title: IDG-SW3+TG-cre-rep1


title: IDG-SW3+TG-DTA-rep1

status: Public on Sep 01 2022

type: SRA

city: San Antonio

first: Katherine

middle: Vivian

last: Lillis

state: TX

address: 7703 Floyd Curl Dr

department: Endodontics

country: USA

institute: UNIVERSITY OF TEXAS HLTH SCI CTR SAN ANTONIO

library_source: transcriptomic

data_processing:
The base called files were converted to fastq, demultiplexed, and mm10 alignments and analysis was done with TopHat-Bowtie and DESeq programs.
Genome_build: mm10
Supplementary_files_format_and_content: read count

molecule: total RNA

organism: Mus musculus

source_name: CellLine from Dmp1-GFP  bones +  SensoryNerve Deleted TG Preparations

extract_protocol: Total RNA was isolated from IDG-SW3 cells after 14 days culture in the presence of differentiation media (n=2 wells/condition) using the RNAeasy Kit (Qiagen, Valencia, CA) following the manufacturer’s recommendation. Total RNA was ribosomal RNA depleted using the NEBNext rRNA Depletion Kit. Libraries were built for the biological duplicates (6 libraries, n=2: IDG-SW3 [d1 and d2], IDG-SW3 +TG-cre [TGd1 and TGd2], and IDG-SW3 +TG-DTA [SNSd1 and SNSd2]). We used the Next Flex Rapid Directional RNA-Seq Kit to prepare libraries as described by the manufactuer with appropriate barcodes (Bioo Scientific).  The total RNA libraries were submitted to the U. Texas Health Science Center Gene Sequencing Facility at the Greehey Childrens Cancer Center, and the paired end libraries were sequenced on one lane with the Illumina Hi-Seq 2000.

treatment_protocol: The osteoblast cell line IDG-SW3 with a GFP expression under the Dmp1 promoter (Kerafast, Boston, MA) was cultured at the concentration of (~1x105/well) in collagen type-1 coated 24 well plated with the addition of ascorbic acid (50 μg/ml) and β-glycerolphosphate (4mM). Once cells reached 80% confluency, inserts of TG-cre or TG-DTA cultures were transferred to the plates and incubated for 14 days at 37ºC and 5% CO2 with media replaced every 2 days and new TG-cre or TG-DTA cultures were replaced every 7 days.

tag: strain

tag: osteoblast cell

tag: tg insert

value: Nav1.8 sensory nerve depleted TG


title: 5_ChIP_OPC_H3K4me3_3

city: Paris

first: Carlos

last: Parras

address: 47 boulevard de l'hôpital

country: France

institute: Paris Brain Institute

description: H3K4me3 ChIP in OLglia

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2
Data were filtered using SAMtools and PCR-derived duplicates removed by using PICARD MarkDuplicates
peaks were called using MACS (Model-based Analysis of ChIP-Seq)with options: keep-dup all, nolambda, broad, nomodel, extsize 75 -q 0.01 and filtered according to the following criteria: (i) length>=100bp and (ii) p-value<=5%
Assembly: mm10
Supplementary files format and content: narrowpeaks and broadpeaks files with in this order: chrom, chromStart, chromEnd, peak name, score, signalValue, pValue, qValue; bigwig

molecule: genomic DNA

source_name: O4+ cells

growth_protocol: in vivo Magnetic-activated cell sorting of O4+ cells from P7 or P12 WT mouse cortices using anti-O4 antibodies

extract_protocol:
Lysates were clarified from sonicated nuclei and Olig2-DNA and Histones-DNA complexes were isolated with corresponding antibodies.
The ChIP-seq libraries were prepared using TruSeq ChIP library preparation kit (Illumina ip-202-1012)

tag: tissue

value: Cortex and Corpus callosum

tag: cell type

tag: age

value: Postnatal day 12

tag: chip antibody

value: rabbit anti-H3K4me3 antibody (Active motif, 39060)


title: 10%FBS rep 3

city: Boston

first: Timothy

middle: M

last: O'Shea

state: MA

address: 44 Cummington Mall, ERB Room 521

department: Biomedical Engineering

institute: Boston University

description: 10% FBS 3

data_processing:
The R1 and R2 FASTQ files from lanes 1 and 2 that were obtained directly from the Illumina NovaSeq S2 run were concatenated and cleaned-up using the Trimmomatic tool with default parameters in Galaxy.
Data was then aligned to the M. musculus (mm10) reference genome using the HISAT2 tool applying default parameters in Galaxy
Gene counts from the aligned datasets was performed using the featureCounts tool applying default parameters in Galaxy
Differential expressed gene (DEG) analysis on raw gene count data was conducted using Edge-R in Galaxy applying Benjamini and Hochberg p-value adjustment and TMM normalization
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for every gene and every sample

growth_protocol: mESCs were maintained and expanded on 0.1% gelatin-coated flasks (EmbryoMax™ 0.1% Gelatin Solution, Millipore Sigma, Cat# ES006B) in KnockOut™ DMEM media (Cat# 10829018, ThermoFisher Scientific) containing 15% Fetal bovine serum (FBS) (ES cell tested) (ThermoFisher Sci cat # 10439-016), MEM Non-Essential Amino Acids Solution (100X) (Cat# 11140050, ThermoFisher Scientific), 100X EmbryoMax® Nucelosides (EMD Millipore cat # ES-008-D), Beta-Mercaptoethanol (Sigma Aldrich M3148), Antibiotic-Antimycotic (100X) (Cat# 15240096, ThermoFisher Scientific) and Leukemia inhibitory factor (LIF) (1 million units/mL stock) (EMD Millipore cat # ESG1106). NPC lines were derived from mESCs using a standard 2-/4+ induction protocol followed by a neural expansion protocol. The 2- step of embryoid body (EB) formation involved removing LIF and FBS supplements from the cell media and changing media to a differentiation media consisting of Advanced DMEM/F12 (ThermoFisher Sci cat # 12634-010) supplemented with L-Glutamine (Thermofisher Scientific Cat#25-030-081) (2mM) and Knockout serum replacement (ThermoFisher Sci cat # 10828010) plus the other constituents described above for 2 days. Neural induction (4+) of embryoid bodies (EB) was performed by culturing isolated EB in differentiation media supplemented with retinoic acid (RA) (R2625-50MG, Sigma) (50nM) and purmorphamine (PUR) (sonic hedgehog (SHH) agonist) (SML0868-5MG, Sigma) (500nM) for 4 days. To propagate the neurally induced mESCs, the cells were grown in neural expansion media consisting of Advanced DMEM/F12 supplemented with B27 (no Vitamin A) (50X) (ThermoFisher Sci cat # 12587010) and growth factors EGF (Cat# AF-100-15-100UG, Peprotech) and FGF (Cat# 100-18B-100UG, Peprotech) (100ng/ml for each) for a period of 2-6 weeks resulting in a passagable line of adherent NPC. Samples at defined passages after neural induction (P) were collected for analysis.

extract_protocol:
SCI tissue or cell pellet samples were homogenized in supplemented homogenization buffer (50 mM Tris pH 7.4, 100 mM KCl, 12 mM MgCl2, 1% NP-40, 1 mM Dithiothreitol (DTT), 1X Protease inhibitors, 200 U/ml RNAsin, 100 mg/ml Cyclohexamide, 1 mg/ml Heparin) using 2mL glass Dounce tissue grinders (D8938-1SET, Sigma). Tissue homogenates were centrifuged to remove tissue debris before being incubated with Anti-HA.11 Epitope Tag Antibody (Biolegend, Cat# 901515) for 4 hours in a microcentrifuge tube on a microtube rotator kept at 4°C. At the end of 4 hours, IP solutions were combined with Pierce A/G Magnetic Beads (Thermofisher, #PI88803) and incubated overnight on a microtube rotator at 4°C. On the second day, magnetic beads were washed three times with high salt solution (50 mM Tris pH 7.4, 300 mM KCl, 12 mM MgCl2, 1% NP-40, 1 mM Dithiothreitol (DTT), 100 mg/ml Cyclohexamide). Unpurified RNA was collected from the magnetic beads by addition of RLT Plus buffer with BME and vigorous vortexing. RNA was then purified using RNeasy Plus Mini (for in vitro cell pellets) or Micro Kits (for spinal cord tissue) (QIAGEN Cat# 74134 and 74034). Total mRNA derived from the RiboTag IP was quantified using an automated electrophoresis bioanalyzer. RNA samples with RNA integrity numbers (RIN) greater than seven were processed for RNA-Sequencing. Sequencing was performed on poly-A selected libraries using Illumina NovaSeq S2 (housed in the UCLA Technology Center for Genomics & Bioinformatics) using pair end reads (2x50 – 50bp length) with an average of 50-100M reads per sample.
The workflow for library construciton involved poly(A) RNA selection, RNA fragmentation and double-stranded cDNA synthesis using a mixture of random and oligo(dT) priming, followed by end repair to generate blunt ends, adaptor ligation, strand selection, and PCR amplification to produce the final library.

treatment_protocol: NPC were differentiated spontaneously (Spont) by lowering the EGF/FGF concentration in the neural expansion media from 100ng/ml to 1ng/ml for 4 days. CNTF (Cat# 450-13-100UG, Peprotech) and IGF-1 (Cat#100-11-100UG, Peprotech) differentiation involved adding 100ng/ml of the respective growth factor into the Spont media and culturing for 4 days. FBS differentiation involved adding FBS (Cat# 10437010, ThermoFisher Scientific) at 1, 5, 10 or 20% vol/vol to the Spont media and culturing for 4 days.

value: ES-derived neural progenitor cells

tag: genotype

value: RiboTag +


title: Plate1-m83-RNA

city: Chapel Hill

first: Julia

last: Rager

state: NC

address: 135 Dauer Drive, CB 7431

institute: UNC

data_processing:
The counts of sequencing reads per mRNA within the FASTQ files were aligned to the ENSEMBLE mouse genome database (v98) and organized using the Bowtie algorithm within Tempo-SeqR script.
Count data were normalized by median signal intensity using algorithms enabled within the DESeq2 package, resulting in variance stabilized expression values.
Genome_build: ENSEMBLE database version 98
Supplementary_files_format_and_content: Count data are provided as a .csv, aligned to gene symbols, and represent count values prior to normalization

source_name: Lung tissue from CD-1 mice

extract_protocol:
Lung and heart tissue samples were collected immediately 4 h and 24 h postexposure  and stored at -80 degrees C until further analysis.  RNA molecules with 18 nucleotides or greater were extracted with the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) and quantified with the NanoDrop 1000 Spectrophotometer (Thermo Scientific, Waltham, Ma) and tested for quality based on RNA integrity scores produced by the QIiAxcel system (Qiagen).
Isolated RNA samples were analyzed using next generation sequencing technologies enabled through the BioSpyder TempO-Seq platform. mRNA-seq libraries were prepared using the QuantSeq 3' mRNA-Seq Library Prep Kit for Illumina, and then these libraries were pooled and sequenced (single-end 50 bp) on the Illumina Ultra-High-Throughput Sequencing System (Hiseq) 2500.

tag: treatment

value: PineNeedlesSmolder

tag: treatment duration (hrs)

value: Lung

tag: Sex

value: female


title: Plate2-m82-RNA

value: PeatSmolder


title: Plate1-m89-RNA

value: PineSmolder


title: IDG-SW3-rep2

source_name: CellLine from Dmp1-GFP  bones


title: 10%FBS rep 2

description: 10% FBS 2


title: Plate2-m81-RNA


title: 2_ChIP_OPC_Input_1

description: Control for 1_ChIP_OPC_Olig2_1

value: Postnatal day 7


title: IDG-SW3-rep1


title: WTGF_1

city: Durham

first: John

middle: F

last: Rawls

address: 213 Research Drive

institute: Duke University School of Medicine

data_processing:
Paired read files were concatenated in Galazy and trimmed using Trim Galore
Reads were mapped to the Danio rerio DanRer11 genome using RNAstar
Features counts was used to quanity the number of reads mapped per gene
DESeq was used to determine differential gene expression and statisical significance
Genome_build: DanRer11
Supplementary_files_format_and_content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar

organism: Danio rerio

source_name: dissected GI tract

extract_protocol:
larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit (Invitrogen) was used to extract total RNA
RNA libraries were prepared using standard Illumina protocols

value: dissected GI tract

value: wild type

tag: microbial status

value: Germfree

value: 6 dpf


title: 10%FBS rep 1

description: 10% FBS 1


title: H33S28A, RNA, rep2

city: Gatersleben, Stadt Seeland, Germany

first: Hua

last: Jiang

address: Corrensstraße 3

country: Germany

institute: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben

data_processing:
For RNA-seq analysis, reads were mapped to TAIR10 Col-0 and the Ler‐0 genomes with HISAT2 (Kim et al., 2019) in paired-end mode.
DEGs were analyzed via the Subread (Liao et al., 2019) and DESeq2 R packages (Love et al., 2014) with a 0.05 false discovery rate (FDR).
For ChIP-seq library preparation, the purified ChIP-ed DNA was utilized for the subsequent end repairing, A-tailing, adaptor ligation, and library amplification. The steps were performed with the NEBNext® Ultra™ II DNA Library Prep Kit (NEB).
The library was sequenced on an Illumina Novaseq instrument with 2 × 150 bp reads.
Genome_build: tair10

organism: Arabidopsis thaliana

source_name: 2-week-old seedlings

growth_protocol: Seeds were sown in soil and stratified for 2 days at 4°C. The plants were then grown in a growth chamber with a photoperiod of 16 h of light and 8 h of darkness at 22°C (LDs) or in a chamber with a photoperiod of 8 h of light and 16 h of darkness at 22°C (SDs).

extract_protocol:
For RNA-seq library preparation, total RNA from closed buds was extracted with a RNeasy Plant Mini kit (Qiagen). Afterwards, the total RNA was treated with a Poly(A) mRNA Magnetic Isolation Module Kit (NEB #E7490). Libraries were prepared from the resulting mRNA with a VAHTS mRNA-seq V3 Library Prep Kit (Vazyme #NR611-01) .The ChIP experiments were performed as described by Moreno-Romero et al. (2017), with minor changes. In brief, after the isolation of nuclei, the chromatin was sonicated in Nuclei lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS, 0.1 mM PMSF, 1 μM pepstatin A, Protease Inhibitor Cocktail (Roche, 11836145001)) using a Bioruptor® Plus sonication device (Diagenode) to obtain the desired DNA fragment size (enriched at 300 bp). The following procedures were described by Moreno-Romero [46]. After the de-crosslinking, DNA was purified according to the IPure kit v2 Kit manual (Diagenode, C03010015). ChIP-seq libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645). The following antibodies were used: anti-H3 (Sigma, H9289), anti-H3S28ph (Millipore, 07-145), and anti-H3K27me3 (Millipore, 07-449).
Libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: 2-week-old seedlings


title: H33S28A, RNA, rep1


title: Plate2-m80-RNA


title: 5%FBS rep 4

description: 5% FBS 4


title: H33, RNA, rep2


title: 5%FBS rep 3

description: 5% FBS 3


title: H33, RNA, rep1


title: WTDP_H3K4me3

city: Charlestown

first: Katia

last: Georgopoulos

address: 13th street

department: CBRC

institute: Harvard Medical School

data_processing:
Basecalls were performed using  bcl2fastq v. 1.8.3
Read alignment was performed on the mm10 (mouse genome) assembly using the genome mappers STAR for RNAseq and ChIPseq.
For visualization of sequencing data,  primary sequencing data were sorted, indexed, normalized with reads per kilobase per million mapped reads using DeepTools
Genome_build: mm10
Supplementary_files_format_and_content: fastq, bam, bigwig

source_name: DP thymocytes

extract_protocol:
Thymocytes were isolated by mechanical disruption. WTDP and WTDN3 cells were FACS sorted using cell surface markers (WTDN3; Lin-CD25+CD44-cKit-, WTDP; CD8+CD4+).
ChIP for histone modifications was performed from sorted DN3 and DP cells as described in Hu et al Gene Dev, 2016 (doi: 10.1101)

value: CD8+CD4+ DP thymocytes

value: WT

tag: antibody


title: WTDP_H3K27Ac


title: H31S28A, RNA, rep2


title: 5%FBS rep 2

description: 5% FBS 2


title: LTK_2: LTK-14A 3T3L1

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

data_processing:
NFCORE RNA Seq Pipeline has been used
iGEAK RNA Seq Analysis Analysis Pipeline was used
DAVID online tool was used to analyze the DEGs functional enrichment analysis
Genome_build: mm10
Supplementary_files_format_and_content: Log2 of FPKM Values with Transcript Annotation

source_name: Mouse adipocyte cell line

growth_protocol: The cells were grown in Dulbecco's Modified Eagle's medium (DMEM) supplemented with 10% foetal bovine serum in a 37ᴼC incubator with 5% CO2 and 90% relative humidity.

extract_protocol:
Cells were collected in Trizol followed by RNA isolation using phenol:chloroform method after which contaminating DNA was removed by incubation with DNAse I.
Libraries for RNA-seq were prepared according to KAPA Stranded RNA-Seq Kit with RiboErase (KAPA Biosystems, Wilmington, MA) system. Final library quality and quantity were analyzed by Agilent Bioanalyzer 2100 and Life Technologies Qubit3.0 Fluorometer, respectively

treatment_protocol: The cells were grown to a confluent state and then two days post-confluence , were incubated with differentiation medium (growth medium containing 1 µg/ml insulin, 0.5 mM IBMX and 1 µm dexamethasone) for two days after which they were kept in maintenance medium (growth medium with 1µg/ml insulin) with media change given every two days, until the cells were differentiated into adipocytes characterized by accumulation of lipid droplets

tag: cell line type

value: cell line with fibroblast like morphology differentiated into adipocytes


title: H31S28A, RNA, rep1


title: Plate2-m76-RNA

value: RedOakSmolder


title: 5%FBS rep 1

description: 5% FBS 1

value: ES-derived neural progenitor cells


title: Plate1-m77-RNA


title: 1% FBS rep 4

description: 1% FBS 4

source_name: 1% FBS

value: RiboTag +


title: LTK_1: LTK-14A 3T3L1


title: H3.1, RNA, rep2


title: DMSO_2: DMSO 3T3L1

value: DMSO


title: H3.1, RNA, rep1


title: DMSO_1: DMSO 3T3L1


title: Plate2-m74-RNA

value: Lung


title: Plate2-m75-RNA

value: female


title: Plate2-m79-RNA

value: PeatSmolder


title: 1% FBS rep 2

description: 1% FBS 2


title: H3.3S28A, S28, rep2

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat


title: UI_2: Untreated 3T3L1

value: untreated


title: Plate2-m78-RNA

tag: strain


title: 1% FBS rep 1

description: 1% FBS 1


title: Plate2-m73-RNA


title: UI_1: Untreated 3T3L1


title: IGF rep 4

description: IGF 4

source_name: IGF


title: Plate2-m72-RNA


title: H3.3S28A, K27, rep2


title: IGF rep 3

description: IGF 3


title: H3.3S28A, K27, rep1


title: Plate1-m70-RNA

value: LPS


title: 1% FBS rep 3

description: 1% FBS 3


title: H3.3S28A, H3, rep2

value: Sigma


title: Plate1-m69-RNA


title: IGF rep 1

description: IGF 1


title: IGF rep 2

description: IGF 2


title: H3.3S28A, S28, rep1


title: H3.3, S28, rep2


title: Plate1-m67-RNA


title: CNTF diff rep 4

description: CNTF 4

source_name: CNTF diff


title: H3.3, S28, rep1


title: H3.3, K27, rep2


title: CNTF diff rep 2

description: CNTF 2


title: Plate1-m66-RNA

value: EucalyptusFlame


title: Plate1-m71-RNA


title: H3.3, K27, rep1


title: CNTF diff rep 3

description: CNTF 3


title: old_tissue_4

city: Cologne

first: Peter

last: Tessarz

state: Nordrhein-Westfalen

address: Joseph-Stelzman-Str 9b

institute: Max Planck Institute

description: each sample is data from one animal.

data_processing:
Fastq files were mapped using STAR_2.5.2b (Dobin et al. 2013), sorted using samtools (version 1.9) (Li et al. 2009) and count matrix was created using “featureCounts” from Rsubread (version 1.32.4) (Liao et al. 2013). Reads were mapped to Mus musculus (mm10) and ERCC sequences with Ensembl annotation version GRCm38.91.
Downstream computational analysis was conducted in R (version 3.6.3). The count matrix was normalized and filtered with edgeR (version 3.28.1) (Robinson et al. 2010) using “filterByExpr” with min.count = 3.  Differential expression analysis was performed using DESeq2 (v. 1.26.0) (Love et al, 2014). Genes with an FDR < 5 % were considered to be statistically significant.
Assembly: mm10
Supplementary files format and content: tab delimited count matrix

source_name: Liver tissue

extract_protocol:
total RNA was isolated from 4 young and 4 old murine livers using an RNA extraction kit (Direct-zol RNA Miniprep, Zymoresearch)
Libraries were generated using the NEBNext UltraII Directional RNA Library Prep kit for Illumina.

value: liver

value: 18 months


title: H3.3S28A, H3, rep1

value: 2-week-old seedlings


title: H3.3, H3, rep2


title: old_tissue_3

description: each sample is data from one animal.


title: Plate1-m68-RNA


title: CNTF diff rep 1

description: CNTF 1


title: H3.3, H3, rep1


title: old_tissue_2

description: each sample is data from one animal.


title: Plate1-m65-RNA


title: Plate1-m64-RNA


title: Plate1-m63-RNA


title: Spontaneous diff rep 3

description: Spont 3

source_name: Spontaneous diff


title: Spontaneous diff rep 4

description: Spont 4


title: H3.1S28A, S28, rep2


title: Plate1-m62-RNA


title: old_tissue_1

description: each sample is data from one animal.


title: Plate1-m61-RNA


title: stau2_3

type: RNA

middle: N

last: Hutchinson

state: Massachusetts

address: 201 Wachusett Street

institute: Diamond Age Data Science

description: Stau2 pulldown, replicate 3

hyb_protocol: Affymetrix standard procedure

scan_protocol: Affymetrix standard procedure

data_processing: Arrays were processed using the ‘oligo’ BioConductor package, quality-controlled with arrayQualityMetrics  and normalized with RMA at the transcript level. A linear model for microarray data analysis (LIMMA) was performed to identify mRNAs that were enriched in Staufen2 RNA-IP over total input RNA samples. All probe's p-values were adjusted for multiple testing (by FDR; false discovery rate) and a fold change >1.5 and p<0.05 cutoff  applied.

label: biotin

source_name: Staufen2 pulldown from differentiated immortalized murine podocytes total RNA

label_protocol: 100ng of total input podocyte RNA or 100ng of co-precipitated RNA from Staufen2 RIP was used as starting material. cDNA was amplified and terminal-labeled using an isothermal linear amplification (Ambion WT expression kit).

growth_protocol: Cells were propagated on gelatin (0.2%) coated dishes at 33°C (permissive conditions) in RPMI 1640 medium supplemented with 10% fetal bovine serum, 100 U/ml penicillin, 100 ug/ml streptomycin and 10U/ml mouse recombinant gamma-interferon. To induce differentiation, cells were switched to 37°C (non-permissive conditions) in the absence of gamma-interferon. Cells were grown and differentiated under an atmosphere of 5% (v/v) CO2 and 95%(v/v) air. Stock flasks of proliferating cells were cultured at 33°C. Cells were sub-cultured to maintain them at a logarithmic growth rate such that flasks at approximately 70% confluency were split at a ratio of 1:4.

extract_protocol: Co-precipitated and input RNAs were isolated using Trizol (Invitrogen).

treatment_protocol: Differentiated immortalized murine podocytes were lysed in cytoplasmic extraction buffer (20mM HEPES pH7.9, 50mM KCl, 2mM EDTA, 10% glycerol, 0.1% NP-40, 80U/ml RNase inhibitor, 20U/ml DNase I, 1μg/ml pepstatin, 1μg/ml antipain, 1μg/ml leupeptin, 200μM PMSF). Prior to IPs the salt concentration was increased to 150mM KCl and the lysates were pre-cleared by incubation with Protein G Dynabeads (Invtirogen) at 4°C for 1hr. Beads were removed and lysates incubated with Staufen2 (Sigma Prestige antibody) antibody overnight at 4°C. Antibody was bound by the addition of protein G beads for 2hrs at 4°C. Supernatant was removed and beads washed three times with lysis buffer.


title: stau2_2

description: Stau2 pulldown, replicate 2

value: Differentiated immortalized murine podocytes


title: input_3

description: input, replicate 3

source_name: Differentiated immortalized murine podocytes total RNA


title: Spontaneous diff rep 2

description: Spont 2


title: stau2_1

description: Stau2 pulldown, replicate 1


title: H3.1S28A, S28, rep1


title: Spontaneous diff rep 1

description: Spont 1


title: middle_tissue_4

description: each sample is data from one animal.

value: 12 months


title: input_2

description: input, replicate 2


title: Plate1-m60-RNA

value: PineFlame


title: Neural progenitor cells passage 15 d3 rep 4

description: NPC P15 d3 4

source_name: Neural progenitor cells passage 15 d3

value: ES-derived neural progenitor cells


title: middle_tissue_3

description: each sample is data from one animal.


title: input_1

description: input, replicate 1


title: H3.1S28A, K27, rep2


title: Plate1-m59-RNA


title: Neural progenitor cells passage 15 d3 rep 3

description: NPC P15 d3 3

value: RiboTag +


title: middle_tissue_1

description: each sample is data from one animal.


title: middle_tissue_2

description: each sample is data from one animal.


title: Gene profile of CAMDI KO mice

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: WT vs KO

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: WT

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

extract_protocol: Experimental total RNA samples were isolated from cerebrums at P0 using RNeasy kit (QIAGEN).

tag: genotype/variation

value: WT

source_name: KO

value: CAMDI-KO


title: Neural progenitor cells passage 15 d3 rep 2

description: NPC P15 d3 2


title: Plate1-m58-RNA

value: Lung

value: female


title: Plate1-m57-RNA


title: Plate1-m56-RNA


title: Neural progenitor cells passage 15 d3 rep 1

description: NPC P15 d3 1


title: H3.1S28A, H3, rep1


title: H3.1S28A, K27, rep1

value: Millipore


title: H3.1S28A, H3, rep2


title: young_tissue_3

description: each sample is data from one animal.

value: 3 months


title: Neural progenitor cells passage 15 d2 rep 5

description: NPC P15 d2 5

source_name: Neural progenitor cells passage 15 d2


title: H3.1, S28, rep2


title: Plate1-m54-RNA

source_name: Lung tissue from CD-1 mice

value: PineNeedlesFlame


title: Plate1-m53-RNA


title: Neural progenitor cells passage 15 d2 rep 6

description: NPC P15 d2 6


title: H3.1, S28, rep1


title: Plate1-m55-RNA


title: Neural progenitor cells passage 15 d2 rep 4

description: NPC P15 d2 4


title: Neural progenitor cells passage 15 d2 rep 3

description: NPC P15 d2 3


title: H3.1, K27, rep2


title: young_tissue_1

description: each sample is data from one animal.


title: H3.1, K27, rep1


title: H3.1, H3, rep2

value: Sigma


title: Synbindin siRNA-LPS-4h-3

city: Shanghai

first: Luoyan

last: Ai

state: Shanghai

address: 145 Middle Shandong Road

department: Division of Gastroenterology and Hepatology

country: China

institute: Shanghai Jiao Tong University

data_processing:
The raw data was checked by fastq.gzC.
Clean reads were aligned to the mouse genome using Hisat2
The expression of the transcript was calculated by FPKM using Stringtie.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: RAW264.7 cell line

extract_protocol:
TRIZOL
Stand-specific libraries were constructed using the Hiseq3000SBS&Cluster kit (Illumina).

treatment_protocol: 100ng/ml LPS for 4 hours

tag: cell line

tag: passages

value: Synbindin silence

tag: stimulation

value: with 100ng/ml LPS stimulation for 4 hours


title: Neural progenitor cells passage 15 d2 rep 2

description: NPC P15 d2 2

tag: cell type


title: Plate1-m52-RNA

tag: tissue


title: young_tissue_4

description: each sample is data from one animal.

value: liver

tag: age


title: Synbindin siRNA-LPS-4h-2

tag: genotype


title: Plate1-m51-RNA

tag: treatment

tag: treatment duration (hrs)


title: Plate1-m50-RNA

tag: Sex


title: Neural progenitor cells passage 15 d2 rep 1

description: NPC P15 d2 1


title: Neural progenitor cells passage 30 rep 4

description: NPC P30 4

source_name: Neural progenitor cells passage 30


title: H3.1, H3, rep1

source_name: 2-week-old seedlings

tag: developmental stage

value: 2-week-old seedlings

tag: chip antibody


title: Synbindin siRNA-LPS-4h-1


title: Control siRNA-LPS-4h-3

value: Control


title: Col, H3S28, rep2

value: Col


title: Neural progenitor cells passage 30 rep 3

description: NPC P30 3


title: Neural progenitor cells passage 30 rep 2

description: NPC P30 2


title: Control siRNA-LPS-4h-2


title: Plate1-m49-RNA


title: Control siRNA-LPS-4h-1


title: Col, K27me3, rep2


title: Neural progenitor cells passage 30 rep 1

description: NPC P30 1


title: Synbindin siRNA-LPS-0h-3

value: without LPS


title: Plate1-m46-RNA

value: PeatFlame


title: Col, H3, rep2


title: Plate1-m47-RNA


title: Col, H3S28, rep1


title: Synbindin siRNA-LPS-0h-2


title: Col, H3, rep1


title: Plate1-m45-RNA


title: Synbindin siRNA-LPS-0h-1


title: Col, K27me3, rep1


title: Neural progenitor cells passage 15 rep 3

description: NPC P15 3

source_name: Neural progenitor cells passage 15

value: ES-derived neural progenitor cells

value: RiboTag +


title: Neural progenitor cells passage 15 rep 2

description: NPC P15 2


title: Plate1-m44-RNA


title: Plate1-m48-RNA


title: Control siRNA-LPS-0h-3


title: Neural progenitor cells passage 15 rep 1

description: NPC P15 1


title: Plate1-m43-RNA


title: m17_38_3

city: Hangzhou

first: Juan

last: Gao

address: 866 Yuhangtang Road, Xihu District, Hangzhou

department: College of Life Sciences

institute: Zhejiang University

data_processing:
Cutadapt software is used to remove reads that contain adapter contamination, and to remove low-quality bases and undetermined bases.
The HISAT2 software was used to map the reads to the genome and assembled by StringTie with default parameters.
All transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software.
After the final transcriptome was generated, StringTie and ballgown were used to estimate the expression levels of all transcripts by calculating FPKM (fragments per kilo-base of transcript per million of mapped reads)
Genome_build: tair 10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: flowers

growth_protocol: Plants grew at 22°C under LD condition (16/8-hr day/night).

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent
Libraries were prepared for sequencing using standard Ilumma protocols

treatment_protocol: Plants at flowering stage were treated at 38°C for 6 hours

value: 38C for 6h

value: bzip17 T-DNA  mutant

value: flowers


title: Control siRNA-LPS-0h-2


title: m17_38_2


title: m17_38_1


title: Neural progenitor cells passage 15 rep 4

description: NPC P15 4


title: Control siRNA-LPS-0h-1


title: Neural progenitor cells passage 5 rep 3

description: NPC P5 3

source_name: Neural progenitor cells passage 5


title: Plate1-m40-RNA

value: RedOakFlame

value: Lung

value: female


title: Plate1-m41-RNA


title: m17_22_2

value: 22C for 6h


title: Plate1-m39-RNA


title: m17_22_1


title: Neural progenitor cells passage 5 rep 1

description: NPC P5 1


title: WT_38_3

value: wild type


title: Plate1-m37-RNA


title: C002T5 HiC

city: Singapore

first: Pierce

middle: Kah Hoe

last: Chow

address: 11 Hospital Cres

country: Singapore

institute: National Cancer Center Singapore

data_processing:
Hi-C and H3K27ac HiChIP libraries were analysed using the Juicer pipeline (Durand, et al., 2016). Reads from repeated sequencing libraries were merged to create deeper coverage. Loops were called with HiCCUPS at 10kB resolution. Contact domain were called at 50kB resolution, and differential Topologically Associated Domains (TAD) were analysed using TADCompare (Cresswell & Dozmorov, 2020).
Assembly: hg38
Supplementary files format and content: hic files

organism: Homo sapiens

source_name: HCC

extract_protocol:
HiC and HiChIP were performed using the Arima HiC Protocol described in the Arima Hi-C Kit (Material Part Number: A410110 Document Part Number: A160162 v00). 70 mg of snap frozen liver tissue was excised and pulverized into fine powder in liquid nitrogen.
The experiments were then performed following the Arima-HIC protocol. For the HiChIP, sheared chromatin was immunoprecipitated with 5 µg of H3K27ac antibody (Abcam, ab4729). Library preparation was performed using NEB ultra II library preparation kit, according to manufacturer’s protocol. The libraries were sequenced by Macrogen using 2 x 150 bp read lengths.

value: tumour


title: Plate1-m42-RNA


title: Neural progenitor cells passage 5 rep 4

description: NPC P5 4


title: mouse embryonic stem cells rep 3

source_name: mouse embryonic stem cells

value: mouse embryonic stem cells


title: Plate1-m36-RNA

value: Saline


title: WT_38_2


title: m17_22_3


title: B008T2 HiC


title: mouse embryonic stem cells rep 2


title: mouse embryonic stem cells rep 1


title: WT_22_3


title: B008T2HiChIP H3K27ac

value: H3K27ac (catalogue #:ab4729, Abcam


title: Plate1-m34-RNA


title: B008T1 HiC


title: W121

city: Saint Louis

first: Fumihiko

last: Urano

state: Missouri

address: 660 South Euclid Ave

institute: Washington University School of Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger (10X Genomics)
{"software_version": "cellranger-4.0.0", "format_version": 2}

source_name: iPSC-derived islets

extract_protocol: Library was performed according to the manufacter’s instructions (Chromium Single Cell 3’ Library and Gel Bead Kit v3 (10x Genomics))

tag: disease state

value: Wolfram syndrome

value: iPSC-derived islets


title: CF4 BALB/c Infected

city: Dublin

first: Conor

last: Finlay

address: Trinity Translational Medicine Institute, Trinity College Dublin, St. James' Hospital Campus, Trinity College Dublin, Dublin 8

department: School of Medicine

country: Ireland

institute: Trinity College Dublin

description: Whole cells

data_processing:
Illumina Novaseq S1 software used for basecalling
Initial processing was done using Cell Ranger (v3.0.1) mkfastq and count
Futher processing done using Cell Ranger aggr to create merged counts files
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary files: merged dataset created using Cell Ranger (v3.0.1) aggr;R object for singlecellexperiment; R object for seurat;python anndata object

source_name: Pleural macrophages

growth_protocol: Cells were obtained from pleural lavage with dPBS containing 2% FBS and 2mM EDTA

extract_protocol:
10x genomics protocol (15.7K cells were loaded per each sample)
10x genomics v2 chemistry

treatment_protocol: Cells were FACS purified in 2% FBS and 2 mMEDTA and washed with PBS

value: L. sigmodontis infected BALB/c pleural cavity macrophages

value: BALB/c

value: 113 days old

tag: infection

value: Infected


title: Neural progenitor cells passage 5 rep 2

description: NPC P5 2

value: ES-derived neural progenitor cells

value: RiboTag +


title: WT_22_2

value: flowers


title: mouse embryonic stem cells rep 4


title: C002N HiC

value: adjacent normal


title: B008N HiC


title: CF3 C57BL/6 Infected

description: Whole cells

value: L. sigmodontis infected C57BL/6 pleural cavity macrophages

value: female


title: Plate1-m33-RNA

value: Lung


title: Plate1-m32-RNA


title: B003T2HiChIP H3K27ac

value: tumour


title: WT_22_1

value: 22C for 6h

value: wild type


title: CF2 BALB/c Naïve

description: Whole cells

value: naive BALB/c pleural cavity macrophages

value: naive


title: bZIP17_myc_3

data_processing:
Skewer software was used to remove low-quality and linker sequence fragments, and to filter sequences less than 50 bp.
Bowtie was used to perform unique mapping analysis between the filtered sequencing data and the reference genome to further remove duplicated reads.
MACS software was used to do the peak calling.
The common binding cis-elements were identified by using MEME and GO analysis was performed using the R package edgeR.
Genome_build: tair 10

source_name: seedlings

growth_protocol: Seedlings grew at 22°C under LD condition (6/8-hour day/night).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared for sequencing using standard Ilumma protocols

treatment_protocol: 42°C treated for 2 hours.

value: 42°C for 2h

value: anti-MYC antibody (Sigma-Aldrich, USA)

value: seedling


title: B003T1 HiC


title: Plate1-m31-RNA

value: Saline


title: bZIP17_myc_2


title: CF1 C57BL/6 Naïve

description: Whole cells

value: naive C57BL/6 pleural cavity macrophages

value: 113 days old


title: 194T2HiChIP H3K27ac

value: H3K27ac (catalogue #:ab4729, Abcam


title: 194T1 HiC


title: bZIP17_myc_1


title: Mixed chimera CD45.2 myeloid fraction scRNAseq

city: New York

first: Miriam

last: Merad

state: NY

address: 1470 Madison Ave, 5th Floor

department: Department of Oncological Sciences

institute: cahn School of Medicine at Mount Sinai

description: CD45.2+ Myeloid fractions from 6 biological replicates

data_processing:
Cell Ranger 2.1 for library demultiplexing, alignment to mm10 reference transcriptome, and generating count matrices using the "raw" matrix output
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw and dehashed cell x genes matrix

source_name: Lung Tumor

growth_protocol: Wyld type (c57bl/6) mice were grown in our facilities. All animals used for experiments were age and sex matched between experimental groups. All animal procedures were approved by the Institutional Animal Care and Use Committees (IACUCs) of our institution.

extract_protocol:
Lungs were perfused and processed into a since cell suspension which was immunostained with a cocktail of fluorescent antibodies for FACS-sorting.
For each scRNA-seq experiment, we sorted around 100000 total myeloid CD45.1+ or CD45.2+ cells as further defined as described in the text. Single cell suspensions were pelleted and resuspended in 100 ul diluted hashtag antibodies at 4˚C for 20 minutes (Hashtag antibody conjugated as per New York Genome Center hashing protocol https://citeseq.files.wordpress.com/2019/02/cell_hashing_protocol_190213.pdf ). Stained cells were washed three times in PBS + 0.5% BSA by 4˚C centrifugation at 350 RCF to remove unbound antibodies. Washed cells were resuspended in 150ul wash buffer and counted using a Nexcelom Cellometer Auto2000. Hashed samples were pooled in equal amounts of live cells.   Volume of cell suspension was adjusted to achieve a target of 2 million cells/mL.
Hashed sample pool was counted and loaded on two lanes of the 10x Genomics NextGem 5’v1.1 assay as per the manufacturer’s protocol with a targeted cell recovery of 20,000 cells. Gene expression libraries were made as per the 10x Genomics demonstrated protocol. During cDNA amplification, hashtag oligonucleotides (HTO) were enriched during cDNA amplification.

treatment_protocol: Wyld type mice were lethally irradiated and reconstituted with a mix 1:1 of Trem2+/+ (CD45.1) and Trem2 -/- (CD45.2) bone marrow. 7 weeks later, chimeric mice were injected intravenously with 5*10^5 KP-GFP tumor cells and humanely sacrificed 21 days after tumor delivery

tag: disease

value: GFP-expressing KP lung adenocarcinoma (KP-GFP)

value: day 21

value: Trem2 -/-


title: Plate1-m28-RNA

tag: strain

value: EucalyptusSmolder

value: female


title: muller cell,  Ac-rBc-PI-PLC-A2 protein, 24h rep3

city: wenzhou

first: Bianjin

last: Sun

state: zhejiang

address: No. 270 Xueyuan West Road, Lucheng District

institute: School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1)
Assembly: hg19
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: eye

growth_protocol: Six- to eight-week-old C57BL/6J mice were purchased from the Chinese Academy of Sciences, Shanghai Laboratory Animal Center (SLAC) .The mice were housed in an environment on a 12 h light/12 h dark cycle.Müller glial cells were cultured in DMEM containing 10% heat-inactivated fetal bovine serum (FBS; Ausvin) and penicillin–streptomycin (50 IU/ml and 50 mg/ml, respectively, Beyotime)

extract_protocol:
RNA was harvested using RNAprep pure Cell / Bacteria Kit (Tiangen)
The RNA samples were qualified for library construction. The mRNA SEq library can be constructed in two ways: common library or strand specific library. Common library construction is used for conventional projects, and strand specific library construction is used for distinguishing the directionality of strands.

treatment_protocol: Mice were anesthetized with a mixed solution of xylazine (5 mg/kg body weight) and ketamine (70 mg/kg body weight).Then,1ul of the corresponding solution was injected by intravitreal injection.

value: eye

value: MIO-MI

value: Muller cell

value: WT

value: Ac-rBc-PI-PLC-A2 protein

tag: time


title: Mixed chimera CD45.1 myeloid fraction scRNAseq

description: CD45.1+ Myeloid fractions from 6 biological replicates

value: Trem2 +/+


title: Trem2 Knockout scRNAseq

description: Myeloid (M) and Lymphoid (L) fractions from 2 biological replicates

data_processing:
Cell Ranger 2.1 for library demultiplexing, alignment to mm10 reference transcriptome, and generating count matrices using the "raw" matrix output
Debarcoding of hashtag oligonucleotides (HTO)
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw and dehashed cell x genes matrix

extract_protocol:
Lungs were perfused and processed into a since cell suspension which was immunostained with a cocktail of fluorescent antibodies.
For each scRNA-seq experiment, we sorted around 100000 total myeloid and/or lymphoid cells as further defined as described in the text. Single cell suspensions were pelleted and resuspended in 100 ul diluted hashtag antibodies at 4˚C for 20 minutes (Hashtag antibody conjugated as per New York Genome Center hashing protocol https://citeseq.files.wordpress.com/2019/02/cell_hashing_protocol_190213.pdf ). Stained cells were washed three times in PBS + 0.5% BSA by 4˚C centrifugation at 350 RCF to remove unbound antibodies. Washed cells were resuspended in 150ul wash buffer and counted using a Nexcelom Cellometer Auto2000. Hashed samples were pooled in equal amounts of live cells.   Volume of cell suspension was adjusted to achieve a target of 2 million cells/mL.
Hashed sample pool was counted and loaded on two lanes of the 10x Genomics NextGem 5’v1.1 assay as per the manufacturer’s protocol with a targeted cell recovery of 20,000 cells. Gene expression libraries were made as per the 10x Genomics demonstrated protocol. During cDNA   amplification, hashtag oligonucleotides (HTO) were enriched during cDNA amplification with the addition of 3 pmol of a HTO Additive primer (5’GTGACTGGAGTTCAGACGTGTGCTC).

treatment_protocol: Wyld type mice were injected intravenously with 5*10^5 KP-GFP tumor cells and humanely sacrificed 28 days after tumor delivery

value: day 28


title: muller cell,  Ac-rBc-PI-PLC-A2 protein, 24h rep2

tag: cell line


title: Plate1-m27-RNA

data_processing:
The counts of sequencing reads per mRNA within the FASTQ files were aligned to the ENSEMBLE mouse genome database (v98) and organized using the Bowtie algorithm within Tempo-SeqR script.
Count data were normalized by median signal intensity using algorithms enabled within the DESeq2 package, resulting in variance stabilized expression values.
Genome_build: ENSEMBLE database version 98
Supplementary_files_format_and_content: Count data are provided as a .csv, aligned to gene symbols, and represent count values prior to normalization

extract_protocol:
Lung and heart tissue samples were collected immediately 4 h and 24 h postexposure  and stored at -80 degrees C until further analysis.  RNA molecules with 18 nucleotides or greater were extracted with the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) and quantified with the NanoDrop 1000 Spectrophotometer (Thermo Scientific, Waltham, Ma) and tested for quality based on RNA integrity scores produced by the QIiAxcel system (Qiagen).
Isolated RNA samples were analyzed using next generation sequencing technologies enabled through the BioSpyder TempO-Seq platform. mRNA-seq libraries were prepared using the QuantSeq 3' mRNA-Seq Library Prep Kit for Illumina, and then these libraries were pooled and sequenced (single-end 50 bp) on the Illumina Ultra-High-Throughput Sequencing System (Hiseq) 2500.

value: Lung


title: muller cell,  Ac-rBc-PI-PLC-A1 protein, 24h rep3

value: Ac-rBc-PI-PLC-A1 protein


title: MC_1: WT macrophage rep1

city: Guangzhou

first: Lingyun

last: Zheng

state: Guangdong

address: No. 280, Waihuan East Road, Guangzhou Higher Education Mega Center,Panyu district,

department: School of Life Sciences and Biopharmaceutics

institute: Guangdong Pharmaceutical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: macrophage

extract_protocol:
Macrophage were scratched on ice, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA)  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bone marrow-derived macrophage

value: coculture with MC38 for 48 hours

value: 8 weeks

value: wild type


title: Plate1-m30-RNA


title: Trem2 Wild Type scRNAseq

value: GFP-expressing KP lung adenocarcinoma (KP-GFP)


title: muller cell,  Ac-rBc-PI-PLC-A1 protein, 24h rep2


title: muller cell,  Ac-rBc-PI-PLC-A2 protein, 24h rep1


title: Plate1-m25-RNA


title: MA_2: anti-Act1 macrophage rep2


title: Plate1-m29-RNA


title: Plate1-m24-RNA

value: PineSmolder


title: MC_2: WT macrophage rep2


title: bZIP17input

value: 42°C for 2h

value: seedling


title: Selection 3, 3D7-A-LF parasites, LFCM condition, 40-45hpi

city: Barcelona

first: Anastasia

last: Pickford

state: Barcelona

address: Carrer Rosselló 153

country: Spain

institute: ISGlobal

hyb_protocol: Hybridization performed as previously described (Painter, H. et al., 2013. PMID: 22990780).

scan_protocol: Microarrays images were obtained using the Agilent G2505C Microarray Scanner.

data_processing:
Initial data processing of microarray data, including normalization, was performed using the GE2_1105_Oct12_ACC_2 extraction protocol in Agilent Feature Extraction 11.5.1.1 software. The next steps of the analysis were performed using Bioconductor in an R environment (R version 3.5.3). For each individual microarray, we calculated Cy3 and Cy5 background signal as the median of the 100 lowest signal probes for each channel. Probes with both Cy3 and Cy5 signals below three times the array background were excluded (set to NA). Gene level log2(Cy5/Cy3) values and statistical estimation of parasite age were computed as described (Rovira-Graells et al., 2012. PMID: 22415456). Genes with missing values or genes that in all samples had expression values within the lowest 20th percentile of intensity (Cy5 channel) were excluded from downstream analysis, including identification of differentially expressed genes, because differences in genes expressed at near-background levels are of low confidence. To account for the progression delay induced by HS exposure, which can be a major confounder in the downstream analysis, we estimated the age (hours post-invasion, hpi) of each microarray sample by calculating the most likely time post-invasion along the asexual cycle compared to the HB3 transcriptome as reference, using a statistical likelihood method as previously described [Lemieux et al., 2009, PMID: 19376968].
The file processed_data.txt includes all normalized data, probe name, feature number, gene ID and whether or not the probe was excluded from the analysis.

organism: Plasmodium falciparum

label_protocol: Test sample, Cy5; reference pool, Cy3. As previously described (Painter, H. et al., 2013. PMID: 22990780)

growth_protocol: Parasites were cultured in B+ erythrocytes at a 3 % haematocrit under standard culture conditions in RPMI-based supplemented with either 0,5% AlbuMAX II (3D7-A-Ctrl parasites) or 0,5% BSA (3D7-A-LF parasites) human serum, in a 5% CO2, 3% O2, balance N2 atmosphere at 35ºC. Tight synchronization (5 h age window) was achieved by Percoll purification followed by sorbitol treatment 5 h later.

extract_protocol: RNA was purified using the TRIzol method following the manufacturer instructions.

treatment_protocol: 3D7-A-Ctrl parasites were always maintained in 0,5% AlbuMAX II medium. The 3D7-A-LF parasites were divided into two conditions after the Percoll synchronization: LF0 (3D7-A-LF parasites always maintained in 0,5% BSA medium) and LFCM (3D7-A-LF parasites switched to 0,5% AlbuMAX II medium).

tag: condition

value: LF parasites from selection 3 in LFCM condition

tag: time point

tag: estimated age (hpi)

source_name: 3D7-A mixed stage Reference Pool

value: 3 samples of synchronized cultures covering the whole asexual cycle


title: muller cell,  Ac-rBc-PI-PLC-A1 protein, 24h rep1

tag: tissue

value: eye

value: MIO-MI

tag: cell type

value: Muller cell


title: MA_1: anti-Act1 macrophage rep1

tag: age

tag: genotype


title: Plate1-m23-RNA

last: Rager

address: 135 Dauer Drive, CB 7431

institute: UNC

tag: treatment

tag: treatment duration (hrs)

value: female


title: Selection 3, 3D7-A-LF parasites, LFCM condition, 24-29hpi


title: muller cell,  pbs, 24h rep3

value: WT

value: PBS


title: Plate1-m26-RNA

value: EucalyptusSmolder

value: Lung

tag: Sex


title: Plate1-m22-RNA


title: Selection 3, 3D7-A-LF parasites, LFCM condition, 8-13hpi


title: Selection 3, 3D7-A-LF parasites, LFCM condition, 16-21hpi


title: Selection 3, 3D7-A-LF parasites, LFCM condition, 32-37hpi


title: muller cell,  pbs, 24h rep2


title: Plate1-m21-RNA


title: Selection 3, 3D7-A-LF parasites, LF0 condition, 40-45hpi

value: LF parasites from selection 3 in LF0 condition


title: Plate1-m20-RNA


title: Plate1-m19-RNA


title: Plate2-m18-RNA

value: PineNeedlesSmolder


title: Pcgf-4KO Rep3

city: Nanjing

first: Yaru

last: zhu

address: Xuefu Road

institute: Nanjing University

data_processing:
TopHat (version2.1.1) software used for basecalling.
The sequencing data were mapped to mouse genome (Ensemble GRCm38.p5).
The expression levels of each gene was calculated by FPKM (fragments per kilobase of transcript per million fragments mapped) method. Gene abundances and differential expression analysis were quantified by RSEM and R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R).
Genome_build: GRCm38
Supplementary_files_format_and_content: gene.tpm.matrix.annot.txt: Tab-delimited text file

source_name: mouse embryonic stem cell

extract_protocol:
ES cells were trypsinized and RNA was harvested using Trizol reagent (Invitrogen) following the manufacturer’s instructions.
RNA-seq transcriptome library was prepared using TruSeqTM RNA sample preparation Kit from Illumina.

value: mouse embryonic stem cell


title: Pcgf-6KO Rep1


title: Pcgf-4KO Rep2


title: young_tissue_2

description: each sample is data from one animal.

source_name: Liver tissue

value: liver

value: 3 months


title: Pcgf-6KO Rep3


title: Selection 3, 3D7-A-LF parasites, LF0 condition, 32-37hpi


title: Pcgf-4KO Rep1


title: Plate2-m17-RNA

city: Chapel Hill

first: Julia

source_name: Lung tissue from CD-1 mice


title: Plate2-m16-RNA


title: Ring1a/b-dKO Rep3


title: A549 cells, Treated_3, 72h

city: Shengyang

first: 海蓝

last: 黄

state: Liaoning

address: No.103,Wenhua Street, Shenhe District

institute: Shenyang Pharmaceutical University

data_processing:
Quality control:Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools
Quantification of gene expression level:featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM  values and raw gene counts for each Sample

source_name: Lung

growth_protocol: A549 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol (Invitrogen, USA). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: A549 cells was treated by B35 (2μM) or untreated for 72h

value: Human non-small cell lung cancer cell

value: treated with 2μM B35 for 72h


title: Plate2-m15-RNA


title: Selection 3, 3D7-A-LF parasites, LF0 condition, 8-13hpi


title: muller cell,  pbs, 24h rep1


title: Pcgf-6KO Rep2


title: Selection 3, 3D7-A-LF parasites, LF0 condition, 16-21hpi


title: A549 cells, Treated_2, 72h


title: Selection 3, 3D7-A-LF parasites, LF0 condition, 24-29hpi


title: Selection 3, 3D7-A-Ctrl parasites, 32-37hpi

value: Control parasites from Selection 3


title: Selection 3, 3D7-A-Ctrl parasites, 40-45hpi

value: 3 samples of synchronized cultures covering the whole asexual cycle


title: Plate2-m14-RNA


title: Ring1a/b-dKO Rep1


title: Selection 3, 3D7-A-Ctrl parasites, 24-29hpi


title: A549 cells, Treated_1, 72h


title: W024

description: 10x Genomics

value: Wolfram syndrome

value: iPSC-derived islets


title: Ring1b-KO Rep3


title: Selection 3, 3D7-A-Ctrl parasites, 16-21hpi


title: A549 cells, Control_3, 72h

value: untreated


title: Plate1-m12-RNA

value: PeatSmolder

value: female


title: Ring1b-KO Rep2


title: A549 cells, Control_2, 72h

value: WT


title: Plate1-m11-RNA


title: Ring1a/b-dKO Rep2


title: Ring1b-KO Rep1


title: Selection 3, 3D7-A-Ctrl parasites, 8-13hpi


title: A549 cells, Control_1, 72h


title: Selection 2, 3D7-A-LF parasites, LFCM condition, 40-45hpi

value: LF parasites from selection 2 in LFCM condition


title: Ring1a-KO Rep3


title: Plate1-m10-RNA

value: Lung


title: Selection 2, 3D7-A-LF parasites, LFCM condition, 32-37hpi


title: Plate1-m9-RNA


title: Plate1-m13-RNA


title: TNBC2

city: Stony Brook

first: Jinyu

last: Li

address: 101 Nicolls Rd

department: Cancer Center

institute: Stony Brook University

data_processing:
Single Cell sequencing data were pre-processed by cellranger 6.0.1 from 10X Genomics using default settings.
Downstreaming analysis was performed by Seurat 3.0
Assembly: mm10, GRCh38
Supplementary files format and content: gzipped file format containing "filtered_feature_bc_matrix" folder contents from cellranger outputs

source_name: triple negative breast tumor tissue

extract_protocol:
The tumors were digested both mechanically and enzymatically (Collagenase/Hyaluronidase, and DNaseI) and single cell suspensions of viable cells were prepared. mRNA from each individual cell was captured and tagged with barcodes using 10X Genomics microfluidic platform.
Barcoded cDNA library was prepared using the manufacturer's instructions, 10X Genomics.

tag: tissue of origin for tumor

value: Breast

tag: genetic alteration


title: Ring1a-KO Rep2


title: Plate1-m8-RNA


title: Ring1a-KO Rep1


title: Plate1-m7-RNA


title: Selection 2, 3D7-A-LF parasites, LFCM condition, 24-29hpi


title: Selection 2, 3D7-A-LF parasites, LFCM condition, 16-21hpi


title: WT Rep3


title: Plate1-m6-RNA

value: RedOakSmolder


title: TNBC1


title: sh_WT_2

city: Berkeley

first: Roberto

last: Zoncu

state: California

address: Li Ka Shing Center, 1951 Oxford Street, Rm330F

department: Molecular Cell Biology

institute: University of California Berkeley

description: shLYCHOS + LYCHOS WT_replicate#2

data_processing:
Analysis was performed using a combination of programs including STAR, HTseq, Cufflink and Novogene's wrapped scripts. Alignments were parsed using Tophat program and differential expressions were determined through DESeq2/edgeR. GO and KEGG enrichment were implemented by the ClusterProfiler. Gene fusion and difference of alternative splicing event  were detected by Star-fusion and rMATS software
Indexes of the reference genome was built using STAR  and paired-end clean reads were aligned to the reference genome using STAR (v2.5).
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each  gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq2  R package (2_1.6.3). The resulting P-values were adjusted using the Benjamini and Hochberg’s  approach for controlling the False Discovery Rate(FDR). Genes with an adjusted P-value <0.05  found by DESeq2 were assigned as differentially expressed.
Genome_build: Homo sapiens hg19
Supplementary_files_format_and_content: fpkm and read counts

source_name: mammalian cells

growth_protocol: Cells were grown in DMEM + 10% FBS,  100 U/mL penicillin, 100 mg/mL streptomycin at 37°C and 5% CO2. Cell were grown for 5days post-lentiviral infection and harvested using RNA lysis buffer from Biorad Aurum total RNA extraction kit.

extract_protocol:
Total RNA was extracted using Biorad Aurum total RNA extraction kit (Cat# 7326820). Libraries were made using NEBNext Ultra II Library prep kit for Illumina (E7770). The construction of sequencing libraries was performed by Novogene Corporation Inc.
RNA libraries were prepared for sequencing using NEBNext Ultra II Library prep kit for Illumina.

value: shLYCHOS + LYCHOS WT


title: WT Rep2

value: mouse embryonic stem cell


title: sh_WT_1

description: shLYCHOS + LYCHOS WT_replicate#1


title: Selection 2, 3D7-A-LF parasites, LF0 condition, 40-45hpi

value: LF parasites from selection 2 in LF0 condition


title: WT Rep1


title: Selection 2, 3D7-A-LF parasites, LFCM condition, 8-13hpi


title: Plate1-m5-RNA


title: TNBC3


title: shGpr6_2

value: shLYCHOS


title: Plate1-m4-RNA


title: scRNAseq_BalbC_IL1rnKO

city: Boston

first: Pui

last: Lee

address: 60 Fenwood Rd.

institute: Brigham and Womens Hospital

description: Samples from 3 groups were labeled with hashtag antibodies then pooled for single cell RNAseq. BALBC - Hashtag 9; IL1rnKO vehicle - Hashtag 10; IL1rnKO rapamycin - Hashtag 11. R1 file is composed of a 16 bp barcode and 12 bp UMI. The R2 file contain mRNA reads and the files with I1 contain the library  index. BRI-856 files are from mRNA sequencing. BRI-866 files are generated from sequencing of hashtag (HTO).

data_processing:
Raw base call files (BCL) generated by Illumina sequencers are then de-multiplexed into FASTQ files using cellranger mkfastq.
cellranger count was used to performs alignment, filtering, barcode counting and UMI counting.
Data are processed using Cell Ranger version 3.1.0.
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: Matrix

source_name: peripheral blood

extract_protocol:
Sorted leukocytes were loaded onto a Chromium chip G (10X Genomics) followed by encapsulation in a lipid droplet.
Library construction was performed using the Chromium Single Cell 3' GEM, Library & Gel Bead Kit v3.1 (10X Genomics) according to the manufacturer’s instructions.

treatment_protocol: IL1rn-deficient mice were treated with vehicle (PBS with 5% PEG 400 and 5% Tween 80) or rapamycin (3 mg/kg every 2 days) for 10 weeks.

value: Leukocytes


title: Selection 2, 3D7-A-LF parasites, LF0 condition, 32-37hpi


title: shGpr6_1


title: Selection 2, 3D7-A-LF parasites, LF0 condition, 16-21hpi


title: GFP_Mix

first: Dingcheng

address: 1300 York Ave

department: CT Surgery

institute: Weill Cornell Medical College

description: Single cell 10x Genomics Chromium

data_processing:
The scRNA-seq data were analyzed with the custom Partek Flow software (Partek Inc), based on the Seurat R package. The raw sequencing data were aliagned to the mouse transcriptome reference (mm10) by STAR after Triming the tag sequences. The deduplication of UMIs, filtering of noise signals, and quantification of cell barcodes were performed to generate the single cell counts data of each sample. Single-cell QA/QC was then controlled by the total number of genes (≤ ~6,000), UMIs (≤ ~40,000), and the percentage of mitochondria genes (≤ 10%) according to each sample. The filtered counts were normalized to counts permillion (CPM), added 1.0 and Log2.0 scaled.
Genome_build: mm10

molecule: polyA RNA

source_name: Breast tumor

growth_protocol: GFP+ Tri-PyMT cells were injected into mice through tail vein in in 100 µL of sterile PBS.

extract_protocol:
Single cell suspensions were prepared from lungs and stained for DAPI. DAPI-negative/GFP+ cells were sorted via fluorescence-activated cell sorting (FACS).
10x Genomics Chromium was employed to add barcoded primer gel beads to each single cell.  The captured polyA mRNA from single cells was reversely transcribed, barcoded and amplified following standard protocol of10X Genomics Chromium Single-cell 3' Library RNA-Seq Assays , followed by sequencing in Illumina NovaSeq6000 at the Genomics and Epigenetics Core Facility at Weill Cornell Medicine.

treatment_protocol: At day 15 post-administration of GFP+ Tri-PyMT cells, mice were sacrificed. Tumor bearing lungs were harvested for single cell suspension. GFP+ Tri-PyMT cells were sorted and submitted for single cell sequencing analysis.

value: Mixed strain of FVB and C57BL6

value: MMTV-PyMT breast tumor

value: 15 days after tail vein injection of tumor cells.


title: Plate1-m3-RNA


title: Selection 2, 3D7-A-LF parasites, LF0 condition, 24-29hpi

value: 3 samples of synchronized cultures covering the whole asexual cycle


title: Tri-PyMT_invitro_Mix

description: Single cell RNA sequencing

extract_protocol:
Tri-PyMT cells were cultured in growth medium with 10% FBS. RFP+, GFP+ and Double+ cells were sorted by flow cytometry and re-mixed with same numbers.
10x Genomics Chromium was employed to add barcoded primer gel beads to each single cell.  The captured polyA mRNA from single cells was reversely transcribed, barcoded and amplified following standard protocol of10X Genomics Chromium Single-cell 3' Library RNA-Seq Assays , followed by sequencing in Illumina NovaSeq6000 at the Genomics and Epigenetics Core Facility at Weill Cornell Medicine.

value: Sorted from culture of parental Tri-PyMT cells


title: Plate1-m1-RNA


title: Selection 2, 3D7-A-Ctrl parasites, 40-45hpi

value: Control parasites from Selection 2


title: XX epiblast tet3ko mutant #4

city: San Francisco

first: Barbara

last: Panning

state: CA

address: 600 16th Street

department: Biochemistry and Biophysics

institute: UCSF

data_processing:
Quality Control was performed on the data using FastQC (v0.11.7)
Reads were trimmed using Trimmomatic (v0.35) by removing Illumina TruSeq adapters using Trimmomatic's TruSeq3-PE.fa adapter file, a PHRED quality score of 15, and a minimum length of 20 bases.
Transcript abundance was quantified from the trimmed reads using Salmon (v1.1.0).
Genome_build: GRCm38
Supplementary_files_format_and_content: singular tab-delimited file containing TPM values for all samples

source_name: epiLC

growth_protocol: mESCs were grown in 2i media containing N2B27, GSK3 inhibitor, and MEK1/2 inhibitor, and LIF and passaged at least three rounds.  To transition the mESCs to EpiLCs, the cells were fed using FGF5 and Activin A without LIF for five days.

extract_protocol:
RNA was extracted using the Direct-zol RNA miniprep kit cat#R2051 from Zymo Research
RNA integrity (RIN) was measured for all samples using a Bioanalzyer Agilent 2100. All sequencing libraries analyzed were generated from RNA samples with a RIN score ≥ 9. The Illumina TruSeq Stranded Total RNA Gold protocol was used to deplete cytoplasmic and mitochrondrial rRNA from all samples, capturing coding RNA and multiplex forms for non-coding RNA. A total of 200ng of total RNA was used to construct RNA-seq libraries, and these were quantified and normalized using the Library Quantification Kit from Kapa Biosystems


title: shLuc_1

description: shLuciferase (control)_replicate#1

value: shLuciferase (control)


title: CRC1200_D7

city: Durham

first: Xiling

last: Shen

address: 101 Science Dr., CIEMAS

institute: Duke University

description: original dissociated cells

data_processing:
Drop-seq datasets were analyzed using the Broad Institute Drop-seq pipeline software (https://github.com/broadinstitute/Drop-seq).
10x Genomics datasets were analyzed using the CellRanger pipeline software (version 3.1.0) to demultiplex BCL files, generate fastqs, and generate feature counts.
Gene expression matrices for the drop-seq datasets were produced using the first 4,000 cellular barcodes with the largest number of reads associated with each index.
All default parameter values for both the Drop-seq pipeline and CellRanger v3.1.0 pipeline software were used to generate processed data files.
Genome_build: hg19
Supplementary_files_format_and_content: "tab-separated expression matrix" is the output from the Broad Drop-seq proccessing pipeline and is a gene x cell barcode matrix of integer counts. "hdf5 feature barcode matrix" is the output from the 10x Genomics CellRanger proccessing pipeline and is a binary encoding of a gene x cell barcode matrix of integer counts.

source_name: colorectal

growth_protocol: Micro organospheres were grown in tumor culture medium supplemented with required growth factors in basal medium.

extract_protocol:
We extracted cells from droplets by dissociating 3D matrix using TypLE and incubation.
For drop seq technology, we followed Dolomite Drop-seq scRNA library protocol. For 10X scRNA librariy preparation, we followed 10X Next GEM 3' scRNA seq library kit (V3.1) protocol.

treatment_protocol: We treated micro organospheres with either ESK1* drug or negative control drug, or no drug for 24 hours before the cells were dissociated for singlec ell RNA-seq assays.

tag: patient

value: untreated

value: colorectal

tag: disease state

value: cancer


title: XX epiblast tet3ko mutant #3

tag: strain


title: Selection 2, 3D7-A-LF parasites, LF0 condition, 8-13hpi


title: CRC1200_D3

description: original dissociated cells


title: XX epiblast tet3ko mutant #1


title: DEP-SiglecFlow Neutrophil 2

city: Seoul

first: JAE WOO

last: SHIN

address: 103 Daehak-ro

department: Department of Biomedical Sciences

country: South Korea

institute: Seoul National University

data_processing:
Reads were mapped to the genome (Ensembl GRCm38 release89) using STAR-v2.5.4b with ENCODE option.
RSEM-v1.2.31 was used to calculate read counts and normalization.
Genome_build: mm10
Supplementary_files_format_and_content: tab separated RSEM results
Supplementary_files_format_and_content: matrix table of count from every sample and genes

source_name: DEP-SiglecFlow 2

extract_protocol:
DEP exposed lungs were removed. Eosinophils, SiglecFlow and SiglecFhigh neutrophils were sorted. We extracted total RNA from samples using RNeasy Micro Kit (Qiagen), following the manufacturer’s instructions, and treated DNaseI.
We constructed RNA-seq libraries using the NEXTflex™ Rapid Directional RNA-Seq Kit (Perkin Elmer), following the manufacturer’s instructions. In brief, we selected and fragmented poly-A-tailed mRNA ligated double-stranded cDNA fragments with adapters and amplified them for 9 cycles of PCR. We then performed RNA-seq using the Illumina HiSeq 2500 platform.

treatment_protocol: C57BL/6 female mice were exposed to DEP (150μg) intratracheally for 3 consecutive days and sacrificed on a following day.

value: Lung

value: 7 week


title: DDNSe DN3_DLL1_3

city: Charlestown

first: Katia

last: Georgopoulos

address: 13th street

institute: Harvard Medical School

data_processing:
Basecalls were performed using  bcl2fastq v. 1.8.3
Read alignment was performed on the mm10 (mouse genome) assembly using the genome mappers STAR
Assembly: mm10

source_name: in vitro culture

extract_protocol:
proB, largepreB, smallpreB (BM):  Erythroid, myeloid, T cells, NK cells and mature B lineage (Lin) cells were depleted from bone marrow cell suspensions, and Lin(–)cKitloCD19+CD43+ pro-B cells, Lin(–)CD19+CD43+BP1+ large preB cells, and Lin(–)CD19+CD43–CD25+ small preB cells were sorted by FACSAria (BD Biosciences).    ETP, DN2, DN3, preDP (Thymus):  Erythroid, myeloid, gdT, CD8+CD4+DP, CD8+T, CD4+T, NK and B lineage (Lin) cells were depleted from thymocyte cell suspensions, and Lin(–)CD44+cKit+CD25– ETP, Lin(–)CD44+cKit+CD25+ DN2, Lin(–)CD44–CD25+ DN3, and Lin(–)CD44–CD25– preDP cells were sorted by FACSAria (BD Biosciences).      smallDP, CD8+T, CD4+T (Thymus):  Erythroid, myeloid, NK and B lineage (Lin) cells were depleted from thymocyte cell suspensions, and CD8+CD4+ small DP, CD8+T, and CD4+T were sorted by FACSAria (BD Biosciences).    RNA was isolated using Trizol reagent and Direct-zol RNA prep kit (Zymo Research).
Illumina TruSeq RNA Sample Prep Kit (Illumina) or NEB Next Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB) were used for the construction of sequencing libraries.

value: DNSe-/-


title: XY epiblast rep 3

value: wildtype


title: shLuc_2

description: shLuciferase (control)_replicate#2


title: DEP-SiglecFhigh Neutrophil 2

source_name: DEP-SiglecFhigh 2


title: DEP-SiglecFhigh Neutrophil 1

source_name: DEP-SiglecFhigh 1


title: UiPSM scRNA-seq

city: Hangzhou

first: Xingnan

last: Huang

address: No.18 Shilongshan Road

institute: Westlake University

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
We mapped single-cell sequencing data to human genome by using CellRanger 3.0.2 with setting ‘--localcores=10 --localmem=3 --mempercore=3 --maxjobs=10 --r1-length=26 --r2-length=151’.
We processed mapped data by using Seurat15. The count matrix was generated by using merge() function in Seurat and excluding low quality cells—cells with less than 200 genes and low quality genes—genes expressing less than 10 cells.
Genome_build: hg38

source_name: UiPSM reprogramming cell (teratoma)

growth_protocol: Preparing 1.5x106 UiPSM cells at different passages (p20, p40) derived from three donors, which were harvested by briefly washing with PBS followed by dissociation by 0.25% Trypsin-EDTA(Gibco).

extract_protocol:
Cells suspensions (500-1000 cells per microliter) were loaded on a Chromium Single Cell Controller (10x Genomics) to obtain single-cell gel beads in emulsion (GEMs) by using Single Cell 3’ Library and Gel Bead Kit V2 (10x genomics, 120237). Captured cDNAs were lysed and the released RNA were barcoded through reverse transcription in singular GEMs (Zheng et al., 2017). Barcoded cDNAs were pooled and cleaned by DynaBeads® MyOne Silane Beads (Invitrogen, 37002D).
Single-cell RNA-seq libraries were prepared by Single Cell 3’ Library Gel Bead Kit V2 (10x Genomics, 120237) following the manufacturer’s instruction.

treatment_protocol: After centrifugation and pelleting, cells were resuspended in a small volume(100~150µL) of cold DMEM/F12, counted, and diluted with an equal volume of cold Matrigel, yielding a cell suspension in a 1:1 mixture of DMEM-F12/Matrigel that was kept on ice until transplantation. (The Matrigel was pre-cooled and defrosted in a 4-degree refrigerator for 3 hours) Finally, subcutaneous transplantation into the immunodeficient MITRG mice of 1 months of age.

value: UiPSM reprogramming cell (teratoma)

tag: method

value: scRNA-seq


title: Plate1-m2-RNA

value: RedOakSmolder

value: female


title: Selection 2, 3D7-A-Ctrl parasites, 24-29hpi


title: XY epiblast rep 2


title: DDNSe DN3_DLL1_2


title: WT_38_1

first: Juan

last: Gao

address: 866 Yuhangtang Road, Xihu District, Hangzhou

institute: Zhejiang University

data_processing:
Cutadapt software is used to remove reads that contain adapter contamination, and to remove low-quality bases and undetermined bases.
The HISAT2 software was used to map the reads to the genome and assembled by StringTie with default parameters.
All transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software.
After the final transcriptome was generated, StringTie and ballgown were used to estimate the expression levels of all transcripts by calculating FPKM (fragments per kilo-base of transcript per million of mapped reads)
Genome_build: tair 10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: flowers

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent
Libraries were prepared for sequencing using standard Ilumma protocols

value: 38C for 6h

value: wild type

value: flowers


title: UiPSC scRNA-seq

source_name: Urine induced pluripotent cell (teratoma)


title: scRNA-seq_Day6

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
We mapped single-cell sequencing data to human genome by using CellRanger 3.0.2 with setting ‘--localcores=10 --localmem=3 --mempercore=3 --maxjobs=10 --r1-length=26 --r2-length=151’.
We processed mapped data by using Seurat15. The count matrix was generated by using merge() function in Seurat and excluding low quality cells—cells with less than 200 genes and low quality genes—genes expressing less than 10 cells.
Genome_build: hg38
Supplementary_files_format_and_content: h5 matrix

source_name: UiPSM reprogramming Day6

growth_protocol: UiPSM reprogrammed from Urine cell with a induction medium(DM),Advanced DMEM/F12 supplemented with 5uM EPZ5676,10ng/ml bFGF, 5ng/ml EGF and 3uM CHIR99021

treatment_protocol: UiPSM cells including time-course samples were briefly washed (DPBS), dissociated (0.25% Trypsin-EDTA(Gibco)), strained (100 µm filter) twice, pelleted and resuspended in DPBS containing 0.04% BSA (Sigma) to give a final concentration of 800 cells/ul.

value: UiPSM reprogramming cell

tag: day

value: Day 6


title: Plate1-m38-RNA

value: RedOakFlame


title: Plate1-m35-RNA

value: Saline


title: Selection 2, 3D7-A-Ctrl parasites, 8-13hpi

tag: condition

value: Control parasites from Selection 2

source_name: 3D7-A mixed stage Reference Pool

value: 3 samples of synchronized cultures covering the whole asexual cycle


title: XY epiblast rep 1


title: Sq_ND_5

first: John

middle: Zhong

state: Jiangsu

address: 101 Longmian Avenue, Jiangning District

department: Biochemistry and Molecular Biology

institute: Nanjing Medical University

data_processing:
Raw Data are processed with Perl scripts
The reference genomes and the annotation file were downloaded from ENSEMBL database,and Clean Data were mapped to the reference genome using HISAT2
Read Count for each gene in each sample is counted by HTSeq, and FPKM (Fragments Per Kilobase Millon Mapped Reads) were then calculated to represent the expression level of genes in each sample
DEGseq or DESeq were used for differential expression analysis of two samples with or without replicates.
Genome_build: mm8

source_name: hepatocyte

extract_protocol:
liver were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hepatocyte

tag: diet

value: normal diet

value: post natal week 27


title: DEP-Eos

source_name: DEP-Eos

value: Lung

value: 7 week


title: WT DN3_DLL1_3

value: WT


title: scRNA-seq_Day3

source_name: UiPSM reprogramming Day3

value: Day 3


title: CRC1200_D0

description: original dissociated cells

value: untreated

value: colorectal

value: cancer


title: Sq_HFD_5

value: high fat diet

value: wildtype


title: XX epiblast rep 3


title: WT DN3_DLL1_2


title: Selection 2, 3D7-A-Ctrl parasites, 16-21hpi

tag: time point

tag: estimated age (hpi)


title: scRNA-seq_Day0

source_name: Urine cell

tag: cell type

value: Urine cell


title: S805-O

description:
original dissociated cells
S805-O_S1

source_name: lung

treatment_protocol: We treated micro organospheres with either ESK1* drug or negative control drug, or no drug for 24 hours before the cells were dissociated for singlec cell RNA-seq assays.

tag: subject id

tag: tissue

value: lung


title: WT DN3_DLL1_1

tag: genotype


title: S805-M

description:
negative control
S805-M_S4

tag: treatment


title: B220+CD19+ B_Thymus_2

source_name: Thymus


title: Wild type replicate 2

city: Melbourne

first: Tim

last: Stinear

state: Victoria

address: 792 Elizabeth St, Melbourne

country: Australia

institute: University of Melbourne

data_processing:
RNAseq data was analysed using the S. aureus USA300 FPR3757 reference genome (accession number: NC_007793) and Kallisto, a kmer based pseudoalignment tool, with analysis and visualization using Degust [https://github.com/drpowell/degust]
Assembly: S. aureus USA300 NC_007793

organism: Staphylococcus aureus

growth_protocol: A 10 ml TSB (50 ml tube) culture was grown overnight at 37°C with shaking at 200rpm. The saturated culture was diluted 1:100 into fresh 10 ml TSB and grown to an OD600nm of 0.8-1.0

extract_protocol:
Cells were lysed by bead beating (Precellys 24 instrument - 6000 rpm, 1 min, 100 um zirconium beads) and cell lysates were clarified by centrifugation (20,000xg/10 min/4°C). Subsequently, 700 µl of supernatant was removed and mixed with 700 µl of ethanol. RNA was extracted using a Direct-Zol RNA miniprep plus kit (ZymoResearch) according to manufactures instructions, including the on column DNase I treatment step.
The libraries were sequenced on the Illumina HiSeq platform for 50 bp single end reads.

treatment_protocol: A 5 ml aliquot of culture was removed and added to 10 ml of RNAprotect Bacteria Reagent (Qiagen) and mixed by vortexing. The sample was incubated at room temperature for 5 min. Cells were then harvested by centrifugation (7,000xg/5min/22°C), the supernatant discarded and the cell pellet resuspended in 1 ml of TRIzol (Invitrogen).

tag: time

value: mid-exponential

tag: culture medium

value: TSB broth

tag: growth temp


title: Wild type replicate 3


title: Selection 2, 3D7-A-Ctrl parasites, 32-37hpi

value: Control parasites from Selection 2

value: 3 samples of synchronized cultures covering the whole asexual cycle


title: DDNSe DN3_DLL1_1

state: MA

value: DNSe-/-


title: XX mESC tet3ko mutant #3

source_name: mESC


title: XX mESC tet3ko mutant #4


title: B220+CD19+ B_Thymus_1


title: XX epiblast rep 2

source_name: epiLC


title: XX epiblast rep 1


title: Wild type replicate 1


title: DDNSe DN3_2


title: XX mESC tet3ko mutant #2


title: WalK T389A mutant replicate 2

value: WalK T389A


title: WalK T389A mutant replicate 3


title: S805-E

state: NC

description:
ESK1* treated
S805-E_S3


title: S805-C

description:
no drug treatment control
S805-C_S2


title: WalK T389A mutant replicate 1


title: DDNSe DN3_1


title: XX mESC tet3ko mutant #1


title: XY mESC rep 3


title: HepG2 cell line sh_PCSK9 #5

city: Wuhan

first: Haixin

last: Yu

state: Hubei Province

address: 1277, Jiefang Avenue

institute: Wuhan union hospital

data_processing:
Basecalls performed using Hisat2 v2.0.5
Sequencing read quality was inspected using the FastQC software. Adapter removal and read trimming were performed using Trimmomatic. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 25).
Paired-end reads were aligned to the hg19.featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg19
Supplementary_files_format_and_content: text file include gene name, position,log2(Fold_change),p-value,q-value for each Sample
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes read-counts and FPKM values for each Sample

extract_protocol:
RNA was harvested using Trizol reagent(Life Technologies). Illumina NEB Ultra directional RNA library Prep Kit was used with 1 ug of total RNA for the construction sequencing libraries.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First   Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: cell line


title: IEL Tetramer neg3 TCR

city: Cambridge

first: Damian

last: Plichta

address: 415 Main Street

institute: Broad Institute

data_processing:
Library strategy: TCR-seq
Single-cell RNA sequencing data was processed with Cell Ranger (v3.1.0) as implemented in cellranger_workflow in the Terra platform (https://app.terra.bio/)
Single-cell TCR sequencing data was assembled and the clonotypes were determined using the default settings of Cell Ranger (v3.1.0) VDJ pipeline as implemented in cellranger_workflow in the Terra platform (https://app.terra.bio/)
Genome_build: mm10
Supplementary_files_format_and_content: h5 files with scRNA readout
Supplementary_files_format_and_content: csv tables with TCR contig information

source_name: IELs

growth_protocol: CD4 T cells were isolated and stained from the intraepithelial lymphocytes (IELs) and mLN of mice

extract_protocol:
Stained cells were run on a cell sorter (Sony SH700) and both tetramer positive and tetramer negative CD4+ T-cells were sorted into a tube containing FACS buffer (PBS + 2% FBS), counted and sent for sequencing
Sorted single cells were separated into droplet emulsions using the Chromium Next GEM Single Cell 5′ Solution (v1)
scRNA and TCR seq

treatment_protocol: Epithelial cells were isolated using a PBS buffer containing 2 mM EDTA, 1 mM dithiothreitol and 2% fetal bovine serum (FBS), shaking at 37°C for 30 min.

value: IELs

tag: sorted cells

value: tetramer neg


title: HepG2 cell line sh_PCSK9 #4


title: IEL Tetramer neg2 TCR

tag: strain


title: XY mESC rep 2


title: control_hPi grafts_pooled_CRISPR

first: VICTOR

last: BARRERA BURGOS

address: Landmark 401 Park Drive 3 East

department: Biostatistics

institute: Harvard School of Public Health

data_processing:
PoolQ v3 software was used to deconvolute sequencing files and quantitate gRNA barcodes counts in each sample
Supplementary files format and content: lognorm-JD_GPP2373_2901507_Sintov_20210224.txt. Tab separated columns with the Log-normalized counts matrix.
Supplementary files format and content: correlation-JD_GPP2373_2901507_Sintov_20210224.txt. Tab separated columns with the condition scores correlation matrix
Supplementary files format and content: barcodecounts-JD_GPP2373_2901507_Sintov_20210224.txt. Tab separated columns with counts by condition barcode
Supplementary files format and content: counts-JD_GPP2373_2901507_Sintov_20210224.txt. Tab separated columns with counts matrix.

source_name: LT SC-islet Graft

growth_protocol: Pagliuca et al., 2014

extract_protocol:
Quick-DNA™ Midiprep Plus Kit (Zymo Research, D4075) was used to extract genomic DNA (gDNA).
gDNA was submitted to GPP for PCR amplification of the integrated construct containing a barcode sequence, and Illumuna sequencing to determine the abundance of each gRNA in each sample.
PCR amplification of the integrated construct containing a barcode sequence, and Illumuna sequencing to determine the abundance of each gRNA in each sample.

treatment_protocol: Sintov et al, 2022

tag: cell source

value: hESC S6

value: Control grafts or hPi grafts


title: XX mESC rep 3


title: HepG2 cell line sh_Control #6


title: XY mESC rep 1


title: XX mESC rep 2


title: sBWH4 [re-used]

description: PBMC

data_processing:
BCL files were demultiplexed and fastq files were obtained using Cell Ranger  (v5.0.0) mkfastq function
Filtered count data was generated using Cell Ranger  (v5.0.0) count function
QC, Samples cluster structure, integration and differentially expressed genes were obtained using the Suerat package in R along with custom code
Assembly: GRCh38-v.2020-A
Supplementary files format and content: mtx files. sparse matrix format with genes on the rows and cells on the columns as output by Cell Ranger.
Supplementary files format and content: TSV files with features (genes) and barcode sequences corresponding to row and column indices, respectively.

source_name: PBMC

extract_protocol:
For co-cultured experiment, cells were collected from 96 wells after 48hrs of co-cultured and SC-islets dissociated using TrypLE Express at 37 °C, to form single cells and quenched with S3 media.
Harvested cells from both sources were centrifuged, resuspended in 0.04% BSA in PBS, counted (LUNA-FX7 Automated Cell Counter), adjusted to 1000 cells/μl and sent to the Harvard University Bauer Sequencing Core for 10X Chromium Single Cell 3’ Library preparation and sequencing.
10X Chromium Single Cell 3’ Library preparation and sequencing

value: Peripheral Blood Mononuclear Cell

value: PBMC


title: sBWH7 [re-used]

description: PBMC


title: HepG2 cell line sh_Control #4


title: SCb_BWH7_48h

description: SC-islets culture 48hr with PBMCs

source_name: SC-islets+PBMCs

value: SCb + PBMC


title: XX mESC rep 1


title: HepG2 cell line sh_Control #5


title: mLN Tetramer neg3 TCR

source_name: mLN T cells

value: mLN T cells


title: mLN Tetramer neg2 TCR


title: SCb_BWH7_24h

description: SC-islets culture 24hr with PBMCs


title: HepG2 cell line PCSK9_inr #3


title: HepG2 cell line sh_PCSK9 #6


title: SCb_BWH4_24h

description: SC-islets culture 24hr with PBMCs


title: HepG2 cell line PCSK9_inr #2


title: PLX 5

city: Shanghai

first: Bo

last: Peng

address: 138 Yixueyuan Road

department: Institute for Translational Brain Research

institute: Fudan University

data_processing:
1.filtering:Trimmomatic v0.36  LEADING:3 TRAILING:3 ILLUMINACLIP:TruSeq3-PE-2.fa:
2.alignment:hisat2  v2.2.1.0 --rna-strandness rf --fr
3.quantify:htseq-count v0.9.1 -s reverse
4.differ:DESeq v1.18.0 pvalue<0.05, |log2FoldChange|>1
5.enrichment: R  v3.4
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: The csv file of the raw counts and etc.

source_name: brain

extract_protocol:
Total RNA was extracted using RNeasy Micro Kit the (QIAGEN) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis.
The libraries were constructed using TruePrepTM DNA Library Prep Kit V2  for Illumina® (Vazyme, Nanjing, China) according to the manufacturer’s instructions.

treatment_protocol: Sorted by FACS

value: astrocytes

value: PLX5622-formulated chow diet

value: brain

tag: gender

value: male


title: SCb_BWH4_48h

description: SC-islets culture 48hr with PBMCs


title: mLN Tetramer neg1 TCR


title: mLN Tetramer pos TCR

value: tetramer pos


title: PLX 4


title: IEL Tetramer neg1 TCR


title: HepG2 cell line PCSK9_inr #1


title: PLX 3


title: WTDN3_H3K4me3

data_processing:
Basecalls were performed using  bcl2fastq v. 1.8.3
Read alignment was performed on the mm10 (mouse genome) assembly using the genome mappers STAR for RNAseq and ChIPseq.
For visualization of sequencing data,  primary sequencing data were sorted, indexed, normalized with reads per kilobase per million mapped reads using DeepTools
Genome_build: mm10
Supplementary_files_format_and_content: fastq, bam, bigwig

source_name: DN3 thymocytes

extract_protocol:
Thymocytes were isolated by mechanical disruption. WTDP and WTDN3 cells were FACS sorted using cell surface markers (WTDN3; Lin-CD25+CD44-cKit-, WTDP; CD8+CD4+).
ChIP for histone modifications was performed from sorted DN3 and DP cells as described in Hu et al Gene Dev, 2016 (doi: 10.1101)

value: Lin(-)CD44-cKit-CD25+ DN3 thymocytes

value: WT

tag: antibody


title: HepG2 cell line DMSO #3

value: DMSO


title: SCb_48h

description: SC-islets culture 48hr without PBMCs

source_name: SC-islets

value: SCb


title: SCb_24h

description: SC-islets culture 24hr without PBMCs


title: PLX 2

tag: diet


title: MoMac_GFP high 4

city: New York

first: Miriam

last: Merad

address: 1470 Madison Ave, 5th Floor

institute: cahn School of Medicine at Mount Sinai

data_processing:
Raw bulk RNA sequencing data was processed and aligned to genome reference mm10  using  R  package  ‘Rsubread’  with  default  parameters.
Genome_build: GRCh38
Supplementary_files_format_and_content: R data file of bulk counts

source_name: Lung tumor associated macrophage

extract_protocol:
Lungs were perfused and processed into a since cell suspension which was immunostained with a cocktail of fluorescent antibodies. Monocyte derived macrophages were FACS sorted directly into Trizol.
RNA was extracted using the Rneasy Micro Kits (Qiagen) according to manufacturer’s instructions. RNA was quantified and quality controlled using Qbit and a Bioanalyzer. 0.5–1 ng of RNA was retrotranscribed and processed to cDNA libraries using the Smart-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio).
All samples were pooled together and loaded onto one lane. Libraries were sequenced on an Illumina NextSeq 550 system.

value: Monocyte derived Macrophage

tag: type of tumor

value: KP-GFP day 28

value: Lung

tag: gfp signal

value: High


title: IEL Tetramer pos TCR

tag: cell type

value: IELs


title: MoMac_GFP high 3


title: HepG2 cell line DMSO #1


title: HepG2 cell line DMSO #2


title: circRNA-Seq s324

city: Fuzhou

first: xiandong

last: lin

state: fujian

address: No. 420 Fuma Road, Jinan District

institute: Fujian Cancer Hospital and Fujian Medical University Cancer Hospital

description:
s324
Patient Sample 4

data_processing:
Alignment to reference genome is performed using Hisat2
Transcript assembly is performed using StringTie
Cuffcompare is used to select for known circRNA, miRNA, and Mrna
circRNA identification is performed using find_circ and CIRI2
Genome_build: Homo sapiens Ensemble 97
Supplementary_files_format_and_content: contains read count for all of the samples combined

source_name: non-metastatic nasopharyngeal cariconoma patient sample

growth_protocol: C666,NP69, CNE_2 and SUNE_1 were cultured in RPMI-1640 containing 10% (v/v) heat-inactivated fetal bovine serum (FBS) and 100 U/ ml of streptomycin/ penicillin mixture (all from Gibco; Thermo Fisher Scientific, Inc., Waltham, MA, USA) in a humidified 37°C incubator supplied with 5% of CO2

extract_protocol:
Collect conventionally cultured cells in logarithmic growth phase, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

value: fresh human nasopharyngeal carcinoma tumor

tag: metastasized

value: FALSE


title: sBWH4

state: Massachusetts

data_processing:
BCL files were demultiplexed and fastq files were obtained using Cell Ranger (v5.0.0) mkfastq function
Filtered count data was generated using Cell Ranger (v5.0.0) count function
QC, Samples cluster structure, integration and differentially expressed genes were obtained using the Suerat package in R along with custom code
Assembly: GRCh38-v.2020-A
Supplementary files format and content: mtx files. sparse matrix format with genes on the rows and cells on the columns as output by Cell Ranger.
Supplementary files format and content: TSV files with features (genes) and barcode sequences corresponding to row and column indices, respectively.

extract_protocol:
For graft extraction, mice were euthanized, and the transplanted kidney was removed. SC-islets graft was peeled off the kidney, was sliced into small pieces and digested in 2mg/mL collagenase D (Sigma, 11088858001) in RPMI (GIBCO, 11875-085) for 45 min in 37 °C. Additional breaking was used by pipetting and by filtering through a 40μm cell strainer. Cells were then centrifuged and resuspended in 0.5% BSA in PBS and a magnetic mouse depletion kit (Miltenyi, 130-104-694) was used to remove residual mouse cells.
All samples were loaded into Chip G per the user guide from 10x Genomics, no alterations were made at any step of the protocol (Part No. CG000315). GEMs were formed targeting 10,000 cells and reverse transcription completed immediately after. The cDNA was cleaned from the GEM reagents, amplified for a total of 11 cycles and verified via TapeStation (Agilent Technologies). Amplified cDNA was diluted and ran on the 4200 TapeStation instrument using High Sensitivity D5000 tape and reagents (Part No. 5067-5592 & 5067-5593). The amplified cDNA was fragmented, end repaired, and A-tailed followed by adaptor ligation, and PCR amplification for a total of 12 cycles with each sample receiving a unique set of dual indices (Part No. 1000215). Final libraries were diluted and ran using the High Sensitivity D5000 tape and reagents (Part No. 5067-5592 & 5067-5593) on the 4200 TapeStation (Agilent Technologies). Libraries were quantified via Kapa qPCR using the Complete Universal Kit (Part No. 07960140001, Roche Sequencing Solutions) and the CFX96 Touch Real-Time PCR Detection System (Bio-Rad Laboratories). Libraries were sequenced on an Illumina NovaSeq instrument using the parameters outlined in the user guide (Read1: 28 bp, i7 index: 10 bp, i5 index: 10 bp, Read2: 90 bp).
10X Chromium Single Cell 3’ Library preparation and sequencing

value: Peripheral Blood Mononuclear Cell

tag: immune infiltration

value: PBMCs


title: MoMac_GFP low 3

tag: tissue

value: Low


title: sBWH7


title: CD 5

value: astrocytes

value: control diet

value: brain


title: MoMac_GFP high 2


title: circRNA-Seq s1017

description:
s1017
Patient Sample 2

source_name: metastatic nasopharyngeal carcinoma patient sample

value: TRUE


title: s168

source_name: SC-islet Graft

value: hESC S6

value: No

value: Control grafts


title: CD 4

value: male


title: s167


title: CD 2


title: sG952


title: CD 3


title: MoMac_GFP low 4

value: Monocyte derived Macrophage

value: KP-GFP day 28


title: MoMac_GFP high 1

value: Lung

value: High


title: PLX 1

value: PLX5622-formulated chow diet


title: circRNA-Seq s1029

description:
s1029
Patient Sample 1

value: fresh human nasopharyngeal carcinoma tumor


title: DEP-SiglecFlow Neutrophil 1

source_name: DEP-SiglecFlow 1

tag: age

value: 7 week


title: MoMac_GFP low 2


title: s165


title: circRNA-Seq SUNE

description:
SUNE
Cell Line 4

source_name: nasopharyngeal carcinoma cell line

value: human nasopharyngeal carcinoma cell line


title: s166


title: CD 1


title: s83


title: circRNA-Seq NP69

description:
NP69
Cell Line 3

source_name: non-cancerous immortalized nasopharyngeal epithelial cell line

value: immortalized human nasopharyngeal epithelial cell line


title: circRNA-Seq CNE

description:
CNE
Cell Line 2


title: circRNA-Seq s307

description:
s307
Patient Sample 3

value: FALSE