in PBS


title: MMTV-ErbB2-Par 1

value: parental


title: human Mast cell + PBS (control)

description: SR75 run type

value: hMC treated with PBS , so this is the control for LTA treatments


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A9_AD006

value: THp

value: STR

value: female


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A9_AD004

value: male


title: 41BB CAR, day 6, biol rep 2, ATACseq

value: Primary

value: CD19-directed human CAR T cells containing 41BB

value: Co-culture with Nalm6 cells


title: 41BB CAR, day 13, biol rep 2, ATACseq

value: Day 13


title: AML_70

value: bone marrow

value: leukemic blast cells

value: pretreatment diagnostic


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A9_AD002

value: brain

value: THl


title: S9_5hmC.19_Normalized_Counts

city: Rochester

first: Lilach

middle: O

last: O Lerman

state: Minnesota

address: 200 First St. SW

department: Division of Nephrology & Hypertension

institute: Mayo Clinic

data_processing:
Paired-end sequenced FASTQ files were aligned to the human reference genome (hg38) using Bowtie 2 (v2.3.3.1).
Duplicate reads were removed with MarkDuplicates (PICARD v1.67), and hMeDIP-seq peaks were called using MACS2.
Differential binding analysis of hMeDIP-seq peak data was performed using the DiffBind package (v2.14.0), and the Homer (v4.10) peak annotation tool was used to annotate and assign differential peaks and genomic coverage bins.
5hmC coverage analysis applied per-base coverage of regions of interest, calculated with bedtools (v2.20.0) genomeCoverageBed.
Sequence read values for overall exonic 5hmC coverage per gene were calculated as faux-RNA counts using htseq-count (v0.9.1) and then processed by edgeR (v3.28.1), analagous to differential expression analysis of RNA reads.
Assembly: hg38
Supplementary files format and content: A single tab-delimited text file provides normalized counts describing overall exonic 5hmC coverage per gene for 10 samples
Library strategy: hMeDIP-Seq

source_name: MSCs, human, Lean

growth_protocol: Primary human MSCs isolated from subcutaneous abdominal adipose tissue were expanded in culture. Briefly, adipose tissue was enzymatically digested using collagenase-H, filtered through a 100μm cell strainer, and centrifuged to pellet cells. Cells were then cultured for three weeks in T-75 cm2 flasks (TPP, Cat.#Z707503) placed within a humidified incubator (37°C/5% CO2), using a growth medium consisting of Advanced Minimum Essential Medium (Gibco, Carlsbad, CA, Cat.#12492013) supplemented with 5% platelet lysate (PLTmax, Mill Creek Life Sciences, Rochester, MN) and 2 mM L-glutamine (Gibco, Cat.#25030081). MSCs were passaged at 60-80% confluence using TrypLe (Gibco, Cat.#12604013) for 3-4 passages.

extract_protocol:
DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen, Cat.#69504) with RNase treatment. DNA concentrations were measured by a spectrophotometer (NanoDrop) and diluted to 100ng/μL with TE buffer. The aliquot (100μL) of genomic DNA was sonicated using a Bioruptor® Pico instrument (Diagenode) for 7-10 cycles at 30 seconds on and 30 seconds off. The size of fragmented DNA was determined using a Fragment Analyzer (Advanced Analytical Technologies, Ankeny, IA) with the High Sensitivity NGS Fragment Analysis Kit (Cat.#DNF-486). Fragmented DNA with an average size of 200bp was denatured for 10min at 95°C, after which 2.5-5μg of DNA in 1X DNA immunoprecipitation (DIP) buffer (10mM sodium phosphate, pH 7.0, 140mM NaCl, 0.05% Triton X-100) was incubated with 1μg of anti-5hmC antibody from the hybridoma clone EDL HMC 1A (equivalent to Cat.#MABE1093 from MilliporeSigma) for 3hr at 4°C on a rotator. Dynabeads Protein-G (Thermo-Fisher, Cat.#10003D) were added to the DNA/antibody mixture, and the reaction was incubated at 4°C overnight on a rotator. Collected beads-antibody-DNA complexes were then thoroughly washed with DIP buffer and TE buffer. The enriched DNA fragments were eluted from the beads, purified using the ssDNA/RNA Clean & Concentrator (Zymo Research, Cat.#D7010), and quantified with the Qubit ssDNA High Sensitivity Assay Kit (Thermo-Fisher Scientific, Cat.#Q10212).
DNA libraries were generated from input and enriched DNAs using the Accel-NGS® 1S Plus DNA Library Kit (Swift Biosciences, Cat.#10024), according to the manufacturer’s protocol

value: subcutaneous adipose tissue

value: mesenchymal stem/stromal cells (MSCs)

tag: hmedip-seq antibody

tag: disease state

value: Healthy control:BMI<30kg/m2


title: 41BB CAR, day 6, biol rep 1, ATACseq

value: Day 6


title: AML_69


title: AML_81

source_name: peripheral blood

value: peripheral blood


title: 41BB CAR, day 0, biol rep 2, ATACseq

value: Day 0


title: AML_52


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A9_AD001

source_name: brain

value: STR


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A8_AD010

value: SC

value: P

value: female


title: AML_50


title: AML_55


title: AML_79


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A8_AD012


title: 41BB CAR, day 13, biol rep 1, ATACseq

value: Primary

value: CD19-directed human CAR T cells containing 41BB

value: Co-culture with Nalm6 cells


title: S2_5hmC.17_Normalized_Counts

value: anti-5hmC antibody from the hybridoma clone EDL HMC 1A (equivalent to Cat.#MABE1093 from MilliporeSigma)


title: S5_5hmC.8_Normalized_Counts


title: AML_71

value: bone marrow

value: leukemic blast cells

value: pretreatment diagnostic


title: S4_5hmC.7_Normalized_Counts

value: subcutaneous adipose tissue


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A9_AD007

value: brain

value: male


title: 41BB CAR, day 0, biol rep 1, ATACseq


title: AML_41


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A8_AD008


title: CD28 CAR, day 6, biol rep 3, ATACseq

value: CD19-directed human CAR T cells containing CD28

value: Day 6


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A8_AD007


title: AML_35


title: S8_5hmC.10_Normalized_Counts

source_name: MSCs, human, Obese

value: mesenchymal stem/stromal cells (MSCs)


title: S7_5hmC.18_Normalized_Counts


title: S1_5hmC.16_Normalized_Counts

value: Healthy control:BMI<30kg/m2


title: S6_5hmC.9_Normalized_Counts


title: S3_5hmC.6_Normalized_Counts


title: CD28 CAR, day 0, biol rep 3, ATACseq

value: Day 0


title: AML_44


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A8_AD002

value: THl

value: STR


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A8_AD006

value: THp

value: female


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A8_AD004


title: CD28 CAR, day 6, biol rep 2, ATACseq

value: Primary

value: Co-culture with Nalm6 cells


title: CD28 CAR, day 17, biol rep 2, ATACseq

value: Day 17


title: AML_21

value: bone marrow

value: leukemic blast cells


title: MEPH + BeWo Conditioned Media 4

city: Ann Arbor

first: Kelly

last: Bakulski

state: MI

address: 1415 Washington Heights

department: Department of Epidemiology

institute: University of Michigan

data_processing:
Raw fastq files were first examined using fastQC (version 0.11.5) (Andrews 2010), and reports generated for all 24 samples were collated using multiQC (version 0.9)
Mapped reads to the human reference genome (hg38) were done using the Spliced Transcripts Alignment to a Reference (STAR) (version 2.6.0c)
Following mapping, featureCounts (version 1.6.1) was used to quantify aligned reads mapping to exons.
Quantification output from featureCounts was read into R (version 3.6.0), and analyzed with the DESeq2 package (version 1.24.0)
Genome_build: hg38
Supplementary_files_format_and_content: matrix of normalized counts for each gene and sample

source_name: K-562 hematopoietic stem cell line

growth_protocol: K-562 cells were plated at 100,000 cells/mL in 25 mL of Iscove's Modified Dulbecco's Medium in Corning T-175 flasks. Cell cultures were maintained in a 5% CO2, 37°C controlled and humidified incubator.

extract_protocol:
RNA was extracted from K-562 cells using the RNeasy PLUS Mini Kit from Qiagen (Germantown, MD) following the manufacturer-supplied instructions, with the addition of a 2-minute spin at 15,000 x g in the QIAshredder (Qiagen, Germantown, MD) prior to the genomic DNA elimination step
TruSeq Stranded mRNA Library Prep Kit (lllumina, San Diego, CA) using standard protocol

treatment_protocol: After 72 hours in culture, cells were washed 3x with PBS and treated for 24 hours with either: 1) unconditioned media, 2) BeWo conditioned media or 3) MEHP(10µM)+BeWo conditioned media

value: MEPH + BeWo Conditioned Media

tag: batch


title: AML_20

value: pretreatment diagnostic


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A7_AD010

value: brain

value: SC

value: P


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A7_AD012


title: CD28 CAR, day 0, biol rep 2, ATACseq

value: CD19-directed human CAR T cells containing CD28


title: K562 cells, STIM1::MXD3, replicate 1

data_processing:
Paired-end sequencing reads were aligned to the reference genome (hg19) by HISAT2 (v2.2.1).
Read counts were quantified by featureCounts (v2.0.1).
Data processing was performed using the Galaxy platform.
Assembly: hg19
Supplementary files format and content: tab-delimited text files containing read counts

value: myeloid leukemia

value: no treatment


title: S10_5hmC.20_Normalized_Counts

value: subcutaneous adipose tissue

value: mesenchymal stem/stromal cells (MSCs)

value: anti-5hmC antibody from the hybridoma clone EDL HMC 1A (equivalent to Cat.#MABE1093 from MilliporeSigma)


title: BeWo Conditioned Media 4

value: BeWo Conditioned Media


title: Unconditioned Media 4

value: Unconditioned Media


title: K562 cells, STIM1::MXD3, replicate 2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A7_AD004

value: THp

value: STR

value: male


title: CD28 CAR, day 17, biol rep 1, ATACseq

value: Primary

value: Co-culture with Nalm6 cells

value: Day 17


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A7_AD006

value: brain

value: female


title: K562 cells, MXD3, replicate 2


title: MEPH + BeWo Conditioned Media 3

value: MEPH + BeWo Conditioned Media


title: CD28 CAR, day 17, biol rep 3, ATACseq

value: CD19-directed human CAR T cells containing CD28


title: CD28 CAR, day 0, biol rep 1, ATACseq

value: Day 0


title: AML_27

value: bone marrow

value: leukemic blast cells

value: pretreatment diagnostic


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A7_AD001

value: THl


title: K562 cells, MXD3, replicate 1

value: myeloid leukemia

value: no treatment


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A6_AD012

value: SC

value: P


title: K562 cells, emtpy vector control, replicate 2

value: control


title: NPC, INTS10HET2, replicate 1, scRNAseq

city: Philadelphia

first: Alessandro

last: Gardini

state: PA

address: 3601 Spruce St, Room 230

institute: The Wistar Institute

description: 10x Genomics

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
Base calling: Cell Ranger mkfastq pipeline v6.1.1  ( 10X Genomics)
Count matrix:  Cell Ranger count pipeline v6.1.1 (10X Genomics)
Normalization: Cell Ranger aggr pipeline
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: NPC

growth_protocol: NPCs were differentiated from iPSCs using Neural Induction Medium (98% Neurobasal Meida (ThermoFisher, cat#21103049) and 2% Neuronal Induction Supplementd) for 7 days and maintained in Neural Expansion Medium (49% Neurobasal Meida (ThermoFisher, cat#21103049), 49% Advanced DMEM/F12 (ThermoFisher, cat#12634010) and 2% Neuronal Induction Supplement.

extract_protocol:
To harvest cells for single-cell RNAseq, cultured NPCs were incubated with Accutase (A6964) for 5 min at 37 ℃. An equal volume of DPBS was added to each well to collect the cells. Cell suspension was strained through 40um Cell Strainer (XXXX) twice. The single cell suspension was centrifuged at 400 x g for 5 mins and resuspended in DPBS for counting. Cell viability was examined by 0.4% Trypan blue. Single cell suspension with 98% viability containing 15, 000 viable cells (aiming for recovery of 10, 000 cells) were processed using the Chromium Next GEM Single Cell 3' Kit v3.1 to generate cDNA libraries following manufacture's instructions. The quality of cDNA and libraries were assessed by the Agilent 2100 Bioanalyzer System ( or TapeStation). Libraries were sequenced on IllumniaXXXXX.
Chromium Next GEM Single Cell 3' Kit v3.1

treatment_protocol: Lentiviruses were produced in HEK293T cells by co-transfection 8 ug of pLentiCRISPR v2-INTS10 gRNA3 (Target sequence: TTCTGAGAGCTACGTTTGCT). iPSCs or SH-SY5Y were passaged into a 6-well plate at 30-40 % confluence. When the cells reached 60-70% confluence, 2 ml of virus medium per well (cell medium with 4 ul of lentiviral particles per ml and 8 ug/ml polybrene (Thermo Fisher, cat#TR1003G)) was added to replace old medium. 24 hours after induction, the virus medium was removed and replaced with fresh cell culture medium for another 48 hours. After that, cells were selected with with 0.5 ug/ml of puromycin in fresh medium (InvivoGen, cat#ant-pr-1). 48 hours after selection with puromycin, iPSC colonies were disassociated with Accutase and passed through a 40 uM cell stainer to to generate single cells. Singel cell suspension with 10 μM of ROCK inhibitor and 0.5 ug/ml of puromycin were seeded in Geltrex-coated 10 cm dishes.  ROCK inhibitor was removed 24 hours after the seeding. Single cells were cultured in iPSC medium with 0.5 ug/ml of puromycin for the next 2-3 weeks until iPSC colonies appeared.

value: NPC

value: neuronal progenitor cell differentated from pluripotent stem cells

value: No treatment

tag: age

value: 6-8 weeks old


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A6_AD010

value: brain

value: female


title: CD28 CAR, day 6, biol rep 1, ATACseq

source_name: Engineered T cells

value: Primary

value: CD19-directed human CAR T cells containing CD28

value: Co-culture with Nalm6 cells

value: Day 6


title: K562 cells, emtpy vector control, replicate 1


title: BeWo Conditioned Media 2

value: BeWo Conditioned Media


title: MEPH + BeWo Conditioned Media 2

value: MEPH + BeWo Conditioned Media


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A6_AD008

value: male


title: K562 cells, SRP72 p.R124S, replicate 2

value: myeloid leukemia

value: SRP72 p.R124S

value: no treatment


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A6_AD007

value: SC

value: P


title: iPSC-NK5A, clone 29, replicate 2

city: Granada

first: Verónica

last: Ramos-Mejia

state: Granada

address: P. T. Ciencias de la Salud, Avda. de la Ilustración 114

department: Gene Regulation, Stem cells and Development

country: Spain

institute: GENYO, Centre for Genomics and Oncological Research Pfizer - University of Granada - Andalusian Regional Government

data_processing:
Quality control was carried out using FastQC (version 0.11.5).
Alignment of RNA was performed using RSEM software with default parameters and using the GRCh38.p13 as reference genome.
Two biological replicates were sequenced for each clone. We obtained gene expression data for each replicate (.genes.results files) and collapsed the two replicates of each clone by mean of their expected_counts, resulting in a genes/samples matrix of counts that we used in our analysis.
Assembly: GRCh38.p13
Supplementary files format and content: genes.results files: Tab-delimited text files with processed data of each biological replicate. Including gene_id and transcript_id in Ensembl format, length, effective_length, expected_count, TPM and FPKM. Expected_count was used in the subsequent analysis.
Supplementary files format and content: CSV file: Comma-delimited text file include gene counts values for all samples, obtained by mean of the two biological replicates. Each column corresponds to one sample. Each row corresponds to one Ensembl gene identifier.

growth_protocol: iPSC-NK5A and Control clones were cultured in 5% CO2 at 37ºC on Matrigel® Matrix (Corning; Corning, New York, USA). The cells were maintained using Essential 8 (E8) growth medium with daily media changes.

extract_protocol:
RNA was extracted using the NuceloSpin® RNA kit (Macherey-Nagel) according to the manufacturer’s instructions. Concentration and quality of extracted RNA were measured using the Qubit 4 Fluorometer (Thermo Fisher Scientific, MA, USA) and the 2100 Bioanalyzer Instrument (Agilent Technologies, CA, USA) using an RNA 6000 Nano Kit.
Libraries from mRNA were prepared using 800 ng of RNA starting material and the TruSeq Stranded mRNA Library Prep Kit (Illumina, CA, USA) according to the manufacturer’s protocol. This protocol captures poly-adenylated RNA by transcription by oligo-dT primer, after which the RNA is fragmented. The sample is back transcribed to generate the cDNA, both in the first and second strands. The 3 'ends are adenylated, the adapters and barcodes are ligated, and finally, it is enriched by PCR. Adapters and samples codes (index-barcodes) are added to the libraries to be able to be sequenced simultaneously. mRNA libraries were sequenced on the NextSeq 500 system (Illumina, CA, USA) using the highest output mode and paired-end 75 bp read lengths with a depth of 25 million reads for each sample.

value: Induced Pluripotent Stem Cell


title: iPSC-NK5A, clone 29, replicate 1


title: iPSC-NK5A, clone 27, replicate 2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A6_AD006

value: THp

value: STR


title: K562 cells, SRP72 wt, replicate 3

value: SRP72 wild-type


title: MEPH + BeWo Conditioned Media 1


title: Unconditioned Media 2

value: Unconditioned Media


title: iPSC-NK5A, clone 26, replicate 2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A6_AD004

value: brain


title: iPSC-NK5A, clone 27, replicate 1


title: Unconditioned Media 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A6_AD001

value: THl


title: K562 cells, SRP72 wt, replicate 2


title: BeWo Conditioned Media 3


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A5_AD012

value: female


title: NPC, WT, replicate 1, scRNAseq

description: 10x Genomics

value: NPC

value: neuronal progenitor cell differentated from pluripotent stem cells

value: wt

value: No treatment

value: 6-8 weeks old


title: BeWo Conditioned Media 1

value: BeWo Conditioned Media


title: K562 cells, SRP72 p.R124S, replicate 3

value: myeloid leukemia

value: SRP72 p.R124S

value: no treatment


title: K562 cells, RUNX1::ERG, replicate 2


title: K562 cells, SRP72 wt, replicate 1


title: iPSC-NK5A, clone 26, replicate 1

value: Induced Pluripotent Stem Cell


title: iPSC-control, clone 18, replicate 2


title: Skin, Sitagliptin

city: Leipzig

first: Maria

last: Schmidt

address: Härtelstr. 16-18

country: Germany

institute: IZBI

data_processing:
For further analysis and read alignment CellRanger software v3.1.0 was used.
Assembly: mm10-3.0.0
Supplementary files format and content: Filtered feature-barcode matrices in Market Exchange Format (MEX) outputted by cellranger. Each element of the feature-barcode matrix is the number of UMIs associated with a feature (row) and a cell-associated barcode (column).
Supplementary files format and content: TSV files with feature and barcode sequences corresponding to row and column indices, respectively, outputted by cellranger.

source_name: Skin

growth_protocol: 8 Week old mice C57Bl6, male and female

extract_protocol: Chromium 10X

treatment_protocol: Intradermal injection 100 ng Sitagliptin in 100 µl PBs or PBs alone (control), 48 h after processing of the skin

value: Skin

value: Sitagliptine


title: Unconditioned Media 3


title: Skin, PBS

value: PBS


title: K562 cells, SRP72 p.R124S, replicate 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A5_AD008

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

value: SC

value: P

value: male


title: K562 cells, RUNX1::ERG, replicate 1


title: iPSC-control, clone 2, replicate 2


title: iPSC-control, clone 18, replicate 1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A5_AD007

value: brain


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A5_AD001

value: THl

value: STR


title: iPSC-control, clone 2, replicate 1


title: K562 cells, empty vector, replicate 2

value: control


title: K562 cells, empty vector, replicate 1


title: MCRIi018-B_osteo_D73_rep4

city: Parkville

first: Shireen

last: Lamande

state: Victoria

address: Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

data_processing:
adaptors trimmed with Trimmomatic v.0.35
reads mapped with STAR 2.7.3a
Reads over genes summarized with featureCounts
MultiQC to summarize the analyses
Downstream analyses used the EdgeR Bioconductor package. Genes with expression levels of at least one count per million in at least 3 samples were kept for further analyses
Data were TMM normalized and voom transformed. Differential expression was identified with robust paired moderated t tests using limma.
Assembly: hg38
Supplementary files format and content: comma separated .csv files containing RPKM for each sample

source_name: iPSC-derived osteogenic organoid

growth_protocol:
iPSCs differentiated to sclerotome in APEL2 medium during D1-6, cell pellets formed at D4 and transferred to rotary culture at D20. Pellets were treated with 20 ng/ml FGF2 from the end of D6 for 14 days then with 10nM T3 from D41, then grown for 3 weeks in osteogenic medium supplemented with 10 uM CHIR99021 for the first 7 days.
See individual samples in SAMPLES above

extract_protocol:
RNA extracted with TRIzol followed by purification using Direct-zol RNA Microprep kit spin columns (Zymo Research)
Illumina Stranded mRNA Prep kit

value: iPSC-derived osteogenic organoid

value: WT

value: osteogenic differentiation D73


title: iPSC-control, clone 1, replicate 1


title: iPSC-control, clone 1, replicate 2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A4_AD010

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.) or snmC-seq3 protocol described in (Liu, H. et al., Biorxiv. 2023:2023-04.). The libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

value: female


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A4_AD012


title: MCRIi018-B_osteo_D73_rep2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A4_AD008


title: human Mast cell + human fibroblasts

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Sequence reads were trimmed for adaptor sequence/low-quality sequence (parameter- Quality limit: 0.05)
Chemistry: Single cell 3" v3
Pipeline Version: cellranger-6.0.0
Partek software Loupe Cell browser 3.1.1
Assembly: Transcriptome: hg38rel 105
Supplementary files format and content: Fastaq.gz
Supplementary files format and content: cluope.cloupe

source_name: CD34  positve and dermal fibroblast

extract_protocol:
5. Collect the cells, make the final concentration for each sample is 1000 cells/uL in PBS with 0.04% BSA. For FB collection, TrypLE Express Enzyme from Invitrogen was used to detach the FB from the 6-well plate.
Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3

value: CD34  positve and dermal fibroblast

value: myeloid+mesenchymal


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A4_AD002


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A4_AD006

value: THp


title: MCRIi018-B_osteo_D73_rep1


title: Bone marrow cells harvested from transplanted mice, NT mouse D, scRNA-seq and barcoded antibody (ADT)

city: Cambridge

first: Jorge Diego

last: Martin Rufino

state: MA

address: 415 Main Street

institute: Harvard University / Broad Institute of MIT and Harvard / Boston Children's Hospital

description:
polyA RNA and protein
10x Genomics
mouse_transplant_filtered_feature_bc_matrix.h5
mouse_transplant_NT_mouse_D

library_source: other

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: hg38
Supplementary files format and content: h5 files, contains gene expression matrices and cropseq transcript matrices, and barcoded antibody matrices (if applicable)

molecule: other

organism:
Homo sapiens
Mus musculus

source_name: Hematopoietic system

extract_protocol:
Following final FACS enrichment to remove debris and purify transduced cells, 5-mL PBS-BSA coated tubes described above were spun down at 400 x g for 5 minutes at 4ºC. The entire supernatant was carefully removed and 1mL of PBS_0.05% BSA was added. Cells were then counted twice using an automated Countess 2 cell counter (Thermo Fisher, I-CACC2). Cell viability as determined by Trypan Blue was always >95%. Cells were again washed with 5mL PBS_0.05% BSA and resuspended at a final concentration of 1,000 cells / µL and kept on ice.
Single-cells were immediately processed using v3.1 Chemistry Dual Index kits according to manufacturer’s instructions (10X Genomics), using 20µL of cell suspension and 23.2 µL of water on the cell suspension loading step. Libraries were sequenced using a 28 base pair (Read 1), 10 base pair (Index 1), 10 base pair (Index 2), 90 base pair (Read 2) configuration on Nextseq 500, Nextseq 2000 or Novaseq S2/S4 instruments.

value: Bone marrow

value: Hematopoietic system

tag: library type

value: mRNA, ADT

tag: antibodies/tags

value: TotalSeq™-B0052 anti-human CD33 Antibody


title: Bone marrow cells harvested from transplanted mice, NT mouse C, scRNA-seq and barcoded antibody (ADT)

description:
polyA RNA and protein
10x Genomics
mouse_transplant_filtered_feature_bc_matrix.h5
mouse_transplant_NT_mouse_C

tag: tissue


title: MCRIi018-B_cartilage_D52_rep4

source_name: iPSC-derived cartilage

growth_protocol:
iPSCs differentiated to sclerotome in APEL2 medium during D1-6, cell pellets formed at D4 and transferred to rotary culture at D20. Pellets were treated with 20 ng/ml FGF2 from the end of D6 for 14 days then with 10nM T3 from D41.
See individual samples in SAMPLES above

value: iPSC-derived cartilage

value: chondrogenic differentiation D52


title: MCRIi018-B_cartilage_D52_rep3


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A3_AD012

value: brain

tag: source

value: SC

tag: target

value: P


title: dCISH NK 2

city: Kashihara

first: Tsutomu

last: Nakazawa

state: Nara

address: 840, Shijo-cho

country: Japan

institute: Nara medical university

hyb_protocol: According to Affymetrix Clariom™ S array protocol.

label: biotin

source_name: NK cell

growth_protocol: Human CD3-depleted PBMCs were stimulated by IL-2/IL-18 and following 14 days culture by IL-2.

extract_protocol: RNeasy protocol.

treatment_protocol: CIS genome edition.

value: NK

value: dCISH


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A3_AD010

tag: Sex


title: MCRIi019-A_osteo_D72_rep4

value: iPSC-derived osteogenic organoid

tag: genotype

value: WT

value: osteogenic differentiation D72


title: dCISH NK 1

scan_protocol: According to Affymetrix Clariom™ S array protocol.

tag: cell type


title: MCRIi018-B_cartilage_D52_rep2

tag: cell line


title: dCISH NK 3

data_processing: According to Affymetrix Clariom™ S array protocol.

tag: treatment


title: mock NK 2

label_protocol: According to Affymetrix Clariom™ S array protocol.

value: mock


title: mock NK 1


title: MCRIi019-A_osteo_D72_rep3


title: mock NK 3


title: Bone marrow cells harvested from transplanted mice, CD33 mouse A, scRNA-seq and barcoded antibody (ADT)

description:
polyA RNA and protein
10x Genomics
mouse_transplant_filtered_feature_bc_matrix.h5
mouse_transplant_CD33_mouse_A


title: MCRIi018-B_osteo_D73_rep3

value: osteogenic differentiation D73


title: MCRIi018-B_cartilage_D52_rep1


title: MCRIi019-A_osteo_D72_rep2


title: human fibroblasts only

description: 10x Genomics

source_name: dermis

value: dermis

value: mesenchymal

value: no treatment


title: Dataset D8 lib8

city: New York City

first: Itai

last: Yanai

address: 435 East 30th Street

institute: NYU Langone Health

description:
S. aureus grown to an OD600 of ~0.1 from JE2 WT and gbaA mutant, and sGFP reporter strains
D8_metadata.txt

data_processing:
All analysis was performed using the Tavazoie lab computational pipeline (https://tavazoielab.c2b2.columbia.edu/PETRI-seq/PETRI_Seq_Computational.pdf).
Initial QC was performed using FastQC then unique molecular identifiers were extracted with UMI tools. Initial demultiplexing by cell barcode was performed iteratively using Cutadapt.
After selecting barcodes associated with the highest number of reads, reads from individual barcodes were aligned to the S. aureus USA300-FPR3757 reference genome using BWA.
Numbers of reads mapping to individual genes were quantified using FeatureCounts before counts were collapsed into unique reads based on UMI and used to make the final counts matrix.
Sample annotations were extracted from the number of barcode 1, since this corresponds to the way samples were added in the initial plate during reverse transcription.
Assembly: S. aureus reads were aligned to the USA300_FPR3757 reference assembly (GCF_000013465.1).
Supplementary files format and content: Counts matrices: gzip-compressed tab-separated text files of counts by genes (columns) by cell barcode (rows) ("_counts.txt.gz")
Supplementary files format and content: Metadata files: tab-separated files containing library and sample information for each cell barcode ("_metadata.txt").

organism: Staphylococcus aureus

source_name: Whole bacteria

growth_protocol: Bacteria were streaked out onto agar from frozen stocks overnight then grown overnight in TSB. Samples were then diluted back to grow in the medium and to the densities indicated. There was an initial "back-dilution" step prior to harvesting to improve population homogeneity.

extract_protocol:
Samples were fixed and processed according to the protocol of Blattman et al. (PMID: 32451472). Briefly, cells were fixed overnight with 4% formaldehyde, permeabilized with 50% ethanol followed by enzymatic cell wall digestion (100 µg/ml lysostaphin, 15 min), then treated with DNase to remove genomic DNA.
Reverse transcription and split-pool barcode ligation were carried out in situ in fixed cells according to the protocol of  Blattman et al. (PMID: 32451472). After barcoding, cells were separated into aliquots of ~20,000 cells for further processing. After lysis and reversal of crosslinking, second strand synthesis was performed using the NebNext Second Strand Synthesis module (New England Biolabs) and tagmentation was carried out using the EZ-Tn5 transposase (Lucigen), before final amplification with multiplex indexing primers.

treatment_protocol: After growth as described, most bacteria were not subjected to further treatment.

value: Whole bacteria

value: Bacteria

value: JE2, JE2 PGbaA-L-sGFP, JE2 gbaA PGbaA-L-sGFP, JE2 Phom-sGFP

value: TSB


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A5_AD010

value: brain

value: female


title: MCRIi019-A_cartilage_D48_TGFb_rep4

growth_protocol:
iPSCs differentiated to sclerotome in APEL2 medium during D1-6, cell pellets formed at D4. Pellets were treated with 20 ng/ml FGF2 from the end of D6 for 14 days, and with 10 ng/ml TGFb3 from D13. Pellets transferred to rotary culture at D20.
See individual samples in SAMPLES above

value: iPSC-derived cartilage

value: chondrogenic differentiation D48 treated with TGFb from D13


title: human Mast cell

description: 10x Genomics

value: CD34 positive cells

value: myeloid


title: Dataset D8 lib7


title: Bone marrow cells harvested from transplanted mice, CD33 mouse B, scRNA-seq and barcoded antibody (ADT)

description:
polyA RNA and protein
10x Genomics
mouse_transplant_filtered_feature_bc_matrix.h5
mouse_transplant_CD33_mouse_B

value: Bone marrow

value: Hematopoietic system

value: mRNA, ADT

value: TotalSeq™-B0052 anti-human CD33 Antibody


title: MCRIi019-A_cartilage_D48_TGFb_rep3

value: WT


title: MCRIi019-A_cartilage_D51_rep4

value: chondrogenic differentiation D51


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A3_AD007

value: SC

value: P

value: male


title: Dataset D8 lib6

value: Whole bacteria

value: Bacteria

value: JE2, JE2 PGbaA-L-sGFP, JE2 gbaA PGbaA-L-sGFP, JE2 Phom-sGFP


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A3_AD006

value: brain

value: THp

value: STR

value: female


title: MCRIi019-A_cartilage_D51_rep3

value: iPSC-derived cartilage


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A3_AD004


title: MCRIi019-A_cartilage_D48_TGFb_rep2

value: chondrogenic differentiation D48 treated with TGFb from D13


title: MCRIi019-A_cartilage_D51_rep2


title: MCRIi019-A_cartilage_D51_rep1


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A3_AD002

value: THl


title: MCRIi019-A_cartilage_D48_TGFb_rep1


title: Dataset D8 lib5

value: TSB


title: Dataset D8 lib4


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A3_AD001


title: MCRIi019-A_osteo_D72_rep1

value: iPSC-derived osteogenic organoid

value: osteogenic differentiation D72


title: MCRIi019-A_cartilage_D48_noTGFb_rep4

growth_protocol:
iPSCs differentiated to sclerotome in APEL2 medium during D1-6, cell pellets formed at D4. Pellets were treated with 20 ng/ml FGF2 from the end of D6 for 14 days. Pellets transferred to rotary culture at D20.
See individual samples in SAMPLES above

value: WT

value: chondrogenic differentiation D48


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A3_AD008

value: SC

value: P


title: Dataset D8 lib2

value: Whole bacteria


title: MCRIi019-A_cartilage_D69T3_rep3

growth_protocol:
iPSCs differentiated to sclerotome in APEL2 medium during D1-6, cell pellets formed at D4. From D6 pellets transferred to rotary culture in APEL2 medium +  20 ng/ml FGF2 until D34 then in APEL2 medium alone. From D48 medium supplemented with 10nM T3
See individual samples in SAMPLES above

value: chondrogenic differentiation D69 treated with T3 from D48-D69


title: MCRIi019-A_cartilage_D69T3_rep2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A2_AD010


title: MCRIi019-A_cartilage_D48_noTGFb_rep3


title: MCRIi019-A_cartilage_D69T3_rep1


title: Dataset D8 lib1

value: Bacteria

value: JE2, JE2 PGbaA-L-sGFP, JE2 gbaA PGbaA-L-sGFP, JE2 Phom-sGFP


title: MCRIi019-A_cartilage_D48_noTGFb_rep2


title: MCRIi019-A_cartilage_D48_noTGFb_rep1


title: MCRIi019-A_cartilage_D69_rep3

growth_protocol:
iPSCs differentiated to sclerotome in APEL2 medium during D1-6, cell pellets formed at D4. From D6 pellets transferred to rotary culture in APEL2 medium +  20 ng/ml FGF2 until D34 then in APEL2 medium alone
See individual samples in SAMPLES above

value: chondrogenic differentiation D69


title: Dataset D7 lib8

description: S. aureus grown to an OD600 of ~0.1 then treated with 10 µg/ml vancomycin for 0, 6, 12, and 25 min

data_processing:
All analysis was performed using the Tavazoie lab computational pipeline (https://tavazoielab.c2b2.columbia.edu/PETRI-seq/PETRI_Seq_Computational.pdf).
Initial QC was performed using FastQC then unique molecular identifiers were extracted with UMI tools. Initial demultiplexing by cell barcode was performed iteratively using Cutadapt.
After selecting barcodes associated with the highest number of reads, reads from individual barcodes were aligned to the E. coli MG1655  and S. aureus USA300-FPR3757 reference genomes using BWA.
Numbers of reads mapping to individual genes were quantified using FeatureCounts before counts were collapsed into unique reads based on UMI and used to make the final counts matrix.
Sample annotations were extracted from the number of barcode 1, since this corresponds to the way samples were added in the initial plate during reverse transcription.
Assembly: E. coli reads were aligned to the K-12 MG1655 reference assembly (GCA_000005845.2) and S. aureus to the USA300_FPR3757 reference assembly (GCF_000013465.1).
Supplementary files format and content: Counts matrices: gzip-compressed tab-separated text files of counts by genes (columns) by cell barcode (rows) ("_counts.txt.gz")
Supplementary files format and content: Metadata files: tab-separated files containing library and sample information for each cell barcode ("_metadata.txt").

growth_protocol: Bacteria were streaked out onto agar from frozen stocks overnight then grown overnight in LB or TSB as indicated. Samples were then diluted back to grow in the medium and to the densities indicated. With the exception of Datasets D3 and D4, there was an initial "back-dilution" step prior to harvesting to improve population homogeneity.

extract_protocol:
Samples were fixed and processed according to the protocol of Blattman et al. (PMID: 32451472). Briefly, cells were fixed overnight with 4% formaldehyde, permeabilized with 50% ethanol followed by enzymatic cell wall digestion (100 µg/ml, 15 min using lysozyme for E. coli and lysostaphin for S. aureus), then treated with DNase to remove genomic DNA (this step was ommited for some samples in Dataset D4).
Reverse transcription and split-pool barcode ligation were carried out in situ in fixed cells according to the protocol of  Blattman et al. (PMID: 32451472). After barcoding, cells were separated into aliquots of ~20,000 cells for further processing. After lysis and reversal of crosslinking, second strand synthesis was performed using the NebNext Second Strand Synthesis module (New England Biolabs) and tagmentation was carried out using the EZ-Tn5 transposase (Lucigen), before final amplification with multiplex indexing primers.

treatment_protocol: After growth as described, most bacteria were not subjected to further treatment with the exception of some cells in Dataset D6 that were treated with 10 mM N-acetylcysteine for 90 min, and for cells in Dataset D7 that were treated with 10 µg/ml vancomycin for variable times.

value: USA300 LAC

value: TSB + 10 µg/ml vancomycin


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A2_AD008

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

value: brain

value: male


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A2_AD007


title: AC130_romi

city: St Louis

first: Tiandao

last: Li

address: 4444 Forest Park Ave

institute: Washington University

data_processing:
Raw fastq files were aligned against human genome hg38 assembly using Burrows-Wheeler Alignment tool and then processed using methylQA to generate bed and bigwig files.
The MACS2 peak caller was used to compare the ChIP-Seq signal to a corresponding input control to identify narrow regions of enrichment (peaks) using default parameters.
ChIP-Seq signals and peak locations were further visualized using UCSC Genome Browser.
The top 500-1000 ChIP-Seq peaks were assigned to the nearest genes using the annotatePeaks function from HOMER2, motif binding sites were determined using HOMer2, and GO and pathway enrichment analyses were performed by EnrichR.
Assembly: hg38
Supplementary files format and content: fastq, narrowPeak

growth_protocol: VCaP cells were grown in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 degreeC

extract_protocol:
The lysates were immunoprecipitation with H2A-K130ac antibodies (2 ug) for 3 hours.
Ten nanograms of immunoprecipitated DNA was fragmented to 300 base pairs using a Covaris M220 Focused-ultrasonicator (Covaris, Inc., Woburn, MA) and then used to generate sequencing libraries using the Kapa Hyper Prep Kit (Roche Sequencing Solutions Inc., Pleasanton, CA). The size and quality of the library was evaluated using the Agilent BioAnalyzer (Agilent Technologies, Inc., Santa Clara, CA), and the library was quantitated with the Kapa Library Quantification Kit.  Each enriched DNA library was then sequenced on an Illumina NextSeq 500 sequencer to generate 40-50 million 75-base paired-end reads (Illumina, Inc., San Diego, CA).  The raw sequence data were aligned using BowTie 2 [1], and the binding sites were identified using the MACS peak-finding software

treatment_protocol: 5x10^7 VCaP cells were treated with Romidepsin inhibitor overnight (0.5 uM) and lysates were prepared by sonication in RLB bufffer.

value: Human breast cancer

tag: chip antibody


title: MCRIi019-A_cartilage_D69_rep2

value: iPSC-derived cartilage


title: Dataset D8 lib3

value: TSB


title: Dataset D7 lib7


title: AC130_abi


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A2_AD012

city: La Jolla

first: Joseph

last: Ecker

institute: HHMI-Salk-Institute

value: female


title: MCRIi019-A_cartilage_D69_rep1

value: WT


title: Dataset D7 lib4


title: Hypertension PMBCs, biol reps 1-4

city: Nashville

first: Matthew

last: Alexander

state: TN

address: 1211 Medical Center Drive

institute: Vanderbilt University Medical Center

data_processing:
Alignment, filtering, barcode and UMI detection performed using default parameters in 10X CellRanger
Normalization of RNA assay using Seurat v4 with default settings
Normalization of ADT assay using Seurat v4 with "CLR" method
Normalization of hashtag (HTO) assay using Seurat v4 with "CLR" method
Assembly: GRCh38-3.0.0
Supplementary files format and content: Data processed using CellRanger v 4.0.0 to create features, barcodes, matrix files

source_name: PBMCs

extract_protocol:
PBMCs were isolated from human whole blood, cryopreserved, and 4 control and 4 hypertensive samples were thawed for use. Samples were then stained with hashtags and extracellular antibodies. Finally, samples were washed and experimental groups pooled to run on the 10X Genomics controller.
Libraries were prepared according to manufacturer's instructions for 10X Chromium Single Cell 5' Reagent Kit v2 with the 5' Feature Barcode Library Kit by the Vanderbilt VANTAGE core with sequencing on a NovaSeq 6000 targeting 50,000 reads per cell

value: PBMCs

value: TotalSeqC251-GTCAACTCTTTAGCG; TotalSeqC252-TGATGGCCTATTGGG; TotalSeqC253-TTCCGCCTCTCTTTG; TotalSeqC254-AGTAAGTTCAGCGTA; CD8a-GCGCAACTTGATGAT; CD3-CTCATTGTAACTCCT; CD4-GAGGTTAGTGATGGA; CD45R0-CTCCGAATCATGTTG; PD1-ACAGCGCCGTATTTA; CCR7-AGTTCAGTCAACCGA; Tim3-TGTCCTACCCAACTT; CD62L-GTCCCTGCAACTTGA; CD57-AACTCCCTATGGAGG


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A2_AD001

address: 10010 North Torrey Pines Road

value: THl

value: STR


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A1_AD012

value: SC

value: P


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A2_AD002


title: MCRIi019-A_cartilage_D48_rep2

value: chondrogenic differentiation D48


title: Dataset D7 lib6

value: Whole bacteria

value: Bacteria


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A1_AD010


title: MCRIi019-A_cartilage_D48_rep3


title: MCRIi019-A_cartilage_D48_rep1


title: Control PMBCs, biol reps1-4


title: Dataset D7 lib3

value: USA300 LAC

value: TSB + 10 µg/ml vancomycin


title: Dataset D7 lib2


title: CCR10- Tregs, biol rep 1

data_processing:
Read alignment was performed with the human genome using a STAR based aligner and the Illumina DRAGEN RNA pipeline.
DESeq2 v1.30.1 was used to analyze differential gene expression with a multifactorial design to account for paired CCR10+ and CCR10- samples from the same individuals
Assembly: hg38
Supplementary files format and content: csv file after analysis from DeSeq2

source_name: flow sorted PBMCs

extract_protocol:
Three healthy control individuals donated blood from which PBMCs were isolated and cryopreserved. After thawing, cells underwent staining with antibodies to identify regulatory T cells (live, CD45+CD3+CD4+CD25+CD127-) along with CCR10. Cell were subsequently flow sorted for CCR10+ and CCR10- Tregs. From each cell pellet, RNA was isolated using QiaSymphony RNA extraction kit (Qiagen) according to manufacturer’s instructions.
Library prep was performed with the Ovation low input RNA sequencing kit (Tecan) according to manufacturer’s instructions.

value: blood

value: CCR10- Tregs

tag: individual

value: donor 1


title: CCR10- Tregs, biol rep 3

value: donor 3


title: Dataset D7 lib1


title: MCRIi018-B_cartilage_D69T3_rep3

value: iPSC-derived cartilage

value: chondrogenic differentiation D69 treated with T3 from D48-D69


title: CCR10+ Tregs, biol rep 3

value: CCR10+ Tregs


title: Dataset D6 lib8

description: S. aureus grown to an OD600 of ~0.1 from USA300 LAC (with and without N-acetylcysteine treatment) and JE2 WT and gbaA mutant

value: USA300 LAC, JE2

value: USA300 LAC WT, JE2 WT, JE2 gbaA

value: TSB


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A2_AD004

value: brain

value: THp

value: STR

value: male


title: Dataset D7 lib5

value: Whole bacteria

value: Bacteria

value: WT


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A1_AD008

value: SC

value: P


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A1_AD006

value: female


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A1_AD007


title: MCRIi018-B_cartilage_D69_rep3

value: chondrogenic differentiation D69


title: MCRIi018-B_cartilage_D69T3_rep1

value: iPSC-derived cartilage


title: CCR10+ Tregs, biol rep 2

value: blood

value: donor 2


title: CCR10+ Tregs, biol rep 1

value: CCR10+ Tregs

value: donor 1


title: Dataset D6 lib7

value: USA300 LAC, JE2

value: USA300 LAC WT, JE2 WT, JE2 gbaA

value: TSB


title: CCR10- Tregs, biol rep 2

value: CCR10- Tregs


title: Dataset D6 lib6


title: MCRIi018-B_cartilage_D69_rep2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A1_AD002

value: brain

value: THl

value: STR


title: VCaP Input.

source_name: VCaP

value: VCaP

value: Human prostate cancer


title: Dataset D6 lib5

value: Whole bacteria

value: Bacteria


title: MCRIi018-B_cartilage_D69_rep1

value: WT

value: chondrogenic differentiation D69


title: Dataset D6 lib4


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A1_AD001

value: male


title: MCRIi018-B_cartilage_D69T3_rep2

value: iPSC-derived cartilage

value: chondrogenic differentiation D69 treated with T3 from D48-D69


title: MCRIi018-B_cartilage_D48_rep3

value: chondrogenic differentiation D48


title: VCaP DMSO

value: DMSO


title: MCRIi018-B_cartilage_D48_rep2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A12_AD008

value: SC

value: P


title: Dataset D6 lib3

value: USA300 LAC, JE2

value: USA300 LAC WT, JE2 WT, JE2 gbaA

value: TSB


title: CD3+CD4+Ag-specific non-Tr1 cells (T(DCIns)) EXP87

city: Milano

first: Silvia

last: Gregori

state: Italy

address: Via Olgettina 60

country: Italy

institute: SR-TIGET

data_processing:
Illumina Novaseq reads were trimmed for quality control using Trimgalore (v0.6.6)
Read quality was checked for each sample using FastQC (v0.11.6)
Trimmed reads were aligned to GRCh38.p13 using STAR (v2.7.6a)
Total counts of transcripts per gene were quantified with FeatureCounts (v2.0.1)
Differential gene expression analysis between TIL-10/Ins and TIns cells was computed using the DESeq2.
Assembly: GRCh38
Supplementary files format and content: normalized abundance measurements, txt file, output from DESeq2

source_name: Peripheral Blood

extract_protocol:
RNA-Seq was performed on sorted CD3+CD4+CD49b+LAG3+ Ag-specific   (i.e., proliferation dye negative) Tr1 cells (T(DCIL-10/Ins)) and Ag-specific non-Tr1 cells (T(DCIns)). RNA was extracted with miRNeasy Kit (Qiagen), following manufacturer’s instructions.
Libraries were prepared according to Illumina's instructions.

value: CD4+ T cells

tag: donor

value: Healthy donor


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A12_AD007

source_name: brain

value: brain


title: MCRIi018-B_cartilage_D48_rep1


title: CD3+CD4+Ag-specific non-Tr1 cells (T(DCIns)) EXP86


title: Dataset D6 lib1

value: Whole bacteria


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A1_AD004

value: THp

value: STR


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A12_AD004


title: CD3+CD4+Ag-specific non-Tr1 cells (T(DCIns)) EXP85


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A12_AD006

value: female


title: BC7-924832

city: Adelaide

first: Simon

last: Conn

state: South Australia

address: Sturt Road, Bedford Park

department: College of Medicine and Public Health

institute: Flinders University

data_processing:
Raw reads were trimmed off adapter and low quality reads in the sequencer and generated FASTQ files
The FASTQ files were mapped aganist the human refrence genome (hg19) using STAR spliced alignment algorithm (versions 2.7.0)
Aligned with parameters and –chimericSegmentMin 20, --quantMode GeneCounts
The resulting STAR prduced chemiric junction file for each sample processed by CIRCexplorer2 (version 2.3.3) to estimate circRNA abundance
Alignments were visualised and interrogated using the Integrative Genomics Viewer v2.3.80 (Thorvaldsdóttir et al., 2013).
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include gene counts for each sample
Supplementary files format and content: Tab-delimited text files include CIRCexplorer2 produced number of Junction reads for each sample

source_name: Guthrie cards/neonatal blood spots

extract_protocol:
RNA was extracted from one-half a spot from each Guthrie card with TRIzol
TrioRNA-seq library preparation with custom anydeplete to remove ribosomal RNA and adult and fetal hemoglobin transcripts

value: Guthrie cards/neonatal blood spots

value: Control


title: CD3+CD4+CD49b+LAG3+ Ag-specific Tr1 cells (T(DCIL-10/Ins) EXP87


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A12_AD002

value: THl


title: Dataset D5 lib8

description: S. aureus grown to an OD600 of ~0.1 from USA300 LAC strains WT, sigB and saeQRS mutants

value: USA300 LAC

value: Bacteria

value: WT, sigB, saeQRS


title: BC8-938277


title: VCaP Romi

value: VCaP

value: Human prostate cancer

value: Romidepsin


title: BC6-924812


title: CD3+CD4+CD49b+LAG3+ Ag-specific Tr1 cells (T(DCIL-10/Ins) EXP86


title: BC5-924828


title: Dataset D5 lib6

value: TSB


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A11_AD012

value: SC

value: P


title: CD3+CD4+CD49b+LAG3+ Ag-specific Tr1 cells (T(DCIL-10/Ins) EXP85

value: CD4+ T cells

value: Healthy donor


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A11_AD010

value: brain


title: Dataset D5 lib5

value: Whole bacteria


title: Dataset D5 lib4


title: Dataset D6 lib2

value: USA300 LAC, JE2

value: USA300 LAC WT, JE2 WT, JE2 gbaA


title: Active chronic GVHD patient 3, Untreated

city: Durham

first: Stefanie

last: Sarantopoulos

state: NC

address: 2 Genome Ct, MSRB2

department: Department of Medicine

institute: Duke University Medical Center

description:
act_cGVHD
Poe-9

data_processing:
Raw data were preprocessed by Cellranger v2.1.1
The count matrix was analyzed using R package Seurat v.3.1.4
Genome_build: hg38
Supplementary_files_format_and_content: text file, read counts

source_name: Peripheral blood B cells

growth_protocol: Immediately following purification, B cells were maintained for 18h in RPMI-1640 medium containing 10% FBS and 55 mM 2-mercaptoethanol at 5% CO2, either as resting cells or ATRA-treated cells.

extract_protocol:
Per manufacturer's protocol (10x Genomics)
10x Genomics Chromium 3' Single-Cell

treatment_protocol: 100 nM ATRA (All-trans retinoic acid) was present during the entire culture period for the indicated samples.

value: Peripheral blood B cells

value: untreated

value: Active chronic GVHD


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A11_AD008

value: male


title: Dataset D5 lib3

value: USA300 LAC

value: Bacteria

value: WT, sigB, saeQRS


title: BC8-924824

value: Guthrie cards/neonatal blood spots

value: Control


title: Dataset D5 lib7

value: TSB


title: No chronic GVHD patient 2, ATRA treated

description:
no_cGVHD
Poe-8

value: ATRA

value: No chronic GVHD


title: No chronic GVHD patient 2, Untreated

description:
no_cGVHD
Poe-7


title: No chronic GVHD patient 1, ATRA treated

description:
no_cGVHD
Poe-6


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A11_AD007

value: SC

value: P


title: Dataset D5 lib1

value: Whole bacteria


title: BC5-938214


title: Dataset D5 lib2


title: BC1-908

value: Leukemia


title: Dataset D4 lib8

description: S. aureus grown to an OD600 of 1 (exponential phase) or 6 (stationary phase). Note that samples were split into DNase-treated ("plus") and untreated ("minus") samples as indicated in the metadata sheet

value: WT

value: TSB in exponential or stationary phase


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A12_AD001

value: brain

value: THl

value: STR


title: No chronic GVHD patient 1, Untreated

description:
no_cGVHD
Poe-5

value: Peripheral blood B cells

value: untreated


title: BC4-146


title: BC6-938284


title: Active chronic GVHD patient 2, ATRA treated

description:
act_cGVHD
Poe-4

value: Active chronic GVHD


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A11_AD002

value: female


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A11_AD001

value: male


title: BC4-651

value: Guthrie cards/neonatal blood spots


title: Active chronic GVHD patient 2, Untreated

description:
act_cGVHD
Poe-3


title: BC7-938282

value: Control


title: Dataset D4 lib7

value: USA300 LAC

value: Bacteria


title: Dataset D4 lib6


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A10_AD012

value: SC

value: P


title: Active chronic GVHD patient 1, ATRA treated

description:
act_cGVHD
Poe-2

value: ATRA


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A11_AD006

value: THp


title: 1815002

value: Leukemia


title: Dataset D4 lib5

value: Whole bacteria

value: WT

value: TSB in exponential or stationary phase


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A10_AD010

value: brain


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A11_AD004

value: STR


title: No chronic GVHD patient 4, ATRA treated

description:
no_cGVHD
Poe-16

value: Peripheral blood B cells

value: No chronic GVHD


title: Dataset D4 lib4


title: BC3-716


title: 1729802


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A10_AD008

value: male


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A10_AD007


title: Dataset D4 lib3


title: No chronic GVHD patient 3, ATRA treated

description:
no_cGVHD
Poe-14


title: 1729804

value: Guthrie cards/neonatal blood spots


title: Dataset D4 lib2


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A10_AD006

value: female


title: 1729808


title: No chronic GVHD patient 4, Untreated

description:
no_cGVHD
Poe-15

value: untreated


title: No chronic GVHD patient 3, Untreated

description:
no_cGVHD
Poe-13


title: Dataset D4 lib1

value: USA300 LAC

value: Bacteria


title: Differentiated HSPCs, 4 arrayed lentiviruses, rep 2,  barcoded antibody (ADT)

description: perturb_seq_CD33_rep1_filtered_feature_bc_matrix.h5

molecule: protein

extract_protocol:
Following final FACS enrichment to remove debris and purify transduced cells, 5-mL PBS-BSA coated tubes described above were spun down at 400 x g for 5 minutes at 4ºC. The entire supernatant was carefully removed and 1mL of PBS+0.05% BSA was added. Cells were then counted twice using an automated Countess 2 cell counter (Thermo Fisher, I-CACC2). Cell viability as determined by Trypan Blue was always >95%. Cells were again washed with 5mL PBS+0.05% BSA and resuspended at a final concentration of 1,000 cells / µL and kept on ice.
Single-cells were immediately processed using v3.1 Chemistry Dual Index kits according to manufacturer’s instructions (10X Genomics), using 20µL of cell suspension and 23.2 µL of water on the cell suspension loading step. Libraries were sequenced using a 28 base pair (Read 1), 10 base pair (Index 1), 10 base pair (Index 2), 90 base pair (Read 2) configuration on Nextseq 500, Nextseq 2000 or Novaseq S2/S4 instruments.

value: Differentiated hematopoietic stem and progenitor cells

value: Hematopoietic system

value: ADT

value: TotalSeq™-B0052 anti-human CD33 Antibody


title: Active chronic GVHD patient 4, ATRA treated

description:
act_cGVHD
Poe-12

value: ATRA

value: Active chronic GVHD


title: Dataset D3 lib16

description: S. aureus grown to an OD600 of 1 in TSB

value: Whole bacteria

value: WT

value: TSB


title: Active chronic GVHD patient 4, Untreated

description:
act_cGVHD
Poe-11

value: Peripheral blood B cells


title: Differentiated HSPCs, 4 arrayed lentiviruses, rep 2, scRNA-seq

description:
10x Genomics
perturb_seq_CD33_rep1_filtered_feature_bc_matrix.h5

value: mRNA


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A10_AD004

value: brain

value: THp

value: STR

value: male


title: Dataset D3 lib15

description: S. aureus grown to an OD600 of 1 in TSB

value: USA300 LAC


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A10_AD002

value: THl

value: female


title: Dataset D3 lib14

description: S. aureus grown to an OD600 of 1 in TSB

value: Bacteria


title: Dataset D3 lib13

description: S. aureus grown to an OD600 of 1 in TSB


title: Active chronic GVHD patient 3, ATRA treated

description:
act_cGVHD
Poe-10


title: Differentiated HSPCs, 4 arrayed lentiviruses, rep 1, scRNA-seq

value: Differentiated hematopoietic stem and progenitor cells

value: Hematopoietic system


title: Differentiated HSPCs, 4 arrayed lentiviruses, rep 1, barcoded antibody (ADT)

value: ADT

value: TotalSeq™-B0052 anti-human CD33 Antibody


title: Unlabeled stromal cells 2 HTO

city: New York

first: Siting

last: Gan

address: 417 East 68th Street

institute: MSKCC

description:
3188_SG-602_d27_inh_eg_IGO_12437_195_sparse_counts_barcodes.csv
3188_SG-602_d27_inh_eg_IGO_12437_195_sparse_counts_genes.csv
3188_SG-602_d27_inh_eg_IGO_12437_195_sparse_molecule_counts.csv

data_processing:
GFP+ cancer cell and GFP- non cancer cell samples were mapped to hg38 and mm38 genome references, respectively.
The SEQC pipeline performed read alignment, multi-mapping read resolution, and cell barcode and UMI correction to generate a raw UMI-based (cell × gene) count matrix per sample.
An in-house method called SHARP (https://github.com/hisplan/sharp, version 0.2.1) assigned a cell as labeled by a particular Hashtag oligo and thereby belonging to the specific mouse (bearing either MDA231-BrM metastases or HCC1954-BrM metastases) barcoded with this oligo or as a doublet or low-quality droplet.
Assembly: hg38 and mm38
Supplementary files format and content: barcode gene counts
Supplementary files format and content: gene counts
Supplementary files format and content: molecule counts

extract_protocol:
4 weeks post innoculation with cancer cells, brains were harvested from euthanized mice and processed for enzymatic tissue dissociation with the Adult Brain Dissociation kit, removal of myelin with myelin removal beads II, and removal of debris and dead cells. Single cell suspensions of each sample were incubated with an anti-human Hashtag antibody and an anti-mouse Hashtag antibody, 1:100 TruStain FeX Fc receptor blocking solution, 1:100 TruStain FeX anti-mouse CD16/32 antibody, and 1:20 APC Annexin V. Calcein Violet positive and Annexin V negative cells of each sample were sorted into 3 groups, GFP positive mCherry positive, GFP negative mCherry positive, and GFP negative mCherry negative cells.
Single-cell RNA-Seq of FACS-sorted cell suspensions was performed on the Chromium instrument (10X genomics). Droplet encapsulation was performed on the cells after sorting and viability assessment. After reverse transcription and cell barcoding within droplets, emulsions were broken and cDNA purified using Dynabeads MyOne SILANE followed by PCR amplification per user manual instruction. Resulting libraries were sequenced on Illumina NovaSeq S4 platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles).

value: non-cancer cells in mouse brain

value: wild type


title: Dataset D3 lib12

description: S. aureus grown to an OD600 of 1 in TSB

value: Whole bacteria

value: WT

value: TSB


title: Unlabeled stromal cells 1 HTO

description:
2110_Unlabeled_stromal_cells_IGO_11324_10_sparse_counts_barcodes.csv
2110_Unlabeled_stromal_cells_IGO_11324_10_sparse_counts_genes.csv
2110_Unlabeled_stromal_cells_IGO_11324_10_sparse_molecule_counts.csv

value: brain


title: Active chronic GVHD patient 1, Untreated

description:
act_cGVHD
Poe-1

value: Peripheral blood B cells

value: untreated

value: Active chronic GVHD


title: Liver, sh974, run1 (WGBS)

city: Ghent

first: Jeroen

last: Galle

address: Coupure Links 653

department: Dept. Of Mathematical Modelling, Statistics and Bioinformatics

country: Belgium

institute: Ghent University

data_processing:
Reads were mapped using the bowtie2 option (v 2.3.3.1) of the Bismark software (Brabraham Bioinformatics, v 0.18.1_dev) against the Syrian hamster reference genome provided by Ensembl (MesAur1.0, release 95). FastQC (Brabraham Bioinformatics, v 0.11.2) was used to assess quality of the WGBS samples, indicating good quality (both on the raw and trimmed fastq files). Trim Galore! (Brabraham Bioinformatics, v 0.1.0) was used to trim out bad quality bases (quality score < 20, default) from reads (reads trimmed shorter than 15bp were discarded). Bismark and bismark_methylation_extractor (v 0.18.0) were used to quantify CpG methylation. Finally, coverage files were compiled (bismark2bedGraph, v0.18.0) for downstream analysis.
Assembly: MesAur1.0
Supplementary files format and content: Bismark coverage files including tab seperated files on chromosome, chromosomal position, methylation percentage, methylated counts and unmethylated counts.

organism: Mesocricetus auratus

source_name: Liver

extract_protocol:
Liver was flushed with physiological salt solution, removed and snap-frozen in liquid nitrogen and stored at −80 °C.
Total DNA from liver tissue samples was extracted using Machery Nagel Nucleospin tissue kit and used for whole genome bisulfite sequencing (WGBS) by NXTGNT (www.nxtgnt.com). Concentration of the extracted DNA was measured using Quant-iT PicoGreen kit (Invitrogen). DNA quality was checked on a 1% agarose gel (E-gel EX Invitrogen). 500ng DNA was used from each sample for further analysis. Fragmentation was performed using Covaris model S2 to obtain fragments with a size of approximately 400 bp, followed by bisulfite conversion with the EZ DNA methylation Gold kit (Zymo Research, Irvine, CA, USA) according to manufacturer’s protocol. For library preparation, the NEBNext Ultra II DNA library prep kit (New England Biolabs, Ipswich, MA, USA) was used according to protocol, followed by sequencing on three Hiseq3000 lanes (Illumina), generating PE2x150bp reads.

treatment_protocol: All hibernating animals were kept in darkness until euthanization. Arousal was induced at > 3 days of torpor by gentle handling. The animal's activity pattern accurately identified torpor bouts of hamsters, as evidenced by mouth temperature (Tm) at euthanization, being 9.0±0.9°C and 35.0±2.1°C for TL and AE, respectively, whereas SE animals had a Tm of 35.7±0.5°C.

value: Liver

tag: sample id

tag: hibernation stage

value: euthermic

tag: hibernation stage abbrev

value: EU

tag: run


title: Liver, sh973, run1 (WGBS)


title: Liver, sh970, run1 (WGBS)