title: RNAseq_aCSF_Mg_R3

description:
#REF!
salmon.merged.gene_counts_scaled.tsv
salmon.merged.RAW.gene_counts.tsv
DESEQ2_allsamples_normalized.counts.csv
DESEQ2_allsamples_Log2.normalized.counts.plus1.csv

data_processing:
Paired-end fastq files were processed using the open-access Nextflow RNA-seq pipeline with nextflow v20.12.0-edge in Singularity with default nf-core/rnaseq v3.0 parameters and packages.
Fastq files were mapped to GRCm38.mm10 genome. Gene analyses was performed in R v4.2.0 using DeSeq2 v1.36.0 on the salmon.merged.gene_counts_scaled file. Reads with fewer than 3 counts per gene across replicates were filtered out. Three samples were removed that did not pass RNA and cDNA library quality control testing. One sample was removed due to large deviation on PCA and poor sequence alignment. No samples or animals were excluded from any other analyses.
For differential gene analysis the results function in DeSeq2 was used with contrast to test between two genotypes and treatments of interest. Significance was determined by abs(log2FC) > 0.5 and adjusted P value < 0.1 unless otherwise stated.
Assembly: mm10
Supplementary files format and content: csv,tsv files containing raw (salmon processed) and normalized (DESEQ2) gene counts for all samples

source_name: brain

extract_protocol:
24 h after injection, two mice were pooled per replicate and microglia were isolated from 1 mm tissue blocks spanning the injection sites. Tissues were incubated in lysis buffer (1 mg mL-1 collagenase D (Sigma-Aldrich), 0.05 mg mL-1 DNase1 (Sigma-Aldrich), 3 mM actinomycin D (ActD) diluted in Dulbecco’s phosphate-buffered saline (DPBS) with Ca2+ Mg2+ (Thermo Fisher Scientific)) for 30 min at 37°C. Myelin was depleted using the debris removal kit (Miltenyi Biotec). Cells were treated with Fc-block in FACS buffer (DPBS supplemented with 0.2% BSA, Thermo Fisher Scientific) for 5 min at 4°C, then incubated with primary antibodies for 30 min at 4°C. The following primary antibodies were used at 1:200 dilution and purchased from Biolegend: CD11b (M1/70) and CD45 (30-F11). 15,000 to 20,000 CD45loCD11b+ microglia were FACS sorted into tubes containing RLT plus lysis buffer (Qiagen) supplemented with 1% 2-mercaptoethanol and 0.25% reagent DX (Qiagen) using FACSAria II with BD FACSDiva v8 software. Cells were first gated on SSC-A and FSC-A size and then doublet discrimination was performed with FSC-H and FSC-W parameters. Microglia lysates were frozen and stored at -80°C until processed for RNA-seq.
Samples from plasma injection experiment were processed for RNA-seq using the Ovation RNA-seq System V2 low input kit (NuGEN). Libraries were equimolar pooled and sequenced on NovaSeq6000 S4 with 200 paired-end (Illumnia) to a depth of >50 million reads per library.

value: brain

tag: Sex

value: Male

tag: cell type

value: Microglia (Mg)

value: 24h post aCSF injection


title: BMDM_unstim_batch1_scRNAseq_rep1

status: Public on Jun 02 2023

type: SRA

city: San Francisco, CA

first: Katerina

last: akassoglou

state: CA

address: 1650 Owens st

country: USA

institute: Gladstone Institutes

description: 10X Genomics

library_source: transcriptomic

data_processing:
Samples were demultiplexed and fastq files were used to align reads to the mm10 reference assembly (downloaded 2019) and aggregated using Cellranger count and Aggr packages (10x Genomics).
The R toolkit Seurat was used for QC, clustering analysis, and differential gene expression analysis of scRNA-seq data and performed in R v.4.0.2 unless otherwise stated. For scRNA-seq data visualizations, dittoseq package v1 was used to produce UMAPs, dot plots, and violin plots.
For BMDM scRNA-seq analysis, two independent experiments were integrated together and corrected for batch effect. Batch-corrected dataset QC parameters were: nFeature_RNA > 200; nFeature_RNA < 5000; < 5% and 25% mitochondrial and ribosomal genes, respectively. 17,625 QC-passed BMDMs were used with seurat integration workflow using default parameters. Jackstraw was performed with num.replicate of 100. RunUMAP, FindNeighbors and FindClusters functions were used with the first 20 significant PCs and a resolution of 0.5. DEGs were determined by FindAllMarkers with default parameters. Genes that met log2fc.threshold,0.25 with adjusted P value < 0.05 (Benjamini-Hochberg correction) were used for downstream analysis
For microglia scRNA-seq analysis, QC parameters were: nFeature_RNA > 1000; nFeature_RNA < 5500; < 5% and 20% mitochondrial and ribosomal genes, respectively. nCount_RNA in the 93rd percentile (nCount_RNA < 26,206) were used for downstream analysis. Data were normalized, scaled, and percent of mitochondrial and cell cycle genes regressed out following Seurat SCTransform. Jackstraw was performed with num.replicate of 100. FindNeighbors and FindClusters functions in seurat were used with the first 8 significant PCs and a resolution of 0.4 resolution, respectively. 16,186 microglial cells passed QC with an average of 3,469 genes per cell with 20,228 genes. Cluster DEGs were determined by FindAllMarkers with default parameters. Genes that met log2fc.threshold > 0.25 with adjusted P value < 0.05 (Benjamini-Hochberg correction) were used for downstream analysis.
Assembly: mm10
Supplementary files format and content: tsv files containing barcodes, features, matrix

molecule: total RNA

organism: Mus musculus

source_name: bone marrow

extract_protocol:
Following stimulation, adherent cells were lifted with accutase (StemCell Technologies), viable cells were counted by trypan blue method, then resuspended in RPMI with 5% FBS and used for scRNA-seq.
For scRNA-seq library preparation, BMDMs or primary microglia were processed with Chromium Single Cell 3’ v2 kit according to manufactures guidelines (10x Genomics).
Libraries were balanced to achieve a minimum of 75,000 reads per cell and run on a NovaSeq 6000 (Illumnia) at 150 paired-end reads.

treatment_protocol: Fibrin-coated 24-well culture plates (Corning) were prepared Mendiola et al Nat Immunol 2020. 10 mg mL-1 iC3b (CompTech; A115) in HEPES pH 7.2 buffer was immobilized on culture plates by 1 hr incubation at 37°C followed by overnight incubation in a 37°C humified chamber to dry. For fibrin or iC3b stimulation, BMDMs or primary microglia were seeded into fibrin- or iC3b-coated wells at 5.0 x 105 cells mL-1. Control wells were treated with the same buffer void of fibrin or iC3b. For LPS stimulation, BMDMs or microglia were seeded into 24-well tissue culture treated plates at 5.0 x 10^5 cells mL-1, allowed to adhere overnight, then treated with 100 ng mL-1 LPS (Sigma-Aldrich, O55:B5)

tag: tissue

value: bone marrow

tag: batch number

value: BMDM

tag: genotype

value: C57Bl/6 wild type

tag: treatment

value: unstimulated


title: Res-T_wT_3_PFC

city: Rome

first: Daniela

last: Laricchiuta

state: Rome

address: Via del fosso di fiorano, 64

department: Preclinical neuroscience

country: Italy

institute: IRCCS Fondazione Santa Lucia

data_processing:
For the processing of raw data (format conversion and de-multiplexing), Bcl2Fastq 2.20 version of the Illumina pipeline was used.
GRCm38.p6 genome was used to map the reads, and transcript abundances were estimated using Salmon v1.2
To obtain gene-level count matrices the quantification data were imported using tximport.
From here on, we separated the samples in four tables (one for each comparison, namely Res-T vs Sus-T woT; Res-T vs Sus-T wT; woT vs wT Sus-T; woT vs wT Res-T)  due to the following preprocessing strategies being dependent on the design matrix in use.
Differences in RNA composition between samples were corrected by the Trimmed mean of M-values (TMM) normalization (Robinson and Oshlack, 2010), and filtered for low counts based on a count per million reads (CPM) criteria.
Subsequently, ARSyNseq was used to remove the technical batch effect and NOISeqBIO was used to assess differential gene expression (q>0.95, equivalent to FDR-corrected P<0.05)
Assembly: GRCm38.p6
Supplementary files format and content: Matrix table with preprocessed gene counts for every gene and every sample

source_name: Medial Prefrontal Cortex

extract_protocol:
Amygdalae were punched and manual and enzymatic dissociations were performed using the Neural Tissue Dissociation Kit (P) (Miltenyi Biotec, Bergisch Gladbach, Germany). Pyramidal neurons were then sorted by using the MoFlo Astrios EQ (Beckman Coulter, California, USA) into ice-cold lysis buffer (Reliaprep RNA Cell Miniprep System, Promega, Wisconsin, USA) and then stored at -80°C until RNA extraction.
RNA were prepared using the Ovation SoLo RNA-seq kit for Ultra-low input, with Ribosomal RNA removal, for Illumina PE sequencing

value: Pyramidal neurons

tag: strain

value: B6.Cg-Tg(Thy1-YFP)HJrs/J (Thy1-YFP)

tag: group

value: Res-T

tag: condition

value: with trauma


title: CSF, sample 38

city: Providence

first: Zachary

last: Levin

state: RI

address: 185 Meeting Street

institute: Brown University

data_processing:
Illumina adapter sequences removed by Trim Galore! (version 0.5.0) and QC performed using FastQC (version 0.11.5).
Reads were aligned with HiSat2 (version 2.1.0).
Samtools (version 1.9) view and sort commands were used to convert sam files to bam files.
Alignments were assembled into transcripts using StringTie (version 1.3.4) according to the differential expression workflow in StringTie manual.
Coverage tables were converted to read counts using tximport (version 1.22.0) for analysis using DESeq2 (version 1.34.0).
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing matrix of raw read counts of genes (rows) for each sample (columns).

molecule: polyA RNA

organism: Homo sapiens

source_name: CSF

extract_protocol:
CSF was centrifuged at 2000 g for 20 minutes at room temperature and stored at -80°C. 10 mL frozen aliquots were thawed on ice and diluted 1:1 in PBS. Extracellular vesicles were isolated by ultracentrifugation at 100,000 g for 70 minutes at 4°C, resuspended in 100 µL of PBS supplemented with 1% DMSO, and stored at -80°C. RNA was extracted using the miRNeasy Micro Kit according to the manufacturer’s protocol (Qiagen, ID: 217084).
cDNA was prepared according to a standard protocol for Illumina RNA sequencing.

treatment_protocol: CSF was centrifuged at 1500 relative centrifugal force (RCF) for 10 minutes at 4°C to remove debris. Supernatant was collected, flash frozen in liquid nitrogen, and stored at -80°C.

value: CSF


title: Res-T_wT_2_PFC

description: This subject was removed from differential expression analysis


title: Res-T_wT_4_PFC


title: CSF, sample 36


title: Res-T_wT_1_PFC


title: C2C12-Nkd cells, no Dplate, biol rep 2

city: Pasadena

first: Rachael

last: Kuintzle

address: 391 S Holliston Ave, Bio 73, MC 140-18

department: Chemistry and Chemical Engineering

institute: California Institute Of Technology

data_processing:
TrimGalore was used to run Cutadapt to trim low-quality ends (with -q 28), to remove adapters, and to clip 3 bp from the 3' ends of reads after adapter/quality trimming, as well as to run FastQC for quality assessment.
Reads were aligned to the Mouse Dec. 2011 (GRCm38/mm10) genome using HISAT2 with default parameters.
Transcript abundances were computed with StringTie using the GENCODE annotation of the mouse genome (GRCm38), version M22 (Ensembl 97), downloaded 2019-06-27.
Assembly: mm10
Supplementary files format and content: tab-delimited text files (.gtf) include FPKM values for each Sample

growth_protocol: C2C12 cells were cultured at ≤ 90% confluency in DMEM with high glucose, no glutamine (Thermo Fisher Scientific) supplemented with 20% FBS, 1X Pen/Strep/L-glutamine, and 1X Sodium Pyruvate at 37 degrees C and 5% CO2.

extract_protocol:
For RT-PCR analysis, total RNA from cell lines was extracted using the RNeasy Mini Kit (Qiagen) following cell-lysate homogenization via QIAshredder column.
mRNA was isolated using polyA selection and converted into sequencing libraries using the NEBNext Ultra II RNA Library Prep Kit following the manufacturer's protocols.

treatment_protocol:
Notch gene-depleted C2C12 cells (C2C12-Nkd clone) were plated at 80k cells/well in a 12-well plated treated with recombinant ligand (2µg/mL Dll1-ext-Fc in PBS) or PBS only (negative control) in 10 µM DAPT (Notch signaling inhibitor).
Cells were allowed to plate down overnight, and DAPT was washed out the next morning. Cells were harvested for RNA extraction 6 hours after DAPT washout.
Wild type C2C12 cells were also plated on Dll1-ext-Fc as described above to compare the response of Notch target genes in the Notch-depleted C2C12-Nkd cell line vs. wild type.

tag: cell line

value: myoblasts

value: Nkd

value: No Dplate treatment

tag: time

value: Day 0


title: RNAseq_aCSF_Mg_R2

value: brain


title: CSF, sample 35


title: RNAseq_aCSF_Mg_R1

value: Male


title: Sus-T_woT_3_PFC

value: Sus-T

value: without trauma


title: Sus-T_woT_2_PFC


title: Res-T_woT_4_PFC


title: RNAseq_WT_Mg_R3

value: Microglia (Mg)

value: 24h post WT plasma injection


title: Sus-T_woT_1_PFC


title: CSF, sample 34


title: RNAseq_WT_Mg_R2


title: Res-T_woT_3_PFC


title: CSF, sample 33


title: Res-T_woT_2_PFC


title: RNAseq_WT_Mg_R1


title: CSF, sample 32


title: RNAseq_Fgg390-396A_Mg_R3

value: 24h post Fgg390-396A plasma injection


title: Rat P0 DRG neuron cells_rep3

city: Zhuhai

first: Bin

last: Wang

state: Zhuhai

address: Room 2007, Building 6, North HuanDao  Road 2515,

country: China

institute: Guangdong institute of intelligence and science technoloty

description: Rat P0 DRG neuron cells replicate3

data_processing:
Check quality of RNA-seq reads using fastqc (version 0.11.8) with default parameters.
Reads were aligned to rat genome assembly (RGSC Rno5_5.0/rn5) using HISAT2 (Kim et al., 2015) (version 2.1.0, parameters: --no-softclip --score-min L,-16,0 --mp 7,7 --rfg 0,7 --rdg 0,7 --max-seeds 20 -k 10) with annotations from Ensembl (release 79) and RefSeq (updated at 2018/08/27).
Bam to Bedgraph using genomeCoverageBed
Bedgraph to bigwig using UCSC bedGraphToBigWig
Genome_build: rn5
Supplementary_files_format_and_content: bigWig file (UCSC bigwig in an indexed binary format. http://genome.ucsc.edu/goldenPath/help/bigWig.html)

organism: Rattus norvegicus

source_name: Cultured P0 DRG neuron cells

growth_protocol: DRGs were dissociated from rats at P0, followed by digestion with a mixture enzyme of Collagenase I, Trypsin and DNaseI. After centrifugation with 15% Percoll to remove non-neuronal cells, the DRG neurons were obtained and cultured in 35 mm dish (Corning) with the neurobasal medium containing 2% B27 supplement, 2 mM L-Glutamine (Invitrogen) , 100 ng/ml NGF (Invitrogen), 10 mM 5-fluoro-2’-deoxyuridine (Sigma).

extract_protocol:
Total RNA from cultured DRG neurons was extracted with Trizol Reagent (Invitrogen) according to the manufacturer’s protocol. DRG neurons were cultured 48h in 35 mm dish before rinsed twice with ice-cold PBS,  0.5 mL Trizol was added to the dish for total RNA extraction.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB)
Poly(A)+ RNA-seq

treatment_protocol: Untreated

value: SD

tag: type

value: cDNA


title: CSF, sample 31


title: Res-T_woT_1_PFC

value: Pyramidal neurons

value: B6.Cg-Tg(Thy1-YFP)HJrs/J (Thy1-YFP)


title: Rat P0 DRG neuron cells_rep2

description: Rat P0 DRG neuron cells replicate2


title: Rat P0 DRG neuron cells_rep1

description: Rat P0 DRG neuron cells replicate1


title: RNAseq_Fgg390-396A_Mg_R2


title: Sus-T_wT_3_AMY

source_name: Amygdala

value: with trauma


title: Sus-T_wT_4_AMY


title: RNAseq_Fgg390-396A_Mg_R1


title: SW620 cells, KRASi, 2hr, biol rep 1

city: New York

first: Dongsung

last: Kim

state: NY

address: 1275 YORK AVE

department: HOPP

institute: Memorial Sloan Kettering Cancer Center

data_processing:
The sequencing output files from different lanes were concatenated, aligned to GRCH38 using HISAT2 and transcripts were counted using HTSeq in Python.
Ribosomal reads represented less than 0.5% of the total reads generated.

growth_protocol: 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 extracted using RNeasy Mini Kit (QIAGEN catalog # 74104) according to manufacturer’s instructions
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500ng of total RNA per sample underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR

treatment_protocol: 5uM of KRASi or DMSO spiked directly into media for 2hrs with biological duplicates for each condition.

value: COAD

value: KRAS G12V

value: KRASi


title: SW620 cells, KRASi, 2hr, biol rep 2


title: CSF, sample 29

value: CSF


title: SW620 cells, DMSO, 2hr, biol rep 2

value: DMSO


title: CSF, sample 30


title: Sus-T_wT_2_AMY


title: CSF, sample 28


title: Sus-T_wT_1_AMY


title: RNAseq_FGNKO_Mg_R3

value: brain

value: 24h post FGNKO plasma injection


title: CSF, sample 27


title: RNAseq_FGNKO_Mg_R1

value: Male


title: Res-T_wT_4_AMY

value: Res-T


title: SW480 cells, KRASi, 2hr, biol rep 2


title: Res-T_wT_3_AMY


title: CSF, sample 26


title: CSF, sample 25


title: RNAseq_C3KO_Mg_R4

value: Microglia (Mg)

value: 24h post C3KO plasma injection


title: RNAseq_C3KO_Mg_R3


title: SW480 cells, KRASi, 2hr, biol rep 1


title: RNAseq_FGNKO_Mg_R2


title: Res-T_wT_2_AMY


title: SW480 cells, DMSO, 2hr, biol rep 2


title: CSF, sample 23


title: Res-T_wT_1_AMY


title: RNAseq_C3KO_Mg_R2


title: CSF, sample 24


title: SW620 cells, DMSO, 2hr, biol rep 1


title: Sus-T_woT_3_AMY

value: Sus-T

value: without trauma


title: RNAseq_C3KO_Mg_R1


title: SW480 cells, DMSO, 2hr, biol rep 1


title: CSF, sample 21


title: CSF, sample 20


title: RNAseq_AlbKO_Mg_R4

value: 24h post AlbKO plasma injection


title: Sus-T_woT_2_AMY

value: Pyramidal neurons


title: PC9 cells, KRASi, 2hr, biol rep 1

value: LUAD

value: KRAS WT


title: Sus-T_woT_1_AMY

value: B6.Cg-Tg(Thy1-YFP)HJrs/J (Thy1-YFP)


title: CSF, sample 18


title: PC9 cells, KRASi, 2hr, biol rep 2


title: RNAseq_AlbKO_Mg_R3


title: RNAseq_AlbKO_Mg_R2


title: PC9 cells, DMSO, 2hr, biol rep 2


title: Res-T_woT_3_AMY


title: CSF, sample 17


title: RNAseq_AlbKO_Mg_R1


title: Res-T_woT_2_AMY


title: CSF, sample 16


title: PANC0403 cells, KRASi, 2hr, biol rep 2

value: PDAC

value: KRAS G12D


title: PANC0403 cells, KRASi, 2hr, biol rep 1

value: KRASi


title: Res-T_woT_1_AMY


title: NP137_sample_B [NP137-E]

city: LYON

first: Nicolas

last: Rama

address: 28 rue Laennec

country: France

institute: CRCL

data_processing:
Fastq files were processed with Star, v2.5.2b (mapped on the reference genome:Mus_musculus.GRCm38 (GENECODE release 25))  and read count  were analysed with R (ver 4.2.0) package DeSEQ2 (ver 1.36.0).
Assembly: Mus_musculus.GRCm38 (GENECODE release 25)
Supplementary files format and content: tab delimited file containing raw count

source_name: tumor tissue

extract_protocol:
Tumor were collected, snap frozen and cryo-grinded. RNAs were extracted with standard kit (Macherey Nagel)
RNA-Seq library was produced from 0.17µg (170ng) RNA with Illumina TruSeq® Stranded Total RNA Library Prep Human/Mouse/Rat according to the manufacturer and then sequenced with Illumina NovaSeq6000.

value: tumor tissue

value: anti-Netrin-1 antibody

tag: sample type

value: frozen sample


title: CSF, sample 14

value: CSF


title: CSF, sample 15


title: NP137_sample_A [NP137-D]


title: CSF, sample 13


title: PANC0403 cells, DMSO, 2hr, biol rep 2

value: DMSO


title: SRSF2 flox/flox MyoD-Cre

city: s

first: ruochen

last: guo

address: 320 Yueyang RD.

institute: Shanghai Institute of Nutrition and Health

data_processing:
Illumina GA Pipeline v1.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2.
The stat of mapped reads was list in MappingStatistic_1WT.xls and MappingStatistic_3KO.xls
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi, 2008.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: SRSF2 flox/flox MyoD-Cre mice hindlimb

extract_protocol:
SRSF2 flox/flox and SRSF2 flox/flox MyoD-Cre mice hindlimbs were collected.Then mRNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Lifetech protocol.

value: hindlimb muscle

value: SRSF2 flox/flox MyoD-Cre


title: PANC0403 cells, DMSO, 2hr, biol rep 1


title: SRSF2 flox/flox

source_name: SRSF2 flox/flox mice hindlimb

value: SRSF2 flox/flox


title: PC9 cells, DMSO, 2hr, biol rep 1


title: CSF, sample 12


title: Ctl_sample_C [ctl-C]

value: control antibody


title: YFP/mCherry-negative (biol rep 4)

city: London

first: Juan Pedro

last: Martinez-Barbera

address: 30 Guilford Street

department: Developmental Biology and Cancer

country: United Kingdom

institute: Institute of Child Health, UCL

description: YFP/mCherry-negative cells (biol rep 4)

data_processing:
Quality control was peformed using fastQC ( v0.11.8)
Sequencing data was aligned in BaseSpace.
Differential expression was performed using DESeq2 (Love et al., 2014)
Assembly: mm10 (GENCODE vM23/Ensembl 98)

source_name: Lung

extract_protocol:
Tumour bearing lungs from KrasG12D/+; p16FDR/+; Rosa26loxP-STOP-loxP-YFP/+ mice were dissected into 1 mm3 pieces and dissociated in a solution of 0.5% w/v collagenase type 2 (Lorne Laboratories Ltd.), 0.1x Trypsin (Gibco), 50 μg/ml DNaseI (Worthington) and 2.5 μg/ml fungizone (Gibco) in Hank’s Balanced Salt Solution (HBSS (Gibco) for 45 minutes at 37°C. Tissue fragments were further dissociated into single cells through mechanical trituration using a pipette and filtration through a 70 μm filter. Single cells were washed in HBSS and suspended in FACS media (PBS supplemented with 1% foetal calf serum (PAA), 25 mM HEPES and 10 μg/ml of 4′,6-diamidino-2-phenylindole (DAPI, BD Pharmingen) for live/dead cell discrimination) before being analysed using a BD FACS AriaIII Flow Cytometer. Cells were collected into 4°C RLT lysis buffer (Qiagen RNeasy Micro Kit) and total RNA was isolated (Qiagen RNeasy Micro Kit). Total RNA was then processed for bulk RNA-sequencing analysis.
Isolated RNA was processed by the SMARTer V4 low input assay kit (Clontech) to generate amplified cDNA using the strand-switching protocol. Library preparation was performed with 200 pg of amplified cDNA using the Nextera XT preparation kit with 12 cycles of PCR. Sequencing was then performed on an Illumina NextSeq 500 with 43 bp paired end reads.

value: Lung

value: KrasG12D/+; p16FDR/+; Rosa26loxP-STOP-loxP-YFP/+ (KY-FDR)


title: Ctl_sample_A [ctl-A]


title: Ctl_sample_B [ctl-B]


title: PANC1 cells, KRASi, 2hr, biol rep 1


title: CSF, sample 11


title: PANC1 cells, KRASi, 2hr, biol rep 2


title: CSF, sample 10


title: YFP/mCherry-negative (biol rep 2)

description: YFP/mCherry-negative cells (biol rep 2)


title: NP137_sample_C [NP137-F]


title: YFP/mCherry-negative (biol rep 1)

description: YFP/mCherry-negative cells (biol rep 1)


title: Macrophage, NB9464 TCM, SJ3

city: La Jolla

first: Shweta

last: Joshi

address: 3855 Health Sciences Drive, MC 0815

department: Department of Pediatrics

institute: UCSD Moores Cancer Center

data_processing:
Reads were processed and aligned to the mm10 mouse genome using the bcbio-nextgen version 1.2.8 pipeline (https://github.com/chapmanb/bcbio-nextgen).
Reads were cleaned using Picard version 2.26.
Alignment was performed to the mm10 mouse genome with STAR version 2.6.1d.
BAM files were sorted using samtools version 1.9.
Read quantification was done with Salmon version 1.4.0.
Quality statistics were collected with QualiMap version 2.2.2d and compiled into a report with MultiQC 1.11.
Assembly: mm10
Supplementary files format and content: CSV file of Salmon transcript quantification counts.

growth_protocol: BMDMs were isolated from C57BL/6 WT mice and after 5 days of culture, BMDMs were incubated with or without tumor-conditioned media from NB9464 (MYCN amp) or NBT3L (non-MYCN amp) for 24 hrs in the presence or absence of 500nM R788.

extract_protocol:
RNA was extracted from BMDMs using the Qiagen RNAeasy kit.
mRNA library preparation (polyA enrichment)
Nova Seq 6000 PE 150 (6 G of raw data per sample)

treatment_protocol: 500 nM R788 was added to the BMDMs incubated with NB9464 or NBT3L TCM for 24 hrs followed by RNA isolation.

value: Macrophage

value: MYCN amp Cell Line TCM


title: CSF, sample 9


title: PANC1 cells, DMSO, 2hr, biol rep 1


title: Macrophage, NBT3L TCM + R788, SJ12

value: non-MYCN amp Cell Line TCM + R788 SYK inhibitor


title: YFP-positive (biol rep 3)

description: YFP-positive cells (biol rep 3)


title: MRC9 cells, KRASi, 2hr, biol rep 2

value: LUNG

value: KRAS WT


title: Macrophage, NB9464 TCM, SJ4


title: Macrophage, NB9464 TCM + R788, SJ10

value: MYCN amp Cell Line TCM + R788 SYK inhibitor


title: YFP/mCherry-negative (biol rep 3)

description: YFP/mCherry-negative cells (biol rep 3)


title: YFP-positive (biol rep 2)

description: YFP-positive cells (biol rep 2)


title: CSF, sample 7


title: CSF, sample 8


title: CSF, sample 6


title: YFP-positive (biol rep 1)

description: YFP-positive cells (biol rep 1)


title: MRC9 cells, KRASi, 2hr, biol rep 1

value: KRASi


title: MRC9 cells, DMSO, 2hr, biol rep 2


title: PANC1 cells, DMSO, 2hr, biol rep 2

value: PDAC

value: KRAS G12D


title: Macrophage, R788, SJ8

value: R788 SYK inhibitor


title: MRC5 cells, KRASi, 2hr, biol rep 2


title: Macrophage, NBT3L TCM, SJ6

value: non-MYCN amp Cell Line TCM


title: MRC5 cells, KRASi, 2hr, biol rep 1


title: MRC9 cells, DMSO, 2hr, biol rep 1

value: DMSO


title: CSF, sample 4

value: CSF


title: Macrophage, R788, SJ7


title: CSF, sample 3


title: CSF, sample 5


title: Macrophage, NBT3L TCM, SJ5


title: mCherry-positive (biol rep 2)

description: mCherry-positive cells (biol rep 2)


title: mCherry-positive (biol rep 3)

description: mCherry-positive cells (biol rep 3)


title: MRC5 cells, DMSO, 2hr, biol rep 2


title: Macrophage, NS, SJ1

value: NS


title: MRC5 cells, DMSO, 2hr, biol rep 1


title: Macrophage, NBT3L TCM + R788, SJ11


title: mCherry-positive (biol rep 4)

description: mCherry-positive cells (biol rep 4)


title: Macrophage, NB9464 TCM + R788, SJ9


title: Miapaca2 cells, KRASi, 2hr, biol rep 2

value: KRAS G12C


title: iCMs treated with 6uL siPitx2

city: Charleston

first: Allison

last: Trouten

state: SC

address: 173 Ashley Ave Room BSB 642

department: Regenerative Medicine and Cell Biology

institute: Medical University of South Carolina

data_processing:
Raw fastq files were aligned using STAR 2.7.0 aligner
Differential expression analysis run using DEseq2 (BioConductor 3.12)
Heatmaps created using pheatmap (1.0.12)

source_name: MONO-ALLELIC mEGFP-TAGGED TTN WTC iPSC LINE (TAG AT C-TERM)

growth_protocol: SCVI15 hiPSCs were purchased from Stanford Cardiovascular Institute (SCVI) Biobank and maintained in mTeSR1 before differentiation protocol..

extract_protocol:
Standard Trizol phenol chloroform extraction
Total RNA samples were sent to Novogene for library prep and sequencing (mRNA library preparation poly A enrichment)

treatment_protocol:
Cardiogenic differentiation was induced by treating induced pluripotent stem cells (iPSCs) with RPMI media + B27 supplement without insulin followed by treatment with Glycogen synthase kinase 3 (GSK3) inhibitor to drive mesoderm differentiation. After recovery, cells are treated with RPMI + B27 without insulin with Wnt-inhibitor to drive mesoderm specification. After another recovery period, cells are treated with RPMI media + B27 supplement with insulin to complete differentiation. Multiple rounds of glucose starvation are carried out to ensure purity.
Once fully differentiated into iCMs, cultures were treated with various doses of siRNA targeting Pitx2 or a scramble control. Some cultures were subject to oxidative challenge via H2O2 treatment for 4 hours.

value: wild type

value: cardiogenic differentiation of stem cells to iCMs


title: iCMs treated with 6uL siscr

value: MONO-ALLELIC mEGFP-TAGGED TTN WTC iPSC LINE (TAG AT C-TERM)


title: iCMs treated with 3uL siPitx2


title: iCMs treated with 9uL siPitx2


title: Macrophage SYK KO, SJ_M10

description: SYK_WT_KO_macrophages_adoptive_transfer_ENMUSG.csv

source_name: macrophages SYK KO

growth_protocol: 4 million NB9464 cells were implanted in myeloid Syk WT and KO mice and the experiment was terminated on day 40.

extract_protocol:
TAMs were isolated from the NB9464 tumors (isolated on day 40 of tumor inoculation) using CD11b and F4/80 magnetic beads(Milltenyi Biotech) according to the manufacturer's protocol. RNA was extracted from BMDMs using the Qiagen RNAeasy kit.
mRNA library preparation (polyA enrichment)
Nova Seq 6000 PE 150 (6 G of raw data per sample)

treatment_protocol: No treatment was given

value: Macrophage

value: SYK KO


title: Miapaca2 cells, DMSO, 2hr, biol rep 2


title: Macrophage, NS, SJ2


title: Rpl11 heterozygous Cell 96 [96-SCP-1706080]

city: Seattle

first: Raymond

last: Doty

state: WA

department: Division of Hematology

institute: University of Washington

data_processing:
Illumina BaseSpace Informatics Suite was used for basecalling and demultiplexing.
Raw sequence reads were aligned to the mouse genome (NCBI build 37.2) using TopHat v2.0.9.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each cell

source_name: Murine marrow

extract_protocol:
single-cell isolation protocol: Individual cells were isolated for mRNA sequencing using the C1 Single-Cell Auto Prep System (Fluidigm).
imaging protocol : Each cell isolation chamber was imaged at 20X (Leica DMI 6000) with bright-field illumination and fluorescent channels. The Ter119 antibody was labeled with PCP-Cy5.5 and imaged using a 488/705 nm (excitation/emission) fluorescence filter cube.
Cells were lysed, their mRNA reversely transcribed into cDNA, and the cDNA amplifed using the SMART-Seq whole-transcriptome amplification method on the C1 System according to the manufacturer's instructions.
The cDNA libraries were collected from the C1 and prepared for sequencing using a Nextera XT DNA Sample preparation kit (Illumina).

tag: strain background

value: Rpl11 +/lox

value: erythroid precursor


title: Rpl11 heterozygous Cell 92 [92-SCP-1706080]


title: mCherry-positive (biol rep 1)

description: mCherry-positive cells (biol rep 1)

value: Lung

value: KrasG12D/+; p16FDR/+; Rosa26loxP-STOP-loxP-YFP/+ (KY-FDR)


title: Rpl11 heterozygous Cell 95 [95-SCP-1706080]


title: Rpl11 heterozygous Cell 93 [93-SCP-1706080]


title: Rpl11 heterozygous Cell 94 [94-SCP-1706080]


title: iCMs treated with 3uL siscr


title: Bb B31 MOI 1 24 hrs, Rep_G [MS8_90]

city: Baltimore

first: Mark

middle: J

last: Soloski

state: Maryland

address: 5200 Eastern Avenue

department: Medicine

institute: Johns Hopkins University School of Medicine

data_processing:
Sequencing reads were mapped to the human genome version GRCh38 with the alignment tool STAR v.2.4.2a.
The aligned reads were assembled with PsiCLASS v.1.0.0 to create gene and transcript models
Transcripts were then assigned to known genes from the GENCODE v.27 reference gene set, retaining only those corresponding to protein-coding genes
DESeq2 was used to quantify the expression levels and determine differentially expressed genes
Assembly: GRCh38
Supplementary files format and content: Text matrix file of linear notation expression count values from DESeq2

source_name: moDCs

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from donor leukopacks by Ficoll-Paque density gradient centrifugation from ~100 mL of leukocytes isolated by leukapheresis. CD14 MicroBeads (MACS Miltenyi Biotec) were used for CD14+ selection according to manufacturer’s instructions and isolated monocytes were differentiated into mo-DCs in Mo-DC Differentiation Medium (MACS Miltenyi Biotec) at 106 cells/ml for 7 days as described previously {Gutierrez-Hoffmann, 2020 #6472;Tiniakow, 2017 #6344}. Cells were incubated at 37°C, 5% CO2, and >95% humidity. At the end of the culture period the resulting cell population was routinely >95% CD14-/CD11c+, as assessed by flow cytometry.

extract_protocol:
Total RNA was extracted from 107 mo-DCs using RLT Lysis Buffer (Qiagen) by following manufacturer's instructions
NEBNext Poly(A) Magnetic Isolation Module (NEB #E7490) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (Cat# E7765) were used to generate libraries.  Specifically, Poly A RNAs were isolated from total RNAs and fragmented for cDNA synthesis. End repair is performed where 3' to 5' exonuclease activity of enzymes removes 3' overhangs and the polymerase activity fills in the 5' overhangs. An ‘A’ base is then added to the 3' end of the blunt phosphorylated DNA fragments which prepares the DNA fragments for ligation to the sequencing adapters, which have a single ‘T’ base overhang at their 3' end. Ligated fragments are subsequently size selected through purification using the Sample Purification Beads included in the kit and undergo PCR amplification techniques to prepare the libraries. The BioAnalyzer is used for quality control of the libraries to ensure adequate concentration and appropriate fragment size.  The resulting library insert size is 200bp-500bp with a median size around 300bp. Libraries were uniquely barcoded and pooled for NovaSeq6000 sequencing.

treatment_protocol: Immature mo-DCs were seeded in 6-well plates at a density of 1 x 106 cells in 1 mL of RPMI 1640 and 10% fetal bovine serum, supplemented with 2 mM L-glutamine and 20 µM ß-mercaptoethanol in duplicate. Immature mo-DCs were left at rest or stimulated with 1 µg/mL purified lipoteichoic acid (LTA) from Staphylococcus aureus (InvivoGen, San Diego, CA) or live B. burgdorferi strains A3 or B31 at multiplicities of infection of 1 or 10 bacteria per cell for 8 and 24 hours. Cells were incubated at 37°C, 5% CO2, and >95% humidity. At the end of the incubation period, cells and/or supernatants were harvested a

value: moDCs

tag: subject

value: Subject G

tag: timepoint

value: 24 hrs

tag: moi

value: MOI 1


title: LS513 cells, KRASi, 2hr, biol rep 2

value: COAD

value: KRAS G12D

value: KRASi


title: Macrophage SYK KO, SJ_M9


title: Macrophage SYK WT, SJ_M8

source_name: macrophages SYK WT

value: SYK WT


title: Rpl11 heterozygous Cell 90 [90-SCP-1706080]


title: LS513 cells, KRASi, 2hr, biol rep 1


title: Macrophage SYK WT, SJ_M7


title: Miapaca2 cells, KRASi, 2hr, biol rep 1

value: PDAC

value: KRAS G12C


title: Rpl11 heterozygous Cell 89 [89-SCP-1706080]


title: Whole Tumor, V3

source_name: Whole Tumor

growth_protocol: 4 million NB9464 cells were implanted subcutaneously in C57BL/6 WT mice and when tumors reached 250 mm3, mice were randomized into three groups and treated with R788 and PDL1 mAb and radiation.

treatment_protocol: Mice bearing 250 mm3 NB9464 tumors were treated with 50 mg/kg R788 (5 times a week) or anti-PDL1 mAb ((clone 10F.9G2, Bio-X-cell, 4 times a week) or 10Gy radiation.

value: Whole Tumor

value: WT

value: Vehicle


title: LS513 cells, DMSO, 2hr, biol rep 2

value: DMSO


title: Bb A3 MOI 1 24 hrs, Rep_G [MS8_88]


title: Miapaca2 cells, DMSO, 2hr, biol rep 1


title: LTA Stim 1 ug/mL 24 hrs, Rep_G [MS8_87]


title: Whole Tumor, V2


title: Rpl11 heterozygous Cell 91 [91-SCP-1706080]

value: Rpl11 +/lox

value: erythroid precursor


title: LOVO cells, KRASi, 2hr, biol rep 2

source_name: LOVO

value: LOVO

value: KRAS G13D


title: LOVO cells, DMSO, 2hr, biol rep 2


title: Immature DCs 24 hrs, Rep_G [MS8_86]

value: moDCs

value: Subject G


title: Bb B31 MOI 1 8 hrs, Rep_G [MS8_84]

value: 8 hrs

value: MOI 1


title: Bb A3 MOI 10 24 hrs, Rep_G [MS8_89]

value: 24 hrs

value: MOI 10


title: Bb B31 MOI 10 8 hrs, Rep_G [MS8_85]


title: Whole Tumor, RP1


title: LOVO cells, KRASi, 2hr, biol rep 1

value: COAD

value: KRASi


title: LOVO cells, DMSO, 2hr, biol rep 1


title: Bb B31 MOI 10 24 hrs, Rep_G [MS8_91]


title: HPAC cells, KRASi, 2hr, biol rep 2

source_name: HPAC

value: HPAC

value: PDAC

value: KRAS G12D


title: LS513 cells, DMSO, 2hr, biol rep 1


title: Whole Tumor, IRRP3

value: Whole Tumor

value: WT

value: Radiation + R788 + PD-L1


title: Rpl11 heterozygous Cell 87 [87-SCP-1706080]

value: Rpl11 +/lox

value: erythroid precursor


title: Rpl11 heterozygous Cell 83 [83-SCP-1706080]


title: Rpl11 heterozygous Cell 84 [84-SCP-1706080]


title: Rpl11 heterozygous Cell 85 [85-SCP-1706080]


title: Rpl11 heterozygous Cell 86 [86-SCP-1706080]


title: Rpl11 heterozygous Cell 82 [82-SCP-1706080]


title: Whole Tumor, IRRP2


title: Rpl11 heterozygous Cell 81 [81-SCP-1706080]


title: HPAC cells, KRASi, 2hr, biol rep 1


title: HPAC cells, DMSO, 2hr, biol rep 2

value: DMSO


title: Whole Tumor, RP2


title: Whole Tumor, IRRP1


title: HPAC cells, DMSO, 2hr, biol rep 1


title: Bb A3 MOI 10 8 hrs, Rep_G [MS8_83]

value: moDCs


title: Bb A3 MOI 1 8 hrs, Rep_G [MS8_82]

value: Subject G


title: LTA Stim 1 ug/mL 8 hrs, Rep_G [MS8_81]

value: 8 hrs


title: Rpl11 heterozygous Cell 88 [88-SCP-1706080]


title: Rpl11 heterozygous Cell 80 [80-SCP-1706080]


title: Whole Tumor, RP3


title: Immature DCs 8 hrs, Rep_G [MS8_80]


title: Bb B31 MOI 10 8 hrs, Rep_F [MS8_78]

value: Subject F


title: Immature DCs 0 hrs, Rep_G [MS8_79]

value: 0 hrs


title: Wild-type LSKs, derived from CreER+ Stat3f/f-containing BM chimera [SKO-Com]

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

library_source: transcriptomic single cell

data_processing:
scRNA-seq libraries were sequenced using a NovaSeq6000 SP 100-cycle flow cell (Illumina).
Raw reads were aligned to the mouse genome (mm10), and the digital expression matrix was generated using cellranger count.
Assembly: mm10
Supplementary files format and content: expression matrix

source_name: Bone marrow

extract_protocol:
Bone marrow (BM) cells were flushed from femoral and tibial bones of chimeric mice into Dulbecco's Minimal Essential Medium (DMEM) supplemented with 1% fetal bovine serum. Single cell suspensions of BM cells were treated with red blood cell lysis buffer (Tonbo Bioscience) and incubated with biotinylated antibodies against hematopoietic lineage markers (CD11b, Gr1, CD3, B220, Ter119; Thermo Scientific) for 30 mins. BM cells were then washed with 1X phosphate buffered saline (PBS) and incubated with goat anti-rat IgG microbeads (Miltenyi Biotec). After 30 mins of incubation, the cells were washed in PBS and passed though magnetic-activated cell sorting (MACS) columns (Miltenyi Biotec) to purifiy Lineage- hematopoietic stem and progenitor cells (HSPCs) by negative selection. Lineage- HSPCs were then subjected to FACS to purify Lin-ckit+Sca1+ cells (LSKs). The following LSKs were purified: CD45.2+ CreER+ and CD45.1+ CD45.2+ wild type competitors from control mice containing a 1:1 ratio of CreER+ and wild type competitor cells; and CD45.2+ CreER+ Stat3f/f and CD45.1+ CD45.2+ wild type competitors from test mice containing a 1:1 ratio of CreER+ Stat3f/f and wild type competitor cells. LSKs were purified 8 weeks following tamoxifen treatment to induce Stat3 gene deletion in CreER+ Stat3f/f cells. Single cell suspensions of LSKs (1000 cells/mL) were prepared in PBS supplemented with 0.04% bovine serum albumin (BSA) and used for single cell RNA sequencing.
Purified LSKs were loaded onto a Chromium Single Cell Chip (10X Genomics, Pleasanton, CA) and processed for 3’ single cell RNA seq libraries. The cells were lysed and barcoded for reverse transcription at a target capture rate of 10000 single cells per sample. Bar coded libraries were pooled and sequenced using Novoseq 6000 SP 100-cycle flow cell (Illumina, CA) to an average depth of 100,000 reads per cell.

value: Bone marrow

value: Lin-ckit+Sca1+ cells (LSKs)

value: Wild-type


title: Rpl11 heterozygous Cell 78 [78-SCP-1706080]


title: Bb B31 MOI 10 24 hrs, Rep_F [MS8_77]

value: 24 hrs

value: MOI 10


title: HEK293 cells, DMSO, 2hr, biol rep 2

value: KIDNEY

value: KRAS WT


title: HEK293 cells, KRASi, 2hr, biol rep 1

value: KRASi


title: Wild-type LSKs, derived from CreER+-containing BM chimera [R-Com]


title: CreER+ LSKs, derived from CreER+-containing BM chimera [R-Tt]

value: CreER


title: Rpl11 heterozygous Cell 76 [76-SCP-1706080]

value: Rpl11 +/lox


title: Bb B31 MOI 1 24 hrs, Rep_F [MS8_75]

value: MOI 1


title: HEK293 cells, DMSO, 2hr, biol rep 1

value: DMSO


title: hashed HSPC samples +-APEX1 inhibitors, ADT-derived cDNA

city: Leuven

first: Samantha

last: Zaunz

address: ON4 – Herestraat 49

department: Stem Cell Institute

country: Belgium

institute: KU Leuven

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

library_source: other

data_processing:
The Cell Ranger pipeline (10x Genomics, version 6.1.2) was used to perform sample demultiplexing and to generate FASTQ files for read 1, read 2 and the i7 sample index for  the gene expression and cell surface protein libraries. Read 2 of the gene expression libraries was mapped to the reference genome (mouse GRCm38) using Cell Ranger. Filtered count matrices for RNA, HTO and ADT expression generated by Cell Ranger pipeline, were used for downstream analysis.
Further processing was done with scater (QC steps) and Seurat v4.1.0 (additional cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: mm10
Supplementary files format and content: 10x Genomics filtered cell ranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: protein

source_name: Bone Marrow

extract_protocol:
Bone marrow lin-Sca1+ckit+ (LSK) cells were cultured for 7 days in presence or not of APEX1 inhibitors
Cells stained for the ADT and HTO tags, were pooled together and resuspended  at an estimated final concentration of 1000 cells/µl and loaded on a Chromium GemCode Single Cell Instrument (10x Genomics) to generate single-cell gel beads-in-emulsion (GEM). The scRNA-Seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead and Library kit, version NextGEM 3.1 (10x Genomics) according to the manufacturer’s instructions with the addition of amplification primers (3nM, 5’CCTTGGCACCCGAGAATT*C*C and 5’GTGACTGGAGTTCAGACGTGTGC*T*C) during cDNA amplification to enrich the TotalSeq-A cell surface protein and hashtag oligos.  Size selection with SPRIselect Reagent Kit (Beckman Coulter, B23318) was used to separate amplified cDNA molecules for 3’ gene expression and cell surface protein construction. TotalSeq-A protein library construction including sample index PCR using Illumina’s Truseq Small RNA primer sets and SPRIselect size selection was performed according to the manufacturer’s instructions. The cDNA content of pre-fragmentation and post-sample index PCR samples was analyzed using the 2100 BioAnalyzer (Agilent). Sequencing libraries were loaded on an Illumina NovaSeq flow cell at VIB Nucleomics core with sequencing settings according to the recommendations of 10x Genomics, pooled in a 80:25 ratio for the combined 3’ gene expression and cell surface protein samples, respectively.
OTHER: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

treatment_protocol: ex vivo cultured LSK with and without APEX1 inhibitors

value: Bone Marrow

value: primary LSK culture

value: Hematopoietic Stem and Progenitor Cells (HSPCs)

value: WT

value: ex vivo culture with APEX1 inhibitors or DMSO

tag: antibodies/tags

value: BioLegend TotalSeq™-A antibodies (see file barcode ADT HTO.csv)


title: hashed HSPC samples +-APEX1 inhibitors, HTO-derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

tag: cell type

value: Anti CD45 + Anti MHC class I (BioLegend TotalSeq™-A) :DMSO/TotalSeq-A0311 (hashtag1); E3330/TotalSeq-A0312 (hashtag2); APX2009/TotalSeq-A0313(hashtag3); Inhibitor III/TotalSeq-A0314 (hashtag4) (see file barcode ADT HTO.csv)


title: HCT116 cells, KRASi, 2hr, biol rep 2

value: COAD

value: KRAS G13D


title: Bb A3 MOI 10 8 hrs, Rep_F [MS8_74]

value: moDCs

value: Subject F

value: 8 hrs

value: MOI 10


title: HEK293 cells, KRASi, 2hr, biol rep 2

value: KIDNEY

value: KRAS WT

value: KRASi


title: Rpl11 heterozygous Cell 79 [79-SCP-1706080]

value: Rpl11 +/lox

value: erythroid precursor


title: Bb A3 MOI 10 24 hrs, Rep_F [MS8_73]

value: 24 hrs


title: Rpl11 heterozygous Cell 75 [75-SCP-1706080]


title: Bb A3 MOI 1 8 hrs, Rep_F [MS8_72]

value: MOI 1


title: Rpl11 heterozygous Cell 74 [74-SCP-1706080]


title: HCT116 cells, DMSO, 2hr, biol rep 2

value: DMSO


title: HCT116 cells, KRASi, 2hr, biol rep 1


title: hashed HSPC samples +-APEX1 inhibitors, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

tag: tissue

value: Bone Marrow

value: primary LSK culture

value: Hematopoietic Stem and Progenitor Cells (HSPCs)

value: WT

value: ex vivo culture with APEX1 inhibitors or DMSO


title: Rpl11 heterozygous Cell 73 [73-SCP-1706080]


title: Rpl11 heterozygous Cell 72 [72-SCP-1706080]


title: Bb A3 MOI 1 24 hrs, Rep_F [MS8_71]

value: moDCs


title: PS19, replicate 6, 4 months, bulkRNAseq

city: HOUSTON

first: chuangye

last: Qi

state: Texas

address: One plaza

department: Huffington Center

institute: Baylor College of Medicine

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt
trimmed reads mapped to reference genome by STAR
Read count caculated by featurecounts
DEGs identified by DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: hippocampus

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: hippocampus

tag: age

value: 4 months old


title: Rpl11 heterozygous Cell 77 [77-SCP-1706080]

tag: genotype


title: Bb B31 MOI 1 8 hrs, Rep_F [MS8_76]

value: Subject F

tag: treatment

value: 8 hrs


title: HCT116 cells, DMSO, 2hr, biol rep 1

value: COAD

value: KRAS G13D


title: PS19, replicate 5, 4 months, bulkRNAseq

tag: strain


title: Rpl11 heterozygous Cell 71 [71-SCP-1706080]

value: Rpl11 +/lox


title: HCC827 cells, KRASi, 2hr, biol rep 2

value: LUAD

value: KRAS WT

value: KRASi


title: LTA Stim 1 ug/mL 8 hrs, Rep_F [MS8_70]


title: PS19, replicate 4, 4 months, bulkRNAseq


title: PS19, replicate 3, 4 months, bulkRNAseq


title: HCC827 cells, DMSO, 2hr, biol rep 2

value: DMSO


title: Rpl11 heterozygous Cell 69 [69-SCP-1706080]

value: erythroid precursor


title: Rpl11 heterozygous Cell 68 [68-SCP-1706080]


title: PS19, replicate 2, 4 months, bulkRNAseq


title: Immature DCs 8 hrs, Rep_F [MS8_67]


title: Rpl11 heterozygous Cell 67 [67-SCP-1706080]


title: H2122 cells, KRASi, 2hr, biol rep 2

value: KRAS G12C


title: Immature DCs 24 hrs, Rep_F [MS8_66]

value: 24 hrs


title: PS19, replicate 1, 4 months, bulkRNAseq


title: Rpl11 heterozygous Cell 66 [66-SCP-1706080]


title: H2122 cells, KRASi, 2hr, biol rep 1


title: Bb B31 MOI 10 8 hrs, Rep_E [MS8_65]

value: Subject E

value: MOI 10


title: Bb B31 MOI 10 24 hrs, Rep_E [MS8_64]

value: moDCs


title: WT, replicate 5, 4 months, bulkRNAseq

value: WT

value: hippocampus


title: LTA Stim 1 ug/mL 24 hrs, Rep_F [MS8_69]

value: Subject F


title: Rpl11 heterozygous Cell 65 [65-SCP-1706080]


title: HCC827 cells, KRASi, 2hr, biol rep 1


title: WT, replicate 4, 4 months, bulkRNAseq

value: 4 months old


title: H2122 cells, DMSO, 2hr, biol rep 2


title: H2122 cells, DMSO, 2hr, biol rep 1


title: Immature DCs 0 hrs, Rep_F [MS8_68]

value: 0 hrs


title: Rpl11 heterozygous Cell 70 [70-SCP-1706080]


title: Rpl11 heterozygous Cell 64 [64-SCP-1706080]


title: Bb B31 MOI 1 8 hrs, Rep_E [MS8_63]

value: 8 hrs

value: MOI 1


title: WT, replicate 3, 4 months, bulkRNAseq


title: Rpl11 heterozygous Cell 63 [63-SCP-1706080]

value: Rpl11 +/lox


title: HCC827 cells, DMSO, 2hr, biol rep 1

value: LUAD

value: KRAS WT


title: H1650 cells, KRASi, 2hr, biol rep 2

value: KRASi


title: Bb B31 MOI 1 24 hrs, Rep_E [MS8_62]


title: Rpl11 heterozygous Cell 62 [62-SCP-1706080]

value: erythroid precursor


title: WT, replicate 2, 4 months, bulkRNAseq


title: Bb A3 MOI 10 8 hrs, Rep_E [MS8_61]


title: WT, replicate 1, 4 months, bulkRNAseq


title: H1650 cells, KRASi, 2hr, biol rep 1


title: PS19, replicate 5, 9 months, bulkRNAseq

value: 9 months old


title: WT, replicate 6, 4 months, bulkRNAseq


title: Bb A3 MOI 10 24 hrs, Rep_E [MS8_60]

value: 24 hrs


title: Rpl11 heterozygous Cell 60 [60-SCP-1706080]


title: Bb A3 MOI 1 8 hrs, Rep_E [MS8_59]

value: Subject E


title: H1650 cells, DMSO, 2hr, biol rep 2

value: DMSO


title: Rpl11 heterozygous Cell 61 [61-SCP-1706080]


title: PS19, replicate 4, 9 months, bulkRNAseq


title: LTA Stim 1 ug/mL 24 hrs, Rep_E [MS8_56]

value: moDCs


title: PS19, replicate 3, 9 months, bulkRNAseq


title: Rpl11 heterozygous Cell 59 [59-SCP-1706080]


title: Bb A3 MOI 1 24 hrs, Rep_E [MS8_58]


title: H727 cells, KRASi, 2hr, biol rep 2

value: KRAS G12V


title: Rpl11 heterozygous Cell 58 [58-SCP-1706080]


title: H1650 cells, DMSO, 2hr, biol rep 1


title: Rpl11 heterozygous Cell 56 [56-SCP-1706080]


title: H727 cells, KRASi, 2hr, biol rep 1


title: LTA Stim 1 ug/mL 8 hrs, Rep_E [MS8_57]


title: Rpl11 heterozygous Cell 55 [55-SCP-1706080]


title: WT, replicate 5, 9 months, bulkRNAseq

value: WT

value: hippocampus


title: WT, replicate 4, 9 months, bulkRNAseq


title: Immature DCs 8 hrs, Rep_E [MS8_54]


title: Rpl11 heterozygous Cell 57 [57-SCP-1706080]


title: Rpl11 heterozygous Cell 54 [54-SCP-1706080]


title: Immature DCs 24 hrs, Rep_E [MS8_53]


title: H358 cells, KRASi, 2hr, biol rep 1

value: KRAS G12C


title: H727 cells, DMSO, 2hr, biol rep 2


title: H727 cells, DMSO, 2hr, biol rep 1


title: Immature DCs 0 hrs, Rep_E [MS8_55]

value: 0 hrs


title: H358 cells, KRASi, 2hr, biol rep 2


title: WT, replicate 3, 9 months, bulkRNAseq


title: Bb B31 MOI 10 8 hrs, Rep_D [MS8_52]

value: Subject D

value: 8 hrs

value: MOI 10


title: WT, replicate 2, 9 months, bulkRNAseq


title: Bb B31 MOI 1 8 hrs, Rep_D [MS8_50]

value: MOI 1


title: H358 cells, DMSO, 2hr, biol rep 2

value: LUAD


title: CLEAR mutant crossing with PS19 , replicate 4, snRNAseq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting were made using CellRanger
removing ambient RNA by decountX
removing doublets by DoubletFinder
cell cluster umap analysis by Seurat
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
For snRNA-seq, single nucleus suspensions were isolated from about 50mg frozen mouse hippocampus following 10x genomics recommendation.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: Sex

value: female


title: PS19, replicate 1, 9 months, bulkRNAseq


title: H358 cells, DMSO, 2hr, biol rep 1


title: WT, replicate 1, 9 months, bulkRNAseq


title: Bb B31 MOI 10 24 hrs, Rep_D [MS8_51]


title: Rpl11 heterozygous Cell 50 [50-SCP-1706080]

value: Rpl11 +/lox

value: erythroid precursor


title: Rpl11 heterozygous Cell 52 [52-SCP-1706080]


title: Rpl11 heterozygous Cell 51 [51-SCP-1706080]


title: Rpl11 heterozygous Cell 49 [49-SCP-1706080]


title: DLD1 cells, KRASi, 2hr, biol rep 2

value: COAD

value: KRAS G13D

value: KRASi


title: Bb B31 MOI 1 24 hrs, Rep_D [MS8_49]

value: moDCs

value: 24 hrs


title: CLEAR mutant crossing with PS19 , replicate 2, snRNAseq

description: 10x Genomics

value: male

value: 9 months old


title: CLEAR mutant crossing with PS19 , replicate 3, snRNAseq

description: 10x Genomics

value: hippocampus


title: CreER+ Stat3f/f LSKs, derived from CreER+ Stat3f/f -containing BM chimera [SKO-Tt]

value: Bone marrow

value: Lin-ckit+Sca1+ cells (LSKs)

value: CreER Stat3f/f


title: Bb A3 MOI 10 8 hrs, Rep_D [MS8_48]

value: Subject D

value: 8 hrs

value: MOI 10


title: DLD1 cells, KRASi, 2hr, biol rep 1


title: DLD1 cells, DMSO, 2hr, biol rep 2

value: DMSO


title: Rpl11 heterozygous Cell 53 [53-SCP-1706080]

value: Rpl11 +/lox


title: Rpl11 heterozygous Cell 48 [48-SCP-1706080]

value: erythroid precursor


title: CLEAR mutant crossing with PS19 , replicate 1, snRNAseq

description: 10x Genomics


title: Rpl11 heterozygous Cell 47 [47-SCP-1706080]


title: Bb A3 MOI 10 24 hrs, Rep_D [MS8_47]


title: Bb A3 MOI 1 8 hrs, Rep_D [MS8_46]

value: MOI 1


title: CAPAN1 cells, KRASi, 2hr, biol rep 2

value: PDAC

value: KRAS G12V


title: DLD1 cells, DMSO, 2hr, biol rep 1

value: COAD

value: KRAS G13D


title: CLEAR mutant, replicate 3, snRNAseq

description: 10x Genomics

value: male


title: CLEAR mutant, replicate 4, snRNAseq

description: 10x Genomics

value: female

value: 9 months old


title: Rpl11 heterozygous Cell 46 [46-SCP-1706080]


title: CAPAN1 cells, KRASi, 2hr, biol rep 1

value: KRASi


title: LTA Stim 1 ug/mL 8 hrs, Rep_D [MS8_44]

value: moDCs


title: Rpl11 heterozygous Cell 45 [45-SCP-1706080]


title: CLEAR mutant, replicate 1, snRNAseq

description: 10x Genomics

value: hippocampus


title: CLEAR mutant, replicate 2, snRNAseq

description: 10x Genomics


title: CAPAN1 cells, DMSO, 2hr, biol rep 2


title: CALU1 cells, KRASi, 2hr, biol rep 2

value: LUAD

value: KRAS G12C


title: Rpl11 heterozygous Cell 43 [43-SCP-1706080]


title: Immature DCs 0 hrs, Rep_D [MS8_42]

value: Subject D

value: 0 hrs


title: Rpl11 heterozygous Cell 42 [42-SCP-1706080]

value: Rpl11 +/lox


title: PS19, replicate 3, snRNAseq

description: 10x Genomics


title: Immature DCs 8 hrs, Rep_D [MS8_41]

value: 8 hrs


title: CALU1 cells, KRASi, 2hr, biol rep 1


title: CAPAN1 cells, DMSO, 2hr, biol rep 1

value: DMSO


title: Rpl11 heterozygous Cell 41 [41-SCP-1706080]

value: erythroid precursor


title: Immature DCs 24 hrs, Rep_D [MS8_40]

value: 24 hrs


title: PS19, replicate 2, snRNAseq

description: 10x Genomics


title: Whole Tumor, V1

value: Whole Tumor

value: WT

value: Vehicle


title: PS19, replicate 1, snRNAseq

description: 10x Genomics

value: male


title: Bb B31 MOI 10 8 hrs, Rep_C [MS8_39]

value: Subject C

value: MOI 10


title: WT, replicate 3, snRNAseq

description: 10x Genomics

value: female

value: 9 months old


title: CALU1 cells, DMSO, 2hr, biol rep 1

value: LUAD


title: Rpl11 heterozygous Cell 40 [40-SCP-1706080]


title: CALU1 cells, DMSO, 2hr, biol rep 2

value: KRAS G12C


title: Bb A3 MOI 1 24 hrs, Rep_D [MS8_45]

value: moDCs

value: Subject D

value: MOI 1


title: LTA Stim 1 ug/mL 24 hrs, Rep_D [MS8_43]


title: Rpl11 heterozygous Cell 44 [44-SCP-1706080]

value: Rpl11 +/lox


title: Rpl11 heterozygous Cell 39 [39-SCP-1706080]


title: WT, replicate 2, snRNAseq

description: 10x Genomics

value: hippocampus


title: Bb B31 MOI 10 24 hrs, Rep_C [MS8_38]


title: ASPC1 cells, KRASi, 2hr, biol rep 2

value: PDAC

value: KRAS G12D

value: KRASi


title: Rpl11 heterozygous Cell 38 [38-SCP-1706080]

value: erythroid precursor


title: WT, replicate 1, snRNAseq

description: 10x Genomics


title: Bb B31 MOI 1 8 hrs, Rep_C [MS8_37]

value: 8 hrs


title: P7-AR-day 7-2-CD45+

city: Shanghai

first: Zhenzhen

last: Zhan

address: Jimo Road 150

department: Research Center for Translational Medicine

institute: Shanghai East Hospital, Tongji University School of Medicine,

description: 10X Genomics Chromium X

data_processing:
Single cell RNA-seq data processing Reads were processed using the Cell Ranger 2.1.0 pipeline with default and recommended parameters. FASTQs generated from Illumina sequencing output were aligned to the mouse genome, version GRCm38, using the STAR algorithm
We excluded cells with fewer than 200 or more than 6000 detected genes (where each gene had to have at least one UMI aligned in at least three cells). The expression of mitochondria genes was calculated using PercentageFeatureSet function of the seurat package.
To remove low activity cells, cells with more than 10 percent expression of mitochondria genes were excluded.
we performed principal component analysis (PCA) and reduced the data to the top 30 PCA components after scaled the data.
Identification of cell types and subtypes by nonlinear dimensional reduction (t-SNE) Cells were clustered using graph-based clustering of the PCA reduced data with the Louvain Method
Assembly: GRCm38
Supplementary files format and content: matrix table with raw gene counts for every gene and every cell

source_name: heart

extract_protocol:
The heart tissues at day 7 after AR operated on postnatal day 1 (P1) and 7 (P7) mice were collected and minced into fine pieces. Tissues were enzymatically digested with a mixture of trypsin and collagenase. After dissociation, cell suspensions were passed through a 40 μm Cell Strainer, followed by red blood cells lysis. Then single cell suspensions were incubated with CD45 MicroBeads, mouse for 15 min at 4 °C, and isolated by a MACS Separator.
10× library preparation and sequencing Beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation,so that each cell was paired with a bead in a Gel Beads-in emulsion(GEM). After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA synthesis, each cDNA molecule was tagged on the 5’end (that is, the 3’end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin. Briefly, 10× beads that were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification. Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ end of the transcripts linked with the cell barcode and UMI. All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (CG000206 RevD). Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific).

value: heart

value: 15 days old

value: CD45+ cells

value: apical resection


title: Rpl11 heterozygous Cell 37 [37-SCP-1706080]


title: ASPC1 cells, KRASi, 2hr, biol rep 1


title: Bb B31 MOI 1 24 hrs, Rep_C [MS8_36]

value: Subject C

value: 24 hrs


title: ASPC1 cells, DMSO, 2hr, biol rep 2

value: DMSO


title: Bb A3 MOI 10 8 hrs, Rep_C [MS8_35]

value: moDCs

value: MOI 10


title: P7-AR-day 7-1-CD45+

description: 10X Genomics Chromium X


title: Rpl11 heterozygous Cell 36 [36-SCP-1706080]


title: ASPC1 cells, DMSO, 2hr, biol rep 1


title: P1-AR-day 7-2-CD45+

description: 10X Genomics Chromium X

value: 8 days old


title: NTG, CD11b, M, 6m, scRNAseq, rep3

city: San Francisco, CA

first: Katerina

last: akassoglou

institute: Gladstone Institutes

description: 10X Genomics

data_processing:
The R toolkit Seurat was used for QC, clustering analysis, and differential gene expression analysis of scRNA-seq data and performed in R v.4.0.2 unless otherwise stated. For scRNA-seq data visualizations, dittoseq package v1 was used to produce UMAPs, dot plots, and violin plots
For brain CD11b+ scRNA-seq analysis, QC parameters used were: 1,000 – 4,000 nFeature_RNA, < 12,000 nCount_RNA, < 10% mitochrondrial genes. Batch correction was performed using FindIntegrationAnchors for “batch1” and “batch2”, ScaleData function was performed on integrated object regression out known microglia immediate response genes. The vars.to.regress function used was set to c(‘Fos’,‘Egr1’,‘Jun’,‘Junb’,‘Zfp36’,‘Jund’,‘H3f3b’, ‘Btg2’,‘Rhob’,‘Fosb’,‘Dusp1’,‘Ier2’,‘Socs3’,‘Ier5’,‘Nfkbia’,‘Zfp36l1’,‘Btg1’,‘Ptma’,‘Sgk1’,‘Klf6’). FindNeighbors and FindClusters were used with the first 20 significant PCs and a 0.2 resolution, respectively. Differential gene analysis was performed using FindMarkers or FindAllMarkers with MAST or Wilcoxon test for p_val_adj < 0.05 and avg_log2FC > 0.25.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain

extract_protocol:
Brains from male and female 6-month-old 5XFAD, 5XFAD:Fggg390-396A, NTG and Fggg390-396A mice were processed for FACS. Live Sytox blue–CD11b+ cells from cortical/hippocampal tissues were sorted into tubes containing DPBS supplemented with 5% FBS at 4°C and then were resuspended in 4°C DPBS supplemented with 2% FBS at 333 cells mL-1 and processed for scRNA-seq.
For scRNA-seq library preparation, live Sytox blue–CD11b+ cells were processed with the Chromium Single Cell 3’ v3 kit following manufactures instructions (10X Genomics).

value: brain

value: Male

value: NTG


title: Bb A3 MOI 10 24 hrs, Rep_C [MS8_34]


title: Rpl11 heterozygous Cell 34 [34-SCP-1706080]

value: Rpl11 +/lox


title: Bb A3 MOI 1 8 hrs, Rep_C [MS8_33]

value: MOI 1


title: P1-AR-day 7-1-CD45+

description: 10X Genomics Chromium X


title: in vivo 3M (E7)

first: Charles

middle: E

last: Murry

address: 850 Republican Street

department: Pathology

description:
3M_invivo_rep_2
253G1-GCaMP3 human PSC-cardiomyocytes three months after transplation into infarcted rat heart

data_processing:
a hybrid of human (hg38) and rat genome (Rnor_6.0) was constructed
reads were mapped to either human (for the hPSC-CMs) only or to the human-rat hybrid genome using STAR program (2.5.3a)
the STAR output were name-sorted using samtools sort
A customized python scripts were used to separate human from the rat reads and only the reads uniquely mapped to human genome were used for downstream analysis
Cufflinks was used to quantify reads and FPKM were calculated for genes
Genome_build: a hybrid of human  (hg38) and rat (Rnor_6.0) genome
Supplementary_files_format_and_content: FPKM table

organism:
Homo sapiens
Rattus norvegicus

growth_protocol: 253G1-GCaMP3 hPSC-CMs were differentiated as previously described  (Kadota et al, Stem Cell Reports, 2017, PMID:28065644), and cultured in RPMI-1640 supplemented with B-27 until different time points after differentiation

extract_protocol:
Laser capture technique was used to localize the grafts in the rat heart slices
SMART-Seq v4 Ultra Low Input RNA kit for sequencing was used to establish library from the heart slices and Nextera XT DNA library preparation kit was used for library construction for the hPSC-CMs

treatment_protocol: 253G1-GCaMP3 hPSC-CMs were cultured in vitro for different period and some were transplanted into infarct rat hearts and harvested at different time points after transplantation

value: Sprague-Dawley

tag: condition

value: athymic

value: hPSC-derived cardiomyocytes


title: Rpl11 heterozygous Cell 33 [33-SCP-1706080]

value: erythroid precursor


title: NTG, CD11b, M, 6m, scRNAseq, rep2

address: 1650 Owens st

description: 10X Genomics


title: Bb A3 MOI 1 24 hrs, Rep_C [MS8_32]


title: NTG, CD11b, F, 6m, scRNAseq, rep1

description: 10X Genomics

value: Female


title: in vivo 1M (E6)

description:
1M_invivo_rep_2
253G1-GCaMP3 human PSC-cardiomyocytes one month after transplation into infarcted rat heart

tag: cell line


title: Rpl11 heterozygous Cell 32 [32-SCP-1706080]


title: LTA Stim 1 ug/mL 8 hrs, Rep_C [MS8_31]

value: 8 hrs


title: Rpl11 heterozygous Cell 35 [35-SCP-1706080]


title: in vivo 7D (E5)

description:
7D_invivo_rep_2
253G1-GCaMP3 human PSC-cardiomyocytes one week after transplation into infarcted rat heart

tag: time


title: 5XFAD, CD11b, M, 6m, scRNAseq, rep3

description: 10X Genomics


title: Rpl11 heterozygous Cell 31 [31-SCP-1706080]


title: LTA Stim 1 ug/mL 24 hrs, Rep_C [MS8_30]

value: Subject C


title: in vivo 1D (E4)

description:
1D_invivo_rep_2
253G1-GCaMP3 human PSC-cardiomyocytes one day after transplation into infarcted rat heart


title: 5XFAD, CD11b, M, 6m, scRNAseq, rep2

description: 10X Genomics


title: in vivo 3M (A10)

description:
3M_invivo_rep_1
253G1-GCaMP3 human PSC-cardiomyocytes three months after transplation into infarcted rat heart


title: Rpl11 heterozygous Cell 30 [30-SCP-1706080]


title: Immature DCs 0 hrs, Rep_C [MS8_29]

value: 0 hrs


title: 5XFAD, CD11b, F, 6m, scRNAseq, rep1

description: 10X Genomics


title: Rpl11 heterozygous Cell 29 [29-SCP-1706080]


title: in vivo 1M (A9)

description:
1M_invivo_rep_1
253G1-GCaMP3 human PSC-cardiomyocytes one month after transplation into infarcted rat heart


title: Immature DCs 8 hrs, Rep_C [MS8_28]


title: Immature DCs 24 hrs, Rep_C [MS8_27]

value: 24 hrs


title: Rpl11 heterozygous Cell 28 [28-SCP-1706080]


title: Fgg390-396A, CD11b, F, 6m, scRNAseq, rep3

description: 10X Genomics


title: in vivo 7D (A8)

description:
7D_invivo_rep_1
253G1-GCaMP3 human PSC-cardiomyocytes one week after transplation into infarcted rat heart


title: Rpl11 heterozygous Cell 27 [27-SCP-1706080]


title: Fgg390-396A, CD11b, M, 6m, scRNAseq, rep2

description: 10X Genomics


title: in vivo 1D (A7)

description:
1D_invivo_rep_1
253G1-GCaMP3 human PSC-cardiomyocytes one day after transplation into infarcted rat heart


title: Rpl11 heterozygous Cell 26 [26-SCP-1706080]


title: Bb B31 MOI 10 24 hrs, Rep_B [MS8_25]

value: moDCs

value: Subject B


title: Bb B31 MOI 10 8 hrs, Rep_B [MS8_26]

value: MOI 10


title: Fgg390-396A, CD11b, M, 6m, scRNAseq, rep1

description: 10X Genomics

value: brain


title: 4C_mES_Chd9_ZBTB21_degron_6h_rep2

city: Beijing

first: Xiong

last: Ji

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Sciences

institute: Peking University

library_source: genomic

data_processing:
Raw 4C reads were firstly filtered and trimmed by the enzyme sites using trimLinker from ChIA-PET2 software. The pair-end reads were selected for downstream analysis by cutadapt software if 5’ end of reads1 contains bait sites.
The processed reads2 were then mapped to mm10 genome by bowtie2 software using ‘--very-sensitive-local’ parameters. PCR duplicates, self-religations and reads longer than the library size were discarded.
The bigwig files were generated by bamCoverage of deepTools software and normalized to the 1x coverage of mm10 genome using ‘--binSize 10 --normalizeUsing RPGC’ parameters.
Assembly: mm10
Library strategy: 4C-Seq

molecule: genomic DNA

source_name: mouse embryonic stem cells

growth_protocol: The V6.5 mouse ES (mES) cell line was cultured with irradiated mouse embryonic fibroblasts in DMEM-KO containing 15% FBS, leukaemia inhibiting factor (LIF), L-glutamine, β-mercaptoethanol, non-essential amino acids and penicillin/ streptomycin at 37 ℃ with 5% CO2, and passage twice for experiments.

extract_protocol:
The 4C-seq referred to a previous publication. Briefly, the cells were first treated properly and then crosslinked with 1% formaldehyde for 10 min at room temperature. The nuclei were isolated and treated with 25 μl 10×cutsmart buffer and 100 U NlaIII (NEB, #R0125S), incubated overnight at 37℃, 900 rpm to digest the chromatin. The next day, the restriction enzyme was inactivated by heat. The proximal, digested chromatin fragments were ligated by T4 DNA ligase (NEB, M0202) by incubating the reaction for at least 6 h at room temperature. After ligation, the DNA was reverse crosslinked and extracted by an equal volume of phenol:chloroform:isoamyl alcohol (Solarbio, P1013). The purified DNA was fragmented by sonication with Biorupter at high energy 30s on, 60s off, for 2 cycles. The fragmented DNA was examined by 1% DNA agarose gel electrophoresis. The size of DNA product was about 0.2 kb-2 kb.
A biotin-labeled primer targeting the region of interest was used for primer extension. The amplified DNA was purified by biotin-streptavidin pulldown. The biotin-labeled single strand DNA was ligated to an adapter by bridge linker-mediated ligation. The ligated DNA products were amplified by nest PCR, and 500 bp-900 bp DNA products were purified by Magen gel purification kit.

treatment_protocol: All degron mES cells were pre-treated with 1 μg/ml Doxycycline for 12 hours. ZBTB21 degron mES was treated with or without 500 μM indole-3-acetic acid (IAA) for 6 hours.

value: mouse embryonic stem cells

value: ZBTB21 degron 6h

tag: bait

value: Chd9 promoter


title: Bb B31 MOI 1 8 hrs, Rep_B [MS8_24]

value: MOI 1


title: Rpl11 heterozygous Cell 25 [25-SCP-1706080]

value: Rpl11 +/lox


title: 4C_mES_Chd9_ZBTB21_degron_6h_rep1


title: Bb B31 MOI 1 24 hrs, Rep_B [MS8_23]


title: 5XFAD, Fgg390-396A, CD11b, M, 6m, scRNAseq, rep3

description: 10X Genomics

value: Male


title: 5XFAD, Fgg390-396A, CD11b, M, 6m, scRNAseq, rep4

description: 10X Genomics


title: 4C_mES_Chd9_ZBTB21_degron_0h_rep2

value: untreated


title: Bb A3 MOI 10 8 hrs, Rep_B [MS8_22]


title: 5XFAD, Fgg390-396A, CD11b, F, 6m, scRNAseq, rep2

description: 10X Genomics


title: Fgg390-396A, CD11b, F, 6m, scRNAseq, rep4

description: 10X Genomics


title: 4C_mES_Chd9_ZBTB21_degron_0h_rep1


title: Rpl11 heterozygous Cell 23 [23-SCP-1706080]

value: erythroid precursor


title: Rpl11 heterozygous Cell 22 [22-SCP-1706080]


title: Bb A3 MOI 10 24 hrs, Rep_B [MS8_21]


title: Rpl11 heterozygous Cell 21 [21-SCP-1706080]


title: 5XFAD, Fgg390-396A, CD11b, F, 6m, scRNAseq, rep1

description: 10X Genomics

value: Female


title: NTG, 12m, CD11bpositive, ROSpositive, male, rep3

description: 10X Genomics

data_processing:
QC parameters were 200 – 5,000 nFeature_RNA, < 7,500 nCount_RNA, < 5% and 20% mitochrondrial and ribosomal genes, respectively. Data were normalized, scaled and percent of mitochondrial genes regressed out following the Seurat SCTransform. Jackstraw was performed with num.replicate of 100. FindNeighbors and FindClusters Seurat functions were used with the first 30 significant PCs and a resolution of 0.6 resolution, respectively. To remove variation in sex-linked genes, the dataset was integrated with Harmony algorithm with runHarmony: group.by.vars = sex and assay.use = SCT. Clustering analysis was performed using the Harmony dimensions with dims = 15 and resolution = 0.4. Based on cell type gene expression markers and in accordance with prior literature, all four CD11b+ cell clusters had high expression of core microglial genes. DEGs for each cluster were determined by FindAllMarkers with default parameters using MAST statistical test. Genes that met log2fc.threshold,0.25 with adjusted P value < 0.05 (Benjamini-Hochberg correction) were used for downstream analyses.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Male and female 12-month-old 5XFAD and NTG mice were perfused with 4°C DPBS and then cortical and hippocampal brain regions were dissected from each animal. Tissues were  incubated with lysis buffer without ActD for 30 min at 37°C. Using a FACSAria II (BD Biosciences), Live Sytox blue–CD11b+ROS– and live Sytox blue–CD11b+ROS+ cell populations were sorted into tubes containing FACS buffer. Sorted cells were resuspended in 4°C DPBS supplemented with 2% FBS and immediately processed for scRNA-seq
For scRNA-seq library preparation, live Sytox blue–CD11b+ROS– and live Sytox blue–CD11b+ROS+ sorted cell populations from 5XFAD and NTG brains were processed using the Chromium Single Cell 3’ v2 following manufactures instructions (10X Genomics)

value: male

value: NTG


title: ChIP-Seq_mES_RPB1_ZBTB21_degron_24h_rep2

data_processing:
Raw ChIP-Seq reads were firstly trimmed using Cutadapt (v2.6) software and then mapped to the mm10 or hg19 genome using Bowtie2 (v2.3.5.1) software in ‘--very-sensitive-local’ mode.
RCR duplicates and discordant reads were filtered for further analysis.
Peaks were called by MACS2 (v2.1.1) software using a q threshold of 0.05. The two replicates were filtered by IDR (v.2.0.3) software using an idr threshold of 0.05 to obtain repeatable peaks.
Assembly: mm10, hg19
Supplementary files format and content: Bigwig files were generated by deepTools2 (v.3.5.0)  software in 10 bp bins normalized by reads mapped to hg19 genome.

growth_protocol:
The mouse embryonic stem cells (mESCs) (obtained from Richard Young’s lab, MIT) were cultured in Knock out DMEM (Gibco, #10829018-018), supplemented with 10% FBS,1x PenStrep (Gibco, #15140-122),1x nucleoside (Sigma, #ES-008),1x L-glutamine (Gibco, #25030-149),1x NEAA (non-essential amino acids, Milipore, #TMS-001-C), 3 μM CHIR99021 (Selleck, #S1036), 0.5 μM PD0325901 (Selleck, #S1263), 143 μM β-mercaptoethanol (Sigma, #M3148),1000 U/ml mLIF (Milipore, #ESG1107) at 37 ℃ with 5% CO2 in a humidified incubator.
HEK293T (ATCC, CRL-3216) cells were cultured in DMEM (Gibco, #11995-065) supplemented with 10% FCS (FBS, Gibco, #10099-141) and 1% PenStrep (Gibco, #15140-122) at 37 °C with 5% CO2 in a humidified incubator.

extract_protocol:
The soluable chromatin fractions were extracted as previously reported (Ji et al., 2015).
DNA library was constructed by previous publication TELP library construction protocol (Peng et al., 2015) and NEBNext®UltraTMII DNA Library Prep Kit for Illumina (NEB, #E765S).

treatment_protocol: We treated the degron-mESCs with 1 μg/ml Doxycycline  (Sigma Aldrich,#D9891) for 24 hours, then added 500 μM IAA (Sigma Aldrich, #115148) for indicated time points for different analyses.

value: mouse embryonic stem cell (mESC)

tag: chip antibody

value: ZBTB21 degron 24h


title: ChIP-Seq_mES_RPB1_ZBTB21_degron_24h_rep1


title: ChIP-Seq_mES_RPB1_ZBTB21_degron_0h_rep2

value: ZBTB21 untreated


title: Rpl11 heterozygous Cell 19 [19-SCP-1706080]

tag: strain background


title: NTG, 12m, CD11bpositive, ROSnegative, male, rep3

description: 10X Genomics


title: ChIP-Seq_mES_RPB1_ZBTB21_degron_0h_rep1


title: LTA Stim 1 ug/mL 8 hrs, Rep_B [MS8_18]

value: moDCs

tag: subject

value: Subject B

value: 8 hrs


title: Bb A3 MOI 1 24 hrs, Rep_B [MS8_19]

tag: timepoint

value: 24 hrs


title: NTG, 12m, CD11bpositive, ROSpositive, male, rep2

description: 10X Genomics

value: brain


title: Rpl11 heterozygous Cell 18 [18-SCP-1706080]


title: Rpl11 heterozygous Cell 24 [24-SCP-1706080]


title: NTG, 12m, CD11bpositive, ROSnegative, male, rep2

description: 10X Genomics


title: LTA Stim 1 ug/mL 24 hrs, Rep_B [MS8_17]


title: Immature DCs 0 hrs, Rep_B [MS8_16]

value: 0 hrs


title: ChIP-Seq_mES_CTCF_ZBTB21_degron_6h_rep2

value: Ctcf

value: ZBTB21 degron 6h


title: ChIP-Seq_mES_CTCF_ZBTB21_degron_6h_rep1


title: NTG, 12m, CD11bpositive, ROSpositive, female, rep1

description: 10X Genomics

value: female


title: Rpl11 heterozygous Cell 17 [17-SCP-1706080]

value: Rpl11 +/lox


title: Rpl11 heterozygous Cell 16 [16-SCP-1706080]

value: erythroid precursor


title: ChIP-Seq_mES_CTCF_ZBTB21_degron_0h_rep2


title: Rpl11 heterozygous Cell 20 [20-SCP-1706080]


title: NTG, 12m, CD11bpositive, ROSnegative, female, rep1

description: 10X Genomics


title: 5xFAD, 12m, CD11bpositive, ROSpositive, female, rep3

description: 10X Genomics


title: ChIP-Seq_mES_CTCF_ZBTB21_degron_0h_rep1


title: Rpl11 heterozygous Cell 14 [14-SCP-1706080]


title: Immature DCs 24 hrs, Rep_B [MS8_14]


title: Rpl11 heterozygous Cell 15 [15-SCP-1706080]


title: Bb A3 MOI 1 8 hrs, Rep_B [MS8_20]

tag: moi

value: MOI 1


title: Bb B31 MOI 10 8 hrs, Rep_A [MS8_13]

value: Subject A

value: MOI 10


title: ATAC-Seq_ZBTB21_degron_6h_spikein_rep2

data_processing:
Raw ChIP-Seq reads were firstly trimmed using Cutadapt (v2.6) software and then mapped to the mm10 or hg19 genome using Bowtie2 (v2.3.5.1) software with default parameters.
RCR duplicates, discordant reads and reads mapped to chrM were discarded for further analysis.
Bigwig files were generated using deepTools software normalized by the spikein reads (reads that mapped to hg19 genome)
Assembly: mm10
Supplementary files format and content: Peak files were generated by MACS2 (v2.1.1) software using a q threshold of 0.05. Peaks between two replicates were merged together by IDR (v.2.0.3) using a idr threshold of 0.05 to obtain repeatable peaks.

extract_protocol:
ATAC-seq were performed according to the protocol from (Corces M.R et al., 2017).
50,000 viable cells were used for library preparation using TruePrep DNA Library Prep Kit V2 for Illumina Kit (Vazyme #TD501), PCR amplified libraries were extracted with Megen gel purification kit (Megen # D2111-03) with size selection for mono and dinucleosome.

treatment_protocol: Degron mES cells were treated with 1 μg/ml Doxycycline for 24 hours

value: mouse embryonic stem cell (mESC)


title: Rpl11 heterozygous Cell 13 [13-SCP-1706080]


title: 5xFAD, 12m, CD11bpositive, ROSpositive, male, rep2

description: 10X Genomics

value: male


title: ATAC-Seq_ZBTB21_degron_6h_spikein_rep1


title: Bb B31 MOI 1 8 hrs, Rep_A [MS8_11]


title: Immature DCs 8 hrs, Rep_B [MS8_15]


title: Rpl11 heterozygous Cell 11 [11-SCP-1706080]


title: ATAC-Seq_ZBTB21_degron_0h_spikein_rep2

value: ZBTB21 untreated


title: 5xFAD, 12m, CD11bpositive, ROSpositive, male, rep1

description: 10X Genomics


title: Rpl11 heterozygous Cell 10 [10-SCP-1706080]


title: Bb A3 MOI 10 8 hrs, Rep_A [MS8_9]

value: moDCs


title: 5xFAD, 12m, CD11bpositive, ROSnegative, male, rep1

description: 10X Genomics


title: EMT_3

city: Wuhan

first: Yuehan

last: Li

address: No. 1095, Jiefang Ave.

institute: Huazhong University of Scicence and Technology

data_processing:
Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, the paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq X ten/NovaSeq 6000 sequencer.
The raw reads were aligned to genome sequences, and the mapped reads of each sample were assembled by StringTie (https://ccb.jhu.edu/software/stringtie/index.shtml? t=example) in a reference-based approach
Assembly: mm10
Supplementary files format and content: excel, expression profiles that include FPKM values for each Sample

source_name: blastocyst

extract_protocol:
Total RNA was isolated from three replicates of 10 blastocysts using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions. The quality and concentration of the RNA samples were determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies).
Transcriptome library preparation was done following the TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. In brief, messenger RNA was isolated using the polyA selection method by oligo(dT) beads, followed by fragmentation in the buffer. Afterward, double-stranded cDNA was synthesized by a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation, and ‘A’ base addition according to Illumina’s library construction protocol.

treatment_protocol: Murine two-cell embryos were obitained from female ICR mice oviducts. Embryos were cultured in CZB culture medium, and the culture media were supplemented with extracelluar vesicles from human Fallopian tubes. The recruited patients are either with fibroids or with endometriosis.

value: blastocyst

value: WT

value: Fallopian tube extracellular vesicles from women with endometriosis


title: Bb A3 MOI 1 8 hrs, Rep_A [MS8_7]

value: 8 hrs


title: Rpl11 heterozygous Cell 07 [07-SCP-1706080]


title: EMT_2


title: Bb A3 MOI 10 24 hrs, Rep_A [MS8_8]

value: 24 hrs


title: NK92_SAHA_H3K27ac_HiChIP_rep2

city: Seoul

first: Hyoung-Pyo

address: Yonsei-ro 50-1

department: Department of Tropical Medicine

country: South Korea

institute: Yonsei University College of Medicine

data_processing:
Sequenced using Illumina HiSeq 2500 platform
Raw reads were processed using HiC-Pro pipeline v2.11.4 with DpnII restriction sites
Assembly: hg19
Supplementary files format and content: hic contaning validpairs
Library strategy: HiChIP

growth_protocol: NK92 cells were cultured α-MEM medium supplemented with 20% FBS, 55μM 2-mercaptoethanoland 100U/ml IL-2, 100U/ml Penicillin and 100μg/ml Streptomycin.

extract_protocol:
Fixed chromatin was digested using DpnII enzyme, followed by biotin incorporation with Biotin-14-dATP. After DNA ligation, the DNA was sonicated and immunoprecipitated with antibody recognizing specific protein. Antibody-chromatin complexed were captured with protein A&G beads. Reverse-crosslinked DNA was captured with Streptavidin C-1 beads.
Tagmentation was performed using Nextera DNA library preparation kit (illumina #15028212) according to manufacturer's instructions. Purified DNA was amplified using Nextera PCR primers. Libraries were paired-end sequenced on Illumina HiSeq 2500 platform.

treatment_protocol: NK92 was treated with 1000nM SAHA for 24 hours.

value: NK Cells

tag: passages

value: 12 passages

value: SAHA treated

value: H3K27ac (Abcam #ab4729)


title: 5xFAD, 12m, CD11bpositive, ROSnegative, female, rep3

description: 10X Genomics

value: brain

value: female

tag: cell type


title: Rpl11 heterozygous Cell 08 [08-SCP-1706080]

value: Rpl11 +/lox

value: erythroid precursor


title: NK92_SAHA_H3K27ac_HiChIP_rep1


title: Bb A3 MOI 1 24 hrs, Rep_A [MS8_6]

value: Subject A

value: MOI 1


title: EMT_1

tag: tissue


title: Bb B31 MOI 1 24 hrs, Rep_A [MS8_10]


title: NK92_Control_H3K27ac_HiChIP_rep2

value: untreated


title: ctrl_3

value: Fallopian tube extracellular vesicles from women with uterine fibroids


title: Rpl11 heterozygous Cell 12 [12-SCP-1706080]


title: Bb B31 MOI 10 24 hrs, Rep_A [MS8_12]

value: moDCs

value: MOI 10


title: LTA Stim 1 ug/mL 8 hrs, Rep_A [MS8_5]


title: Rpl11 heterozygous Cell 06 [06-SCP-1706080]


title: 5xFAD, 12m, CD11bpositive, ROSnegative, male, rep2

description: 10X Genomics

value: male

tag: age


title: ctrl_2

value: blastocyst

tag: genotype

value: WT


title: ATAC-Seq_ZBTB21_degron_0h_spikein_rep1

value: mouse embryonic stem cell (mESC)

tag: treatment

value: ZBTB21 untreated


title: LTA Stim 1 ug/mL 24 hrs, Rep_A [MS8_4]

value: 24 hrs


title: Rpl11 heterozygous Cell 09 [09-SCP-1706080]


title: Rpl11 heterozygous Cell 05 [05-SCP-1706080]


title: NK92_SAHA_HiC_rep2

data_processing:
Sequenced using Illumina HiSeq 2500 platform
Raw reads were processed using HiC-Pro pipeline v2.11.4 with DpnII restriction sites
Assembly: hg19
Supplementary files format and content: hic contaning validpairs

extract_protocol:
Fixed chromatin was digested using DpnII enzyme, followed by biotin incorporation with Biotin-14-dATP. After DNA ligation, the DNA was sonicated and captured with Streptavidin C-1 beads.
Tagmentation was performed using Nextera DNA library preparation kit (illumina #15028212) according to manufacturer's instructions. Purified DNA was amplified using Nextera PCR primers. Libraries were paired-end sequenced on Illumina HiSeq 2500 platform.

value: NK Cells

value: 12 passages

value: SAHA treated


title: Rpl11 heterozygous Cell 04 [04-SCP-1706080]

value: Rpl11 +/lox


title: ctrl_1


title: Immature DCs 0 hrs1 , Rep_A [MS8_3]

value: 0 hrs


title: ChIP-Seq_mES_SMC1_ZBTB21_degron_spikein_input

extract_protocol:
The soulable chromatin fractions were extracted as previously reported (Ji et al., 2015).
DNA library was constructed by previous publication TELP library construction protocol (Peng et al., 2015) and NEBNext®UltraTMII DNA Library Prep Kit for Illumina (NEB, #E765S).

value: mES


title: Rpl11 heterozygous Cell 03 [03-SCP-1706080]

extract_protocol:
single-cell isolation protocol: Individual cells were isolated for mRNA sequencing using the C1 Single-Cell Auto Prep System (Fluidigm).
imaging protocol : Each cell isolation chamber was imaged at 20X (Leica DMI 6000) with bright-field illumination and fluorescent channels. The Ter119 antibody was labeled with PCP-Cy5.5 and imaged using a 488/705 nm (excitation/emission) fluorescence filter cube.
Cells were lysed, their mRNA reversely transcribed into cDNA, and the cDNA amplifed using the SMART-Seq whole-transcriptome amplification method on the C1 System according to the manufacturer's instructions.
The cDNA libraries were collected from the C1 and prepared for sequencing using a Nextera XT DNA Sample preparation kit (Illumina).

value: erythroid precursor


title: NK92_Control_HiC_rep2

value: untreated


title: Immature DCs 8 hrs, Rep_A [MS8_2]

extract_protocol:
Total RNA was extracted from 107 mo-DCs using RLT Lysis Buffer (Qiagen) by following manufacturer's instructions
NEBNext Poly(A) Magnetic Isolation Module (NEB #E7490) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (Cat# E7765) were used to generate libraries.  Specifically, Poly A RNAs were isolated from total RNAs and fragmented for cDNA synthesis. End repair is performed where 3' to 5' exonuclease activity of enzymes removes 3' overhangs and the polymerase activity fills in the 5' overhangs. An ‘A’ base is then added to the 3' end of the blunt phosphorylated DNA fragments which prepares the DNA fragments for ligation to the sequencing adapters, which have a single ‘T’ base overhang at their 3' end. Ligated fragments are subsequently size selected through purification using the Sample Purification Beads included in the kit and undergo PCR amplification techniques to prepare the libraries. The BioAnalyzer is used for quality control of the libraries to ensure adequate concentration and appropriate fragment size.  The resulting library insert size is 200bp-500bp with a median size around 300bp. Libraries were uniquely barcoded and pooled for NovaSeq6000 sequencing.

value: Subject A

value: 8 hrs


title: Immature DCs 24 hrs, Rep_A [MS8_1]

value: moDCs


title: NK92_Control_HiC_rep1


title: NK92_Control_H3K27ac_HiChIP_rep1

value: H3K27ac (Abcam #ab4729)


title: Rpl11 heterozygous Cell 02 [02-SCP-1706080]


title: Rpl11 heterozygous Cell 01 [01-SCP-1706080]


title: NK92_SAHA_ATAC_rep2

data_processing:
sequnced using Illumina HiSeq 2500 platform
Raw ATAC-seq reads were trimmed for adaptor sequence, and aligned to the hg19 genome assembly using bowtie2 v2.3.5.1 with the following setting: --end-to-end --very-sensitive --maxins 2000
aligned files were filtered for MAPQ > 30 and sorting, deduplication were processed using PICARD  v2.27.4
filtered reads were shifted and reads in nucleome-free regions were extracted using deeptools alignmentSieve with the following setting: --maxFragmentLength 140 --ATACshift
peaks were called using macs2 v2.2.7.1 with the following setting: -f BAMPE -g hs and all peaks in blacklist regions were removed
normalized abundance file, bigwig files were generated applying CPM normalization using deeptools v3.5.1
Assembly: hg19
Supplementary files format and content: narrowPeak, CPM normalized bigwig

extract_protocol:
ATAC-seq was performed using the protocol from Corces et al., 2015 with small modifications. Nuclear pellets at 5x10^4 were permeabilized and tagmented by Tn5 enzyme.
Tagmentation was performed using Nextera DNA library preparation kit (illumina #15028212) according to manufacturer's instructions. Reverse-crosslinked DNA was amplified using Nextera PCR primers. Libraries were paired-end sequenced on Illumina HiSeq 2500 platform.


title: NK92_SAHA_ATAC_rep1


title: KD2-RKO

city: Nanjing

first: Weizhen

last: Liu

state: Jiangsu

address: No.138,Xianlin Avenue,Qixia District

institute: Nanjing University Of Chinese Medicine

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Assembly: GRCh38
Supplementary files format and content: TXT file contain counts for each sample

source_name: RKO cells

growth_protocol: The human CRC cell line RKO were purchased from the National Collection of Authenticated Cell Cultures and cultured in DMEM supplemented with 10% fetal bovine serum (Gibco, USA).

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Two groups of RKO cells  were transfected with siNC and siSRSF2 separately.

value: RKO

tag: group

value: human CRC cell line


title: Plasma and peripheral blood mononuclear cells (PBMCs)  for patient 7 post-treament

type: RNA

city: Pittsburgh

first: Anda

middle: M.

last: Vlad

state: PA

address: 204 Craft Avenue, B403

institute: Magee-Womens Research Institute

description: Two probes were used to detect each transcript: a reporter probe that carries the fluorescent barcode, and a biotinylated capture probe that immobilizes the complex for data collection. The code set contained 770 probe pairs, each pair specific to a particular nucleic acid target

hyb_protocol: according to Nanostring instructions

scan_protocol: according to Nanostring instructions

data_processing: Used NanostringNorm function in NanostringNorm package to normalize the gene expression data to the 20 housekeeping genes, and then keep the endogenous genes.

label: Fluorescent barcode, unique to each probe

source_name: ovarian cancer

label_protocol: according to Nanostring instructions

growth_protocol: Not applicable.

extract_protocol: RNA from peripheral blood mononuclear cells (PBMCs) was isolated using the Qiagen AllPrep DNA/RNA Kit. All RNA isolation was performed according to the manufacturer’s protocol. RNA concentration was measured with a NanoDrop 2000 UV-Vis Spectrophotometer (Thermo Scientific).

treatment_protocol: Samples were not pre-treated in vitro prior to RNA extraction. However, sample collection relative to the patient's treatment is specified in column L.

tag: gender

value: Female

tag: age at diagnosis

tag: tumor histology

value: Serous

tag: Stage

value: IIB


title: ChIP-Seq_mES_SMC1_ZBTB21_degron_spikein_0h_rep1


title: ChIP-Seq_mES_SMC1_ZBTB21_degron_spikein_6h_rep2

value: ZBTB21 degron 6h


title: ChAR-Seq_mES_ZBTB21_untreated_rep2

data_processing:
Raw ChAR-Seq reads were firstly trimmed using Cutadapt (v.2.6) software and then mapped to the mm10 and dm6 genome using STAR (v2.7.6a) software
Only uniquely mapped reads were kept for further analysis.
The raw counts of genes downloaded from GENECODE vM25 were obtained using featureCounts (v.1.6.3) software.
Assembly: mm10,dm6
Supplementary files format and content: Table with raw counts for each sample

growth_protocol: The mouse embryonic stem cells (mESCs) (obtained from Richard Young’s lab, MIT) were cultured in Knock out DMEM (Gibco, #10829018-018), supplemented with 10% FBS,1x PenStrep (Gibco, #15140-122),1x nucleoside (Sigma, #ES-008),1x L-glutamine (Gibco, #25030-149),1x NEAA (non-essential amino acids, Milipore, #TMS-001-C), 3 μM CHIR99021 (Selleck, #S1036), 0.5 μM PD0325901 (Selleck, #S1263), 143 μM β-mercaptoethanol (Sigma, #M3148),1000 U/ml mLIF (Milipore, #ESG1107) at 37 ℃ with 5% CO2 in a humidified incubator.

extract_protocol:
The chromatin was prepared by following the protocol published previously (Ji et al., 2015). Prepare about 10 million cells and incubate with NP40 cell lysis (10 mM Tris-HCl pH 8.0, 10 mM KCl, 1.5 mM MgCl2, 0.01% NP-40, and protease inhibitors) buffer to lysate cell membranes. Transfer the cell suspension to 1.25 ml sucrose cushion (24% sucrose (m/vol) in NP-40 cell lysis buffer to extract the nucleus. Collect the supernatant (cytoplasm fraction). Discard the supernatant and resuspend the nuclei pellet gently with 0.5 ml glycerol buffer (20 mM Tris·HCl pH8.0，75 mM NaCl,0.5 mM EDTA，0.85 mM DTT，50% (vol/vol) glycerol). Add 0.5 ml nuclei lysis buffer (10 mM Hepes pH 7.6，1 mM DTT，7.5 mM MgCl2，0.2 mM EDTA，0.3 M NaCl，1 M Urea，1% Nonidet P-40) to lysate nucleus. Collect the supernatant (nucleoplasm fraction). The pellets were chromatin fractions used in this study. The total chromatin RNA was extracted with TRIzol by following manufacturer's instructions.
RNA library was constructed by Novogene with Illumina lnc RNA-Seq library preparation kit.

treatment_protocol: We treated the degron-mESCs with 1 μg/ml Doxycycline  (Sigma Aldrich,#D9891) for 24 hours, then added 500 μM IAA (Sigma Aldrich, #115148) for indicated 6h for different analyses.


title: ChIP-Seq_mES_SMC1_ZBTB21_degron_spikein_0h_rep2


title: NK92_SAHA_HiC_rep1

last: Kim

value: NK Cells

value: 12 passages

tag: cell line


title: Plasma and peripheral blood mononuclear cells (PBMCs)  for patient 7 pre-treament


title: NK92_Control_ATAC_rep2


title: NK92_Control_ATAC_rep1


title: Plasma and peripheral blood mononuclear cells (PBMCs)  for patient 3 post-treament

value: Clear Cell

value: IA


title: ChAR-Seq_mES_ZBTB21_untreated_rep1

value: mES


title: ChIP-Seq_HEK293T_ZBTB7B_GFP_input

data_processing:
Raw ChIP-Seq reads were firstly trimmed using Cutadapt (v2.6) software and then mapped to the mm10 or hg19 genome using Bowtie2 (v2.3.5.1) software in ‘--very-sensitive-local’ mode.
RCR duplicates and discordant reads were filtered for further analysis.
Peaks were called by MACS2 (v2.1.1) software using a q threshold of 0.05. The two replicates were filtered by IDR (v.2.0.3) software using an idr threshold of 0.05 to obtain repeatable peaks.
Genome_build: mm10, hg19
Supplementary_files_format_and_content: Bigwig files were generated by deepTools2 (v.3.5.0)  software in 10 bp bins with normalized methods using RPGC.

source_name: HEK293T cells

extract_protocol:
The soluble chromatin fractions were extracted as previously reported (Ji et al., 2015).
DNA library was constructed by previous publication TELP library construction protocol (Peng et al., 2015) and NEBNext®UltraTMII DNA Library Prep Kit for Illumina (NEB, #E765S).

tag: sample type

value: GFP tagged HEK293T

tag: chip antibody


title: ChIP-Seq_mES_SMC1_ZBTB21_degron_spikein_6h_rep1


title: ChIP-Seq_HEK293T_ZBTB21_GFP_rep2

value: untreated

value: GFP


title: Plasma and peripheral blood mononuclear cells (PBMCs)  for patient 3 pre-treament


title: Plasma and peripheral blood mononuclear cells (PBMCs)  for patient 9 post-treament

value: Papillary Serous


title: NK92_SAHA_RUNX3_rep2

data_processing:
sequnced using Illumina HiSeq 2500 platform
Raw ChIP-seq reads were trimmed for adaptor sequence, and aligned to the hg19 genome assembly using bwa mem v0.7.12 with default parameters
aligned files were filtered for MAPQ > 30 and sorting, deduplication were processed using PICARD  v2.27.4
peaks were called using macs2 v2.2.7.1 with input reference bam file and the following setting: -f BAMPE -g hs (--broad for H3K27ac ChIP-seq peak calling, -q 0.1 for Runx3 ChIP-seq peak calling) and all peaks in blacklist regions were removed
normalized abundance file, bigwig files were generated applying CPM normalization using deeptools v3.5.1
Assembly: hg19
Supplementary files format and content: narrowPeak, broadPeak, CPM normalized bigwig

extract_protocol:
ChIP-seq was performed using the protocol from Schmidl et al., 2015 with small modifications. Fixed cells were sonicated and immunoprecipitated with antibody recognizing specific protein. Antibody-chromatin complexed were captured with protein A&G beads.
Tagmentation was performed using Nextera DNA library preparation kit (illumina #15028212) according to manufacturer's instructions. Reverse-crosslinked DNA was amplified using Nextera PCR primers. Libraries were paired-end sequenced on Illumina HiSeq2500, NovaSeq6000, HiSeq 2500 platform.

value: SAHA treated

value: RUNX3 (Santa Cruz #sc101553)


title: ChIP-Seq_HEK293T_ZBTB21_GFP_rep1


title: NC-RKO

value: RKO

value: control


title: ChAR-Seq_mES_ZBTB21_degron_6h_rep1


title: RNA-Seq_mES_ZBTB21_degron_24h_rep2

data_processing:
Raw RNA-Seq reads were firstly trimmed using Cutadapt (v.2.6) software and then mapped to the mm10 genome using STAR (v2.7.6a) software
Only uniquely mapped reads were kept for further analysis.
The raw counts of genes downloaded from GENECODE vM25 were obtained using featureCounts (v.1.6.3) software.
Genome_build: mm10
Supplementary_files_format_and_content: Table with raw counts for each sample

extract_protocol:
The total RNA was extracted with TRIzol by following manufacturer's instructions.
RNA library was constructed by Novogene with Illumina Poly (A) RNA-Seq library preparation kit.
Poly (A) RNA-Seq

value: mouse embryonic stem cell (mESC)

value: ZBTB21 degron 24h

value: ZBTB21 degron 24h mES


title: ChIP-Seq_HEK293T_ZBTB35_GFP_rep1


title: ChIP-Seq_HEK293T_ZBTB35_GFP_rep2


title: Plasma and peripheral blood mononuclear cells (PBMCs)  for patient 5 post-treament

value: Female

value: IIIC


title: NK92_SAHA_RUNX3_rep1

value: NK Cells

value: 12 passages


title: NK92_Control_RUNX3_rep2


title: ChIP-Seq_HEK293T_ZBTB11_GFP_rep2


title: NK92_SAHA_H3K27ac_rep2

value: H3K27ac (Abcam #ab4729)


title: NK92_Control_RUNX3_rep1


title: NK92_SAHA_H3K27ac_rep1


title: RNA-Seq_mES_ZBTB21_degron_24h_rep1


title: ChAR-Seq_mES_ZBTB21_degron_6h_rep2

value: mES

value: ZBTB21 degron 6h


title: ChIP-Seq_HEK293T_ZBTB11_GFP_rep1

value: untreated

value: GFP tagged HEK293T


title: RNA-Seq_mES_ZBTB21_untreated_rep2

value: ZBTB21 untreated mES