title: HepG2_MIC26KO_HG_4

city: DUESSELDORF

first: Arun

middle: Kumar

last: Kondadi

address: Universitätsstr. 1

institute: Heinrich Heine University, Dusseldorf

data_processing:
The BCL Convert Tool (version 3.8.4; Illumina Inc. San Diego, CA, USA) was used to convert the bcl files to fastq files as well for adapter trimming and demultiplexing.
Data analyses on fastq files were conducted with CLC Genomics Workbench (version 22.0.2, Qiagen, Venlo, Netherlands).
The reads of all probes were adapter trimmed (Illumina TruSeq) and quality trimmed (using the default parameters: bases below Q13 were trimmed from the end of the reads, ambiguous nucleotides maximal 2).
Mapping was done against the Homo sapiens (hg38; GRCh38.107) (July 20, 2022) genome sequence.
Reads Per Kilobase and per Megabase (RPKM) were calculated using CLC Genomics Workbench v22.0.2 with standard parameters. After grouping of samples (four biological replicates) according to their respective experimental condition, the statistical differential expression was determined using the CLC differential expression for RNA-Seq tool (version 2.6, Qiagen, Venlo, Netherlands). The resulting values were corrected for multiple testing by FDR and Bonferroni-correction. A value of ≤0.05 was considered significant.
Assembly: hg38
Supplementary files format and content: The excel file includes RPKM values for each sample

growth_protocol: Cells were grown in 1 g/L glucose DMEM (PAN-Biotech) supplemented with 10% FBS (Capricorn Scientific), 2 mM stable glutamine (PAN-Biotech) and penstrep (PAN-Biotech, penicillin 100 U/mL and 100 μg/mL streptomycin)

extract_protocol:
RNA isolation from cell pellets was performed using RNeasy Mini Kit (Qiagen) including DNase digestion according to the manufacturer’s protocol.
The library preparation was performed according to the manufacturer's protocol using the 'VAHTS™ Stranded mRNA-Seq Library Prep Kit' for Illumina®. Briefly, 700 ng total RNA were used as input for mRNA capturing, fragmentation, the synthesis of cDNA, adapter ligation and library amplification. Bead purified libraries were normalized and finally sequenced on the NextSeq2000 system (Illumina Inc. San Diego, CA, USA) with a read setup of 1x100 bp.

treatment_protocol: Cells cultured in standard growth media were divided equally into two cell culture flasks and grown in either 1 g/L glucose DMEM (normoglycemia) or 4.5 g/L glucose DMEM (hyperglycemia) (PAN-Biotech) for three weeks.

value: HG


title: KO M1 biol rep 2

status: Public on Dec 01 2023

type: SRA

city: Chicago

first: Sarah

middle: A

last: Tersey

state: IL

department: Medicine

country: USA

institute: University of Chicago

library_source: transcriptomic

data_processing:
Data was analyzed using Rosalind.
Reads were trimmed using catadapt. Quality scores were assessed using FastQC.
Individual sample reads were quantified using Htseq and normalized via Relative Log Expression using DESeq2 R library.
Assembly: mm10
Supplementary files format and content: excel files with raw counts
Supplementary files format and content: excel files with normalized counts

molecule: polyA RNA

organism: Mus musculus

source_name: BMDM

growth_protocol: RPMI containing 10% FBS, 10 mM HEPES, and 100 U/ml penicillin/ streptomycin) supplemented with 10 ng/ml M-CSF

extract_protocol:
RNA was extracted using Qiagen RNAeasy Mini Kit.
RNA quality and quantity was assessed using the Agilent bio-analyzer. Strand-specfiic RNA-seq libraries were prepared using an TruSEQ mRNA-SEQ library protocol (Illumina provided).
Library quality and quantity was assessed using the Agilent bio-analyzer and libraries were seqenced using an Illumina NovaSEQ6000.

treatment_protocol: BMDM were stimulated with 10 ng/ml LPS and 25 ng/mL IFN-γ for M1-like polarization and 10 ng/mL IL-4 for M2-like macrophage polarization for 16 h prior to RNA isolation.

tag: tissue

value: BMDM

tag: cell type

value: mouse macrophage

tag: genotype

tag: group


title: plasma, subject 9cdb94d1T4

type: protein

city: New York

first: Pushkala

last: Jayaraman

state: New York

address: 1 Gustave Levy Pl

department: Charles Bronfman Institute of Personalized Medicine

institute: Icahn School of Medicine at Mount Sinai

description: See https://www.synapse.org/#!Synapse:syn35874390/ for full clinical data and associated metadata including detailed description for process workflow.

hyb_protocol: As described in https://www.somalogic.com/wp-content/uploads/2016/08/SSM-002-Rev-3-SOMAscan-Technical-White-Paper.pdf

data_processing:
As described in Su, C.-Y. et al. Circulating proteins to predict adverse COVID-19 outcomes. medRxiv, 2021.2010.2004.21264015, doi:10.1101/2021.10.04.21264015 (2021).
Preliminary normalization (no log2 transformation) procedure as per Somalogic guidelines. The code workflow creates the normalizations prior to running the linear model.  More details, see Data-Preprocessing section as described in Su, C.-Y. et al. Circulating proteins to predict adverse COVID-19 outcomes. medRxiv, 2021.2010.2004.21264015, doi:10.1101/2021.10.04.21264015 (2021).
Script used to analyze the data is available at:
https://github.com/Nadkarni-Lab/aki_covid_proteomics

molecule: protein

organism: Homo sapiens

source_name: serum

extract_protocol: Blood samples were collected in Serum Separation Tubes (SST) with a polymer gel for serum separation as previously described in Del Valle DM, Kim-Schulze S, Huang HH, et al. An inflammatory cytokine signature predicts COVID-19 severity and survival. Nat Med. 2020. Samples were centrifuged at 1200 g for 10 minutes at 20°C. After centrifugation, serum was pipetted to a 15 mL conical tube. Serum was then aliquoted into cryovials and stored at -80°C.

tag: subject id

tag: blood sample id

tag: Sex

value: Male

tag: age

tag: days since first sample

tag: patient classification at first sample

tag: covid-19 status

value: Positive

value: Yes

tag: instrument model

value: Somascan discovery platform v4


title: plasma, subject 9b77114aT1

scan_protocol: As described in https://www.somalogic.com/wp-content/uploads/2016/08/SSM-002-Rev-3-SOMAscan-Technical-White-Paper.pdf

value: No


title: HepG2_MIC26KO_HG_3

country: Germany

molecule: total RNA

tag: cell line

tag: treatment


title: Multiplexed sample (JN-DSRCT-1 Adherent, JN-DSRCT-1 Sphere, BER-DSRCT Adherent, BER-DSRCT Sphere), CMO

city: New Orleans

first: Sean

middle: Bong

last: Lee

state: LA

address: 1700 Tulane Ave

department: Pathology

institute: Tulane University School of Medicine

description: Multiplexed scRNA-seq Library (JN-DSRCT-1 Adherent, JN-DSRCT-1 Sphere, BER-DSRCT Adherent, BER-DSRCT Sphere)

library_source: other

data_processing:
Raw read processing was carried out using the Cell Ranger Single-Cell Software Suite (version 7.0.1, 10X Genomics Inc., CA, USA)
gene expression matrices generated per sample using CellRanger were imported into R (version 4.2.2) and and analyzed using the Seurat R package
Assembly: GRCh38
Supplementary files format and content: csv file with barcodes corresponding to the cells in each sample
Supplementary files format and content: h5 matrix file of gene expression for each sample

source_name: mixed sample (JN-DSRCT-1, BER-DSRCT)

growth_protocol: Cells were grown for 7 days in sphere or adherent culture.

extract_protocol:
DSRCT cells grown in adherent or sphere culture conditions were harvest by trypsin and centrifugation to create a single cell solution with viability >95%. 2000 viable single cells from each sample were labeled with unique cell multiplexing oligo (CMO) provided by 10x Genomics (10X Genomics Inc, CA). Labeled cells from each sample were pooled and partitioned into nanoliter-scale Gel Beads-In-EMulsion (GEMs). Feature barcode molecules were captured directly by oligonucleotides presented on the Gel Beads inside a GEM during GEM-RT.
Cell multiplexing libraries comprising dual index NN set A (10X Genomics Inc, CA) were generated by index PCR amplification. Meanwhile, Full-length barcoded cDNAs were also generated and amplified by PCR to obtain sufficient mass for library construction. Following enzymatic fragmentation, end-repair, A-tailing, and adaptor ligation, single cell 3’ libraries comprising dual index TT set A (10X Genomics Inc, CA) were generated. Library quality controls were performed by using Agilent High Sensitive DNA kit with Agilent 2100 Bioanalyzer. JN A – CMO307 (AAGCTCGTTGGAAGA), JN S – CMO308 (CGGATTCCACATCAT), BER A – CMO309 (GTTGATCTATAACAG), BER S – CMO310 (GCAGGAGGTATCAAT).

value: mixed sample (JN-DSRCT-1, BER-DSRCT)

value: WT

value: mixed sample (Adherent or Sphere Culture)


title: plasma, subject 9ab573b1T8

label_protocol: As described in https://www.somalogic.com/wp-content/uploads/2016/08/SSM-002-Rev-3-SOMAscan-Technical-White-Paper.pdf

value: Female


title: Multiplexed sample (JN-DSRCT-1 Adherent, JN-DSRCT-1 Sphere, BER-DSRCT Adherent, BER-DSRCT Sphere), GEX

library_source: transcriptomic single cell


title: KO M1 biol rep 1


title: KO M2 biol rep 1


title: HepG2_MIC26KO_HG_2


title: KO M0 biol rep 4


title: R22035325LR02-RKO-shPNP-4G-4h

city: shanghai

first: Yongfeng

last: Liu

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

country: China

institute: The Institute of Health Sciences, SIBS, CAS / SJTUSM

data_processing:
In this project, PE 150 was applied to sequence the samples. However, the length of DNA segment may be less than 150 bp during library preparation, in results of adapter sequences (green region in the figure below) in the raw reads. fastp(v0.20.1) (Chen S, el at. 2018) software was used to remove the adapter sequence of raw data(Fastq) and the reads whose length is longer than 75bp were selected after adapters were removed. Then the selected reads, named as Clean reads, were used for downstream analysis.
Since mature RNA sequences are formed by concatenating different exons of a gene owing to alternative splicing, alignment gap will occur when genome is used as reference sequence. STAR (v2.7.8a) (Dobin A, et al. 2013) software can fastly and accurately align RNA sequences to gene regions (schematic maps below). The alignment analysis can basically be divided into two steps: 1) genemeGenerate Build an index; 2) Sequence alignment. In this project, clean reads of each sample were aligned to reference genome by using STAR software with default parameters.
RSEM (v1.3.3) (Li B, et al. 2011) can accurately quantify gene or transcript expression levels from RNA-seq data. In the analysis of this project, expression estimation of gene and transcript was performed by using RSEM with setting --estimate-rspd parameter to estimate the distribution of the starting position of the sequence (RSPD) and other parameters were set as defalut. Then edgeR (v3.28.1) package in R was used to perform TMM (trimmed mean of M values) (Robinson, MD, & Oshlack, A. 2010) and CPM (count per million) normalization for the the gene expression. TMM is mainly used to normalize the depth of sequencing in different samples and estimate the expression level for each sample. CPM is used to normalize the amount of read count expression between samples. TMM and CPM normalized read counts of genes were applied to compare between two samples in the downstream analysis. Further more, detected genes were annotated with Gene Ontology (gene2go.20141211), GenRef (gene_info.20141211), and GENCODE(v19), respectively.
EdgeR (Robinson, M.D., McCarthy et al. 2010) used the overdispersed Poisson model and empirical Bayes model to estimate the dispersion of all gene expression levels. In this project, raw read counts of gene expression were applied to estimate the differetiation between pair samples or groups by using edgeR package in R. Genes whose CPM and TMM value is greater than 1 in at least one sample were selected. The criteria for significantly differentially expressed genes was: padj < 0.05 and |FC| >= 2. The databases of Ensembl, GO, and KEGG were used to annotate differentially expression genes to illustrate the biological processes related to these differential genes.
Assembly: hg19
Supplementary files format and content: gene expression for each Sample

organism: Homo

source_name: colorectal

extract_protocol:
mRNA was extracted from total RNA using magnetic beads with oligo-dT then were fragmented randomly.
The first strand of cDNA and the second strand are then synthesized using reverse transcriptase. The reverse transcription product is subjected to terminal repair, followed by addition of an A base at the 3' end. Subsequently, the fragments were ligated with a Illumina universal adapter. After PCR amplified, the ligation products were purified in order to remove the incompletely ligated fragment and the self-ligated adapter.
Library sizes were detected using an Agilent 2100 Bioanalyzer and library concentrations were detected using Qubit 2.0. The RNA sequencing was performed according to Illumina's standard protocol.

treatment_protocol: 4 mM guanosine stimulation for 6 hours

value: colorectal

value: RKO

value: epithelial

value: shPNP

value: guanosine stimulation


title: KO M1 biol rep 4


title: HepG2_MIC26KO_HG_1

value: HG


title: Nasopharyngeal carcinoma tissue, replicate 4

type: RNA

city: Shenzhen

first: Feifan

last: Guo

address: No. 33, Zhongyuan Road

institute: Medical Laboratory of the third affiliated hospital of Shenzhen university

hyb_protocol: 5ug of Cy3-labelled cRNA (specific activity 15 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized  for 17 hours at 65Â°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner （G2565CA）using one color scan setting for4x180K microarrays (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and  Tiff is set to 20 bit).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3(Agilent) using default parameters (protocol GE1-107_Sep09 and Grid:  028680_D_20100527) to obtain background subtracted and spatially detrended Processed Signal intensities.   Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Nonkeratinizing undifferentiated NPC

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Agilent One-Color RNA Spike-In Kit according to the manufacturer's instructions, followed by Qiagen’s RNeasy mini spin columns.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 UV-VIS Spectrophotometer.

extract_protocol: Total RNA was isolated using RNeasy Total RNA Isolation Kit (Qiagen, GmBH, Germany)/ TRIzol reagent (Life technologies, Carlsbad, CA, US) according to the manufacturer’s instructions, and purified by using a RNeasy Mini Kit (Qiagen, GmBH, Germany) .Total RNA was checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). RNA samples of each group were then used to generate biotinylated cRNA targets for the Sino Human ceRNA array V3.0. The biotinylated cRNA targets were then hybridized with the slides. After hybridization, slides were scanned on the Agilent Microarray Scanner (Agilent technologies, Santa Clara, CA, US). Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, R package “limma”. The microarray experiments were performed by following the protocol of Agilent technologies Inc at Sinotech Genomics Corporation. Genes with a fold change of at least 2 were selected for further analysis. Heatmap plots were done by a R package “pheatmap” of the target genes. GO\ pathway enrichment analysis were done use Fisher's exact test by a R package “clusterProfiler” of the target genes. GO categories \Pathway with Fisher's exact test P values < 0.05 were selected

value: Tumor

tag: gender

value: female

tag: Stage

value: T4N1M0 (IV Stage)


title: Nasopharyngitis tissue, replicate 4

source_name: Chronic inflammation of the nasopharyngeal mucosa

value: Control

value: control


title: Nasopharyngeal carcinoma tissue, replicate 2

value: male

value: T3N1MO (III Stage)


title: Nasopharyngeal carcinoma tissue, replicate 1

value: T1N0M0 (I Stage)


title: Nasopharyngeal carcinoma tissue, replicate 3

value: T3N2MO (III Stage)


title: Nasopharyngitis tissue, replicate 3


title: plasma, subject 9ab573b1T4

value: Positive

value: No

value: Yes

value: Somascan discovery platform v4


title: KO M0 biol rep 3

value: BMDM

value: mouse macrophage


title: plasma, subject 9a6c775cT1

value: Female


title: BOD-DSRCT, Sphere Culture, Rep 2

description: BOD_Sphere_vs_Adherent_rsem_DGE_results.xlsx

data_processing:
Gene counts were generated by alignment to human transcriptome GRCh38 using STAR in RSEM.
Differential gene expression analysis was performed using DESeq2
Assembly: GRCh38
Supplementary files format and content: Excel file of differential gene expression analysis from DESeq2 within each cell line including base expression, log2FC, and FDR

source_name: BOD-DSRCT

growth_protocol: Cells were grown for 4 days in sphere or adherent culture.

extract_protocol:
RNAs were prepared with RNeasy Plus kit (Qiagen, Hilden, Germany)
libraries were created from 500ng of total RNA using the Illumina TruSeq Stranded Total RNA kit with Ribo-Zero (San Diego, CA)

value: BOD-DSRCT

value: WT

value: Sphere


title: HepG2_MIC26KO_LG_3

value: LG


title: HepG2_MIC26KO_LG_4


title: BOD-DSRCT, Sphere Culture, Rep 1


title: plasma, subject 9a170b5dT4

value: Male


title: Nasopharyngitis tissue, replicate 1

value: Control

value: control


title: BOD-DSRCT, Adherent Culture, Rep 2

value: Adherent


title: HepG2_MIC26KO_LG_2


title: KO M0 biol rep 2


title: KO M0 biol rep 1


title: WT M2 biol rep 3


title: plasma, subject 9a170b5dT1


title: WT M2 biol rep 4


title: BOD-DSRCT, Adherent Culture, Rep 1


title: Nasopharyngitis tissue, replicate 2

value: female


title: BER-DSRCT, Sphere Culture, Rep 2

description: BER_Sphere_vs_Adherent_rsem_DGE_results.xlsx

source_name: BER-DSRCT

value: BER-DSRCT


title: HepG2_MIC26KO_LG_1


title: BER-DSRCT, Sphere Culture, Rep 1


title: plasma, subject 99eb6b42T1

value: Positive


title: HepG2_WT_HG_4

value: HG


title: plasma, subject 998caea5T12

value: Yes


title: WT M2 biol rep 2


title: plasma, subject 998caea5T1

value: No

value: Somascan discovery platform v4


title: WT M2 biol rep 1

value: BMDM

value: mouse macrophage


title: HepG2_WT_HG_2


title: plasma, subject 99159ba5T4


title: HepG2_WT_HG_3


title: BER-DSRCT, Adherent Culture, Rep 2


title: JN-DSRCT-1, Sphere Culture, Rep 2

description: JN_Sphere_vs_Adherent_rsem_DGE_results.xlsx


title: BER-DSRCT, Adherent Culture, Rep 1


title: plasma, subject 99159ba5T1


title: HepG2_WT_HG_1


title: WT M1 biol rep 2


title: HepG2_WT_LG_4


title: WT M1 biol rep 3


title: HepG2_WT_LG_2


title: plasma, subject 990a7cbaT8

value: Female


title: plasma, subject 990a7cbaT4


title: JN-DSRCT-1, Sphere Culture, Rep 1

value: WT


title: HepG2_WT_LG_3


title: WT M1 biol rep 1


title: WT M0 biol rep 4


title: plasma, subject 990a7cbaT12


title: JN-DSRCT-1, Adherent Culture, Rep 1


title: ATAC-seq, BER-DSRCT, Sphere Culture, Rep 2

library_source: genomic

data_processing:
Quality control was performed with FASTQC and deduplication was performed with bbmap-clumpify
Bowtie2 was used to align sequences to GRCh38
Peak calling was performed with MACS2 and differential peak accessibility was calculated by DiffBind R Package.
Motif analysis was performed with HOMER.
Assembly: GRCh38
Supplementary files format and content: narrow peak files for each sample

molecule: genomic DNA

extract_protocol:
Transposition reaction was initiated for 30 minutes followed by purification with Zymo DNA Clean and Concentrator-5 Kit
PCR with appropriate ATAC primers and NEBNext 2x MasterMix followed by purification with Zymo DNA Clean and Concentrator-5 Kit. Library concentration and fragment size was validated with TapeStation D5000.

value: Sphere


title: JN-DSRCT-1, Adherent Culture, Rep 2


title: plasma, subject 990a7cbaT1


title: WT M0 biol rep 3


title: PDA_10X_mixed_healthy_cells

city: Heidelberg

first: Leo

middle: Carl

last: Förster

state: Deutschland

address: Im Neuenheimer Feld 581

institute: DKFZ

data_processing:
Read processing and mapping to hg38 was carried out using Cellranger v7.0.0, generating a deduplicated UMI-count matrix. Low quality cells with <1000 UMIs and <1000 detected genes were excluded. Tumor cells were identified by malignant calling using inferCNV.
hg38
counts: comma separated matrix of deduplicated UMI counts per cell (columns) per gene (rows). Metadata: comma separated matrix relating metdata (columns) per cell (rows)

source_name: Cortical organoid

extract_protocol:
RNA molecules were captured using bead-bound oligo dT(30) primers in droplets. cDNA was prepared using a template switching oligonucleotide to obtain cDNA which was subsequently amplified and purified using AMPureXP beads.
Purified cDNA was used for 10X Chromium 3' sequencing library preparation according to manufacturer's instructions.

value: Cortical organoid

value: mEGFP

tag: library type

value: mRNA


title: plasma, subject 98c815a3T8

value: Male


title: plasma, subject 98c815a3T1


title: ATAC-seq, BER-DSRCT, Sphere Culture, Rep 1


title: PDA_10X_mixed_tumor_cells

source_name: Brain tumor

tag: tissue

value: Brain tumor

value: TCF-Lef EGFP, TCF-Lef SFRP1


title: WT M1 biol rep 4

tag: cell type


title: ATAC-seq, BER-DSRCT, Adherent Culture, Rep 2

value: BER-DSRCT

tag: genotype

value: Adherent


title: PDA_10X_sorted_tumor_cells

value: TCF-Lef EGFP


title: ATAC-seq, BER-DSRCT, Adherent Culture, Rep 1


title: plasma, subject 98c815a3T0

value: Positive

value: Yes


title: PDA_10X_sorted_healthy_cells


title: plasma, subject 987c5784T1

value: No

value: Somascan discovery platform v4


title: hCCS5

city: Salt Lake City

first: Li

last: Li

state: Utah

address: 201 PRESIDENTS CIRCLE

institute: University of Utah

data_processing:
Count matrices were generated using featureCount (version 1.6.3)
differential expression analysis was performed with DESeq2 3.11
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts
Supplementary files format and content: tab-delimited text file includes sample information and deseq results

source_name: Frozen human CCS tumor samples

extract_protocol:
RNA purification is applied with kit (Zymo) and 1.3ug total RNA was used for library construction
RNA-seq libraries were constructed with the TruSeq Stranded mRNA Library Prep kit with Unique Dual Index Primers (Illumina).

value: Frozen human CCS tumor samples


title: HepG2_WT_LG_1

value: LG


title: plasma, subject 97eda4d9T1

value: Negative


title: prostate_tumor_small_cell

city: Seattle

first: John

middle: K.

state: Washington

address: 1100 Fairview Ave N Rm E2-430

institute: Fred Hutch Cancer Research Ctr

data_processing:
Raw sequencing reads were trimmed to the amplicon regions using the awk command. Barcode sequences in the reads were filtered and extracted using UMI-tools
Processed reads were aligned to custom references containing all amplicon sequences using bwa-mem
Samtools was used to extract amplicon counts for each barcode
Assembly: custom built with reference amplicon
Supplementary files format and content: tab-delimited text files include raw count values for each amplicon
Library strategy: scDNA-seq

source_name: primary mouse prostate epithelial cells

extract_protocol:
Single cells (3,000 to 4,000 cells per μl) were resuspended in Tapestri cell buffer and encapsulated using a Tapestri microfluidics cartridge, lysed, and barcoded.
Libraries were generated either from cryopreserved or freshly dissociated tumor cells using the Mission Bio Tapestri Single-cell DNA Custom Kit according to the manufacturer’s recommendations

value: primary mouse prostate epithelial cells

value: prostate tumor cells

tag: phenotype

value: sorted cells with small morphology


title: plasma, subject 977a55ecT1

tag: subject id


title: prostate_tumor_medium_cell

value: sorted cells with medium morphology


title: hCCS3


title: prostate_tumor_large_cell

value: sorted cells with large morphology


title: hCCS2


title: MANC, scRNAseq

city: Berkeley

first: Marietta

middle: Milou

last: Ravesloot-Chavez

state: Alameda

address: 500E Li Ka Shing, 1951 Oxford St

department: Plant and Microbial Biology

institute: University of California Berkeley

description: 10x Genomics

data_processing:
Samples were demultiplexed by the Vincent J. Coates Genomics Sequencing Laboratory at UC, Berkeley. 10X Cell Ranger Software v4.0.0 was used for gene counting and aggregation (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). The Satija lab Seurat toolki (https://satijalab.org/seurat/) was used to project the data from all genotypes of mice as uniform manifold approximation and projection (UMAP) clustering for visualization of the data. The filtered data was annotated using canonical signature genes as well as Immgen informed gene expression (https://www.immgen.org/).
Assembly: mm10
Supplementary files format and content: tab-separated values files and matrix files containing raw counts

source_name: Lung

extract_protocol:
The second largest lung lobes were pooled from five infected mice, tissues dissociated in RPMI containing liberase and Dnase I in gentleMACS tubes using the gentleMACS dissociator and strained through a 70um filter. A total of 10,000 cell per sample were used for single cell RNA sequencing (sc-RNAseq) according to the 10X Genomics protocol. Single cell suspensions were partitioned into Gel Beads in emulsion (GEMs) using the 3' Chromium Next GEM single Cell v3.1 system.
10x barcoded primers were used to reverse transcribe poly-adenylated mRNA to produced barcoded, full-lenght cDNA. Purified DNA was amplified, fragmented and amplified again to attach Illumina adapter sequences by the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley. Libraries were sequenced on Illumina NovaSeq S1 flowcells and demultiplexed.

treatment_protocol: Mice were infected via the aerosol route with M. tuberculosis strain Erdman and lung tissue was harvest at 21 days post infection.

value: Lung

value: MANC

value: Mycobacterium tuberculosis infection


title: B6, scRNAseq

description: 10x Genomics


title: MANA, scRNAseq

description: 10x Genomics

value: MANA


title: plasma, subject 972d9455T12

tag: blood sample id

value: Female


title: WT_Veh_M_L303

city: Rochester

first: Liewei

last: Wang

state: MN

address: 200 2st Str SW

department: Neurology

institute: Mayo Clinic

data_processing:
Quality checked sequencing files in fastq formats were mapped to GRCm39 reference genome using STAR RNA aligner. Raw counts were then called by HTSEQ.
Assembly: GRCm39
Supplementary files format and content: Tab deliminated raw counts file with Ensembl IDs on first column and each following column is a sample.

source_name: brain

extract_protocol:
Trizol-based total RNA extraction kit
Illumina Truseq 2
PolyA-enriched

treatment_protocol: 37-45days old ndufs4-knockout or WT mice were gavage fed with CP2 or vehicle for three consecutive days when the brain tissue was removed for RNA extraction

value: brain

value: WT

value: Vehicle


title: WT M0 biol rep 1

value: BMDM

value: mouse macrophage

tag: group


title: hCCS1

value: Frozen human CCS tumor samples


title: WT M0 biol rep 2


title: plasma, subject 972d9455T1

tag: Sex

tag: age

value: Positive

value: No

value: Yes

value: Somascan discovery platform v4


title: FHBT-7_pLvb4-ms2-tumor B

source_name: primary mouse bladder urothelial cells

value: primary mouse bladder urothelial cells

value: bladder tumor cells

value: mixed


title: plasma, subject 96f8e6acT8

value: Male

tag: days since first sample

tag: patient classification at first sample


title: WT_Veh_M_L300


title: FHBT-7_pLvb4-ms2-tumor A


title: WT_Veh_M_L285


title: plasma, subject 96f8e6acT4

tag: covid-19 status

tag: instrument model


title: siEA1-2-rep2

tag: cell line

value: tumor cell

value: KD EA1-2


title: MANB, scRNAseq

description: 10x Genomics

value: Lung

value: MANB

tag: treatment

value: Mycobacterium tuberculosis infection


title: LOF E9.5 WT_4

city: Madrid

first: Jose Luis

last: de la Pompa

state: MADRID

address: Melchor Fernández Almagro 3

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using bcltofastQ (Illumina).
Sequencing adapter contaminations were removed with cutadapt, discarding those reads that were shorter than 30 nt after trimming.
Resulting reads were aligned against the GRCm38.91 mouse transcriptome, with RSEM v1.3.1, to obtain expression estimates at gene level.
Assembly: GRCm38.91
Supplementary files format and content: Ensembl gene and transcript IDs, and RSEM-estimated raw counts for 53,465 annotated genes, in each sample.

source_name: Heart ventricles

extract_protocol:
Arcturus PicoPure RNA isolation kit (Thermo Fisher Scientific)
200 ng of total RNA were used to generate barcoded RNA-seq libraries using the NEBNext Ultra RNA Library preparation kit (New England Biolabs). Briefly, poly A+ RNA was purified using poly-T oligo- attached magnetic beads followed by fragmentation and then first and second cDNA strand synthesis. Next, cDNA 3’ ends were adenylated and the adapters were ligated followed by PCR library amplification. Finally, the size of the libraries was checked using the Agilent 2100 Bioanalyzer DNA 1000 chip and their concentration was determined using the Qubit® fluorometer (Life Technologies)
Libraries were sequenced on a HiSeq2500 (Illumina) to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software (Illumina).

value: Heart ventricles

value: WT


title: siEA1-1-rep2

value: KD EA1-1


title: LOF E9.5 WT_3


title: siNeg1-rep2

value: KD scramble control


title: plasma, subject 96f8e6acT12

value: Positive


title: hCCS4

value: Frozen human CCS tumor samples


title: WT_CP2_M_L289

value: brain


title: LOF E9.5 WT_2


title: plasma, subject 96f8e6acT1

value: No

value: Yes

value: Somascan discovery platform v4


title: siEA1-2-rep1


title: WT_CP2_M_L263


title: LOF E9.5 WT_1


title: plasma, subject 967e6186T1

value: Female


title: siEA1-1-rep1


title: WT_CP2_M_L262


title: siNeg1-rep1


title: plasma, subject 961c984bT12

value: Male


title: LOF E9.5 KO_4


title: WT_CP2_M_L259


title: SU-CCS-1,H3K27ac-3

data_processing:
Sequencing was performed on an Illumina NovaSeq instrument using the 2 x 50 bp protocol to a depth of approximately 30 million reads per sample. ChIP-seq reads were aligned to the hg38 using BWA-MEM (version 0.7.10-r789) for paired-end reads
Assembly: hg38
Supplementary files format and content: Bigwig files are generated with MACS2 and bdg2bigwig and  Peaks were called from each aligned bam file against input reads using MACS2 version 2.2.6

extract_protocol:
Cell pellet (approximately 5 million cells)  were processed by cryogenic grinding, fixed with formaldehyde, and quenched with glycine. Nuclei were extracted via lysis and douncing, followed by lysis of nuclear pellets. The chromatin was fragmented by sonication, then incubated with primary antibodies (anti-V5, anti-RNAPOL2, or anti-H3K27ac) and DynaBeads, subsequently eluted and purified for DNA analysis using a commercial kit.(Zymo)
Libraries were constructed with the NEBNext ChIP-seq Library Prep kit with Unique Dual Index Primers (New England Biolabs).

value: Human CCS cell

tag: antibody


title: NDUFS4_Veh_M_L322

value: Vehicle


title: plasma, subject 961c984bT1


title: plasma, subject 9615aa1cT1


title: plasma, subject 95569dbaT1


title: LOF E9.5 KO_2


title: SU-CCS-1,H3K27ac-2


title: NDUFS4_Veh_M_L319


title: WT_CP2_M_L267


title: LOF E9.5 KO_3


title: LOF 15.5 WT_4

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
otal RNA (100 ng) was used to generate barcoded RNA-seq libraries using the NEBNext Ultra II Directional RNA Library preparation kit (New England Biolabs) according to manufacturer’s instructions. First, poly A+ RNA was purified using poly-T oligo- attached magnetic beads followed by fragmentation and first and second cDNA strand synthesis. Next, cDNA ends were repaired and adenylated. The NEBNext adaptor was then ligated followed by second strand removal, uracile excision from the adaptor and PCR amplification. The size of the libraries was checked using the Agilent 2100 Bioanalyzer and the concentration was determined using the Qubit® fluorometer (Life Technologies)
Libraries were sequenced on a HiSeq2500 (Illumina) to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software (Illumina).


title: NDUFS4_CP2_M_L299


title: SU-CCS-1,H3K27ac-1


title: LOF E9.5 KO_1


title: SU-CCS-1,Input-3

value: input


title: plasma, subject 946ec1e0T8


title: plasma, subject 948d9b6dT1


title: SU-CCS-1,Input-2


title: plasma, subject 946ec1e0T4


title: NDUFS4_CP2_M_L298


title: LOF 15.5 WT_2


title: LOF 15.5 WT_3


title: SU-CCS-1,Input-1


title: NDUFS4_CP2_M_L292


title: plasma, subject 946a8d61T4


title: LOF 15.5 WT_1


title: Case 1.6-TCR, PBMC after therapy

city: Taaoyuan

first: HUNG

last: SHUENIU

address: 6F, Research building, Wenhua 1st Rd,

country: Taiwan

institute: Chang Gung Memorial Hospital

data_processing:
Data of Case 1.5-GEX/Case 1.5-TCR were processed by CellRanger v4.0 count function to align sequencing reads into a single set of barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Data of Case 1.6-GEX/Case 1.6-TCR were processed by CellRanger v3.1 count function to align sequencing reads into a single set of barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Data of Case 2.5-GEX/Case 2.5-TCR were processed by CellRanger v6.0 count function to align sequencing reads into a single set of barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Data of Case 2.6-GEX/Case 2.6-TCR were processed by CellRanger v6.0 count function to align sequencing reads into a single set of barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Assembly: hg38
Supplementary files format and content: CellRanger output files : Case 1-1_GEX barcodes.tsv.gz, Case 1-1_GEX features.tsv.gz, Case 1-1_GEX matrix.mtx.gz, Case 1-1_TCR filtered_contig_annotations.csv
Supplementary files format and content: CellRanger output files : Case 1-2_GEX barcodes.tsv.gz, Case 1-2_GEX features.tsv.gz, Case 1-2_GEX matrix.mtx.gz, Case 1-2_TCR filtered_contig_annotations.csv
Supplementary files format and content: CellRanger output files : Case 2-1_GEX barcodes.tsv.gz, Case 2-1_GEX features.tsv.gz, Case 2-1_GEX matrix.mtx.gz, Case 2-1_TCR filtered_contig_annotations.csv
Supplementary files format and content: CellRanger output files : Case 2-2_GEX barcodes.tsv.gz, Case 2-2_GEX features.tsv.gz, Case 2-2_GEX matrix.mtx.gz, Case 2-2_TCR filtered_contig_annotations.csv

source_name: PBMC from peripheral blood

extract_protocol:
PBMCs from patients were thawed and sorted using Dead Cell Removal kit(MACS). Single cells were encapsulated in Gel-Beads-in emulsion (GEMs) using the 10x Controller with a Chromium Next GEM Single Cell 5' Kit v2.
GEX and TCR libraries were constructed according to the 10x Genomics manufacturer's instructions.

value: PBMC from peripheral blood

value: primary PBMC, not cell line

value: PBMC


title: NDUFS4_CP2_M_L291


title: LOF 15.5 Flox_4

value: Heart ventricles


title: Case 1.5-TCR, PBMC before therapy


title: NDUFS4_CP2_M_L266


title: NDUFS4_Veh_M_L310


title: LOF 15.5 Flox_2


title: WT_Veh_F_L296

value: WT


title: LOF 15.5 Flox_3


title: Case 2.6-GEX and TCR, PBMC after therapy


title: Case 2.5-GEX and TCR, PBMC before therapy


title: WT_Veh_F_L295


title: LOF 15.5 Flox_1


title: plasma, subject 945ddd9cT1


title: WT_Veh_F_L278


title: plasma, subject 93e555b0T8


title: Case 1.6-GEX, PBMC after therapy


title: plasma, subject 93e555b0T4


title: Case 1.5-GEX, PBMC before therapy


title: 4TO7-3

city: Montreal

first: Jean-Francois

last: Cote

state: Quebec

address: 110 pine avenue

country: Canada

institute: IRCM

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to the reference mouse genome version GRCm38 (gene annotation Ensembl v98) using STAR version 2.5
Gene expressions are obtained with featureCounts v1.5
DESeq2 was used to normalize raw counts and compute differential expression
Assembly: GRCm38
Supplementary files format and content: normalized count matrix from DESeq2

source_name: spontaneous tumor in BALB/c mice

growth_protocol: 10% FBS-supplemented DMEM

extract_protocol:
RNA was extracted and purified using the Qiagen RNeasy column kit (#74104)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Not applicable

tag: strain

value: BALB/c


title: plasma, subject 93e555b0T1

source_name: serum

value: Positive


title: WT_Veh_F_L277

tag: tissue


title: 4TO7-2


title: MCF10A_H1047R_rep2

city: Nashville

first: Adam

middle: Xavier

last: Miranda

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University

data_processing:
*library strategy: CRISPR KO Screen
All sequencing library reads were trimmed of adapters and assessed for quality using the Trim Galore! (version 0.4.0) Wrapper of Cutadapt and FastQC.
Paired trimmed reads were interleaved using the reformat utility of BBTools (version 38.69)
Reads were counted to guide IDs using MAGeCK software package(version 0.5.9.5). Guide IDs found in Mageck_Guide.csv and NTC_IDs.csv
Target gene dropout was calculated using the maximum likelihood estimation (MLE) algorithm within the MAGeCK software package
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing the relative prevalence of gene targeting guides compared between the parental cell line and each of mutant cell lines.

source_name: Breast Epithelium

growth_protocol: All cell lines were grown in 5% CO2 at 37oC with 1% Pen Strep in respective media conditions. MCF-10A parental cell lines were purchased from American Type Culture Collection (ATCC). MCF-10A cell line knock-ins were previously generated as described in Gustin et al. Parental MCF-10A cell lines were cultured in DMEM/F12 (1:1) supplemented with 5% horse serum, 20 ng/ml epidermal growth factor (EGF), 10 µg/ml insulin (Roche), 0.5 µg/mL hydrocortisone (Sigma), and 100 ng/ml cholera toxin (Sigma). Knock-in cell lines were maintained in the same conditions except without EGF. Cells were grown to 80% confluence. Twenty-four hours prior to collection of RNA or nuclei, for RNA-seq or RNA-seq respectively, all MCF-10A cells were transferred to an assay media of phenol red-free DMEM/F12 (1:1) supplemented with 1% charcoal-dextran stripped FBS (Fisher), 0.2 ng/ml EGF, 10 µg/ml insulin, 0.5 µg/mL hydrocortisone, and 100 ng/ml cholera toxin.

extract_protocol:
Genomic DNA was isolated using Qiagen Qiamp Blook Minikit
First, libraries were PCR amplified for 16 cycles using Phusion Flash High-Fidelity (Thermo) with primers to add adaptors for Illumina sequencing. For all libraries, PCR reactions were performed in duplicate and barcoded to allow quantification of bias introduced by PCR. Samples were sequenced on a MiSeq following the manufacturer’s protocol using a v3 150 cycle kit with 10% PhiX (Illumina). PCR replicates were demultiplexed using FASTX-Toolkit (Hannon Lab, CSHL) and adaptors were trimmed using cutadapt to leave only the sgRNA guide sequence (from Sanjana et al. 2014)

value: Breast Epithelium


title: 4TO7-1


title: plasma, subject 9358dc76T1

extract_protocol: Blood samples were collected in Serum Separation Tubes (SST) with a polymer gel for serum separation as previously described in Del Valle DM, Kim-Schulze S, Huang HH, et al. An inflammatory cytokine signature predicts COVID-19 severity and survival. Nat Med. 2020. Samples were centrifuged at 1200 g for 10 minutes at 20°C. After centrifugation, serum was pipetted to a 15 mL conical tube. Serum was then aliquoted into cryovials and stored at -80°C.


title: plasma, subject 945ddd9cT8


title: WT_CP2_F_L311

value: brain


title: MCF10A_H1047R_rep1


title: plasma, subject 945ddd9cT4

value: No


title: WT_CP2_F_L272


title: plasma, subject 9279c5a5T1

value: Yes


title: 4T1-1


title: MCF10A_E545K_rep1


title: WT_CP2_F_L240


title: 15702X6 cPrdm16 KO2

city: salt lake city

first: Sihem

last: Boudina

department: Nutrition and Integrative Physiology

data_processing:
Mouse GRCm38 genome and gene feature files were downloaded from Ensembl release 94
Reference database was created using STAR version 2.6.1b with splice junctions optimized for 50 base pair reads
Reads were trimmed of adapters using cutadapt 1.16 and aligned to the reference database using STAR in two pass mode
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.20.0
Genome_build: GRCm38
Supplementary_files_format_and_content: FeatureCount output files combined into a single tab-delimited raw count matrix

source_name: heart tissue

growth_protocol: whole tissue

extract_protocol: Illumina TruSeq Stranded RNA Kit with Ribo-Zero Gold (human, mouse, rat, etc.)

treatment_protocol: untreated

value: Heart tissue of Embryos age E17

tag: genotype/variation

value: cPrdm16 KO1


title: WT_CP2_F_L228

tag: genotype


title: WT_Veh_F_L252


title: U373 ADAR3 R-Mutant, IP, Rep 3

city: Bloomington

first: Heather

middle: Ann

last: Hundley

state: IN

address: 1001 E. 3rd Street

department: Biology

institute: Indiana University

data_processing:
Reads were aligned to H. sapiens reference genome using STAR (v2.7.7a).
Differential binidng analysis was performed using FeatureCounts and DESEq2 (Ratios of Ratio using a Likelihood Ratio Test).
Assembly: Homo sapiens (GRCh38)
Supplementary files format and content: .csv files include DeSeq2 analysis with normalized read counts

growth_protocol: IMDM, 10% Fetal Bovine Serum, 1X Penicillin/Streptomycin and 0.2 mg/ml G418 (IBI Scientific). Cells were cultured at  37C at 5% CO2.

extract_protocol:
Prior to cell lysis and sonciation, cells were subjected to UV crosslining at 150 mj/cm2 using a Spectrolinker (Spectronic Corp) following which they were subjected to RNA-Immunoprecipitation.
For all RIP-Seq libraries, RNA was first subjected to ribosomal RNA depletion using the NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat) followed by library preparation using the KAPA Strand-Specific RNA Library Kit. For input samples, 1ug of total RNA was used as starting material. For each IP sample, total immunoprecipitated RNA was used. Libraries were amplified for 15 cycles using a thermocycler.

tag: cell type

value: Glioblastoma

value: U373 + ADAR3 R-Mutant


title: MCF10A_WT_rep2


title: plasma, subject 91245297T12

data_processing:
As described in Su, C.-Y. et al. Circulating proteins to predict adverse COVID-19 outcomes. medRxiv, 2021.2010.2004.21264015, doi:10.1101/2021.10.04.21264015 (2021).
Preliminary normalization (no log2 transformation) procedure as per Somalogic guidelines. The code workflow creates the normalizations prior to running the linear model.  More details, see Data-Preprocessing section as described in Su, C.-Y. et al. Circulating proteins to predict adverse COVID-19 outcomes. medRxiv, 2021.2010.2004.21264015, doi:10.1101/2021.10.04.21264015 (2021).
Script used to analyze the data is available at:
https://github.com/Nadkarni-Lab/aki_covid_proteomics

tag: subject id

value: Male

value: Somascan discovery platform v4


title: 15702X3 WT3


title: plasma, subject 9246fa51T1

tag: blood sample id

value: Female

value: Negative


title: 4T1-3


title: MCF10A_WT_rep1


title: 15702X4 cPrdm16 KO1


title: plasma, subject 9203a023T1


title: MCF10A_E545K_rep2


title: U373 ADAR3 R-Mutant, IP, Rep 1


title: NDUFS4_Veh_F_L281

value: Vehicle


title: plasma, subject 9203a023T4


title: 15702X1 WT1


title: NDUFS4_Veh_F_L283


title: U373 ADAR3 R-Mutant, IP, Rep 2


title: plasma, subject 90e38c54T1


title: NDUFS4_Veh_F_L282


title: 4T1-2


title: plasma, subject 92c9144aT1


title: plasma, subject 91245297T1


title: WT_CP2_F_L257


title: NDUFS4_Veh_F_L279


title: ADAR3, IP, Rep 4

data_processing:
Reads were aligned to H. sapiens reference genome using STAR (v2.7.7a).
Differential binidng analysis was performed using FeatureCounts and DESEq2.
Assembly: Homo sapiens (GRCh38)
Supplementary files format and content: .csv files include DeSeq2 analysis with normalized read counts

growth_protocol: IMDM, 10% Fetal Bovine Serum, 1X Penicillin/Streptomycin. Cells were cultured at  37C at 5% CO2.


title: U373 ADAR3 R-Mutant, Input, Rep 1


title: ADAR3, IP, Rep 2


title: NDUFS4_CP2_F_L227


title: plasma, subject 901703c1T1


title: plasma, subject 8fa95a8dT4


title: ADAR3, IP, Rep 3


title: NDUFS4_CP2_F_L216


title: U373 ADAR3 R-Mutant, Input, Rep 2


title: plasma, subject 900d8f3aT12


title: plasma, subject 8f043e6bT21


title: 15702X2 WT2


title: NDUFS4_Veh_F_L246


title: U373 ADAR3 WT, Input, Rep 3

value: U373 + ADAR3 Wild Type


title: plasma, subject 900d8f3aT1


title: U373 ADAR3 WT, IP, Rep 3


title: NDUFS4_CP2_F_L234


title: U373 ADAR3 WT, Input, Rep 2


title: NDUFS4_CP2_F_L233


title: plasma, subject 8f043e6bT20


title: ADAR3, IP, Rep 1


title: U373 ADAR3 WT, IP, Rep 2


title: U373 ADAR3 R-Mutant, Input, Rep 3


title: U373 ADAR3 WT, Input, Rep 1


title: plasma, subject 8fa95a8dT1


title: NDUFS4_CP2_F_L201


title: PreImmune, IP, Rep 3


title: PreImmune, IP, Rep 4


title: U373 ADAR3 WT, IP, Rep 1


title: PreImmune, IP, Rep 2


title: plasma, subject 8f043e6bT1


title: U373 Control, IP, Rep 3

value: U373 + Control


title: U373, Input, Rep 4


title: U373, Input, Rep 3


title: plasma, subject 8ef6c1bcT1


title: U373, Input, Rep 2


title: striatum_YAC128_AON_A1908332

city: Leiden

first: Elsa

last: Kuijper

address: Albinusdreef 2

department: Human Genetics

country: Netherlands

institute: Leiden University Medical Center

data_processing:
RNAseq reads were processed using the opensource BIOWDL RNAseq pipeline v5.0.0 (https://zenodo.org/record/5109461#.Ya2yLFPMJhE) developed at the LUMC. This pipeline performs FASTQ preprocessing (including quality control, quality trimming, and adapter clipping), alignment, read quantification, and optionally transcript assembly. FastQC was used for checking raw read QC. Adapter clipping was performed using Cutadapt (v2.10) with the default settings. RNAseq reads’ alignment was performed using STAR (v2.7.5a) on a customized mouse reference genome where GRCm39 mouse reference genome is combined with the Homo sapiens huntingtin (HTT), transcript variant 1 (NM_001388492). The gene read quantification was performed using HTSeq-count (v0.12.4) with setting “–stranded=yes”. The gene annotation used for quantification was Ensembl version 106 with an added entry for the HTT transcript (NM_001388492).
Assembly: GRCm39 mouse reference genome combined with Homo sapiens huntingtin (HTT) transcript variant 1 (NM_001388492)
Supplementary files format and content: fragments per gene

source_name: striatum

extract_protocol:
RNA was isolated from striatum using the PureLink RNA mini kit (Thermo Fisher Scientific) including a 15 minute DNase treatment step. Tissue was homogenized in 700 µl lysis buffer in MagNA Lyser Green beads tubes (Roche) with bullet blender Storm 24 (Next Advance) for 2-3 minutes at setting 8. RNA was eluted in 30 µl nuclease-free water and concentrations were measured using the Nanodrop (Thermo Fisher Scientific).
Full-length cDNA generation from RNA-seq data was performed using the mcSCRB-seq method with modifications (https://doi.org/10.1038/s41467-018-05347-6). Instead of single cells, 100 ng of isolated total RNA was used. Polyvinylpyrrolidone (PVP) was used instead of PEG8000 to reduce reaction viscosity. 0.5% PVP gave similar results as 7.5% PEG8000. The oligodT primer was replaced with a primer designed for scifi-RNA-seq (https://www.nature.com/articles/s41592-021-01153-z) containing partially Read 2 sequence primer from the Illumina platform, the UMI, and the well/sample barcode (example: SCIFI_LIG384_001 GAGTTCAGACGTGTGCTCTTCCGATCT-NNNNNNNN-AAGTGATTAGCAA-TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN). Samples were uniquely barcoded using the well barcode, and the handle for Read 2 sequence primer allowed further barcoding of a pool of samples by adding the i7 Illumina barcode and the p7 sequence (CAAGCAGAAGACGGCATACGAGAT[i7_barcode]GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT). The pooled cDNA libraries were generated using the 2x Kapa HiFi HotStart mix (Roche). The Illumina library prep was performed using the Kapa Hyper Plus kit (Roche) with fragmentation, end-repair, A-tailing, and double SPRI purification. Custom indexed adapter barcodes were used to barcode the pool of samples using the i5 Illumina barcode and introduce the p5 sequence to complete the Illumina library (top_adapter: AATGATACGGCGACCACCGAGATCTACAC[i5]ACACTCTTTCCCTACACGACGCTCTTCCGATC*T, bot_adapter GATCGGAAGAGCGT/3InvdT/). The ligated products were purified using Ampure beads, and PCR with Kapa Mastermix (Roche) and p5 and p7 primers was performed for enrichment. After double SPRI size selection, the Illumina library was quantified and checked for size distribution. Illumina paired-end sequencing was performed on a NovaSeq 6000 using the manufacturer's instructions.  After sequencing, Read 1 contained the cDNA information, and Read 2 contained only the UMI. To facilitate pipeline analysis, the UMI from the Read 2 fastq file was added to the beginning of the same read ID in the Read 1 fastq file, resulting in a modified Read 1 fastq file starting with the UMI followed by the cDNA sequence, which was used in the RNA-seq pipeline.

treatment_protocol: YAC128 mice on a B6 background and wild-type littermates were included in the study. Starting at approximately 6 months of age, treatment was administered intracerebroventricularly (ICV). Mice were anesthetized using isoflurane and placed in a stereotactic device to enable placement of non-metallic cannulas in the lateral ventricle. 500 µg AON12.1 or 500 µg scrambled AON diluted in 10 µL aCSF or 10 µL aCSF alone was injected and the cannula was fixed to the skull using Diafil dental cement (Diadent). The second and third injection were performed 2 and 4 weeks after surgery under isoflurane anesthesia. At 12 months of age, an MRI scan was made after which the mice were directly sacrificed by CO2 inhalation and brain was isolated.

value: striatum

value: AON


title: striatum_YAC128_AON_A1909391


title: plasma, subject 8e87fba2T4

value: Positive


title: U373 Control, IP, Rep 2


title: plasma, subject 8df7db09T1


title: striatum_YAC128_Scr_A1906955

value: Scr


title: U373 Control, IP, Rep 1


title: PreImmune, IP, Rep 1


title: U373, Input, Rep 1


title: U373 Control, Input, Rep 3


title: striatum_YAC128_aCSF_A1906954

value: aCSF


title: striatum_WT_aCSF_A1908331

value: WT


title: U373 Control, Input, Rep 2


title: igg_ctrl_1

city: Birmingham

first: Rintaro

last: Hashizume

state: Alabama

address: 1670 University Blvd

department: Pediatrics

institute: UAB

data_processing:
Adapter and quality trimming, alignment, normalization (CPM), BAM to bigwig, and peak calling (SEACR) were performed using the nf-core cutandrun pipeline (version 22.10.2)
Supplementary files format and content: Matrix table containing DESeq2 output and DESeq2 normalized abundance measurements for each sample
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

source_name: Cell line

growth_protocol: SF8628 cells were propagated as monolayers in complete medium consisting of Dulbecco's Modified Eagle's medium (DMEM, 11965092) supplemented with 10% fetal bovine serum (FBS, A31604-02) and non-essential amino acids (11140-050) from ThermoFisher

extract_protocol:
DNA was extracted by phenol-chloroform and dissolved in 12 uL low EDTA TE buffer
Libraries were prepared by the ACCEL-NGS 1S plus DNA library kit
Illumina NextSeq 500, 100 bp, paired-end

treatment_protocol: Cells were treated with 500 nM of AZD5153 or DMSO for 48 hours, and 500,000 cells were harvested and fixed with freshly prepared 0.5% PFA for 2 minutes. After stopping the cross-linking using 500 ?L 2.5 M glycine, cells were washed 3 times with digitonin wash buffer (20 mmol/L HEPES, pH 7.4, 150 mmol/L NaCl, 0.5 mmol/L spermidine, protein inhibitor cocktail, 0.02% digitonin, 0.05% SDS, and 1% Triton X-100) and bound to Concanavalin A-coated beads prewashed with binding buffer. Cells on beads were then incubated with antibodies on a nutator overnight at 4°C [1:500 for H3K27 acetylation (H3K27ac) antibody (Cell Signaling 8173)] After overnight incubation, cells were washed 3 times with 0.02% digitonin wash buffer, resuspended in 100 ?L digitonin buffer containing Protein A-Micrococcal Nuclease fusion protein (pA-MNase) and second antibody complex assemblies (pA-MNase and secondantibodies were preassembled at a 2:1 ratio in 50% glycerol at 4°C for 1 hour) and nutated at 4°C for 1 hour. After pA-MNase-second antibody binding, cells were washed 3 times with digitonin wash buffer for 5 minutes. Finally, cells were resuspended in 100 ?Licecold digitonin buffer in a heating block precooled in the ice water bath. Digestion of the chromatin was initiated by the addition of 2 mmol/L CaCl2 in the tube and lasted for 60 minutes at 0°C. The digestion was stopped by addition of 100 ?L 2× STOP buffer(340 mmol/L NaCl, 20 mmol/L EDTA, 4 mmol/L EGTA, 0.02% digitonin, 100 ?g/mL RNase A, and glycogen 50 ?g/mL). Digested DNA was released by incubation at 37°C for 30 minutes, and the supernatant was collected. Then, 5 ?L proteinase K and 200 ?L2× elution buffer [20 mmol/L Tris-HCl (pH = 8.0), 300 mmol/L NaCl, 20 mmol/L EDTA, 2% SDS, 10 mmol/L DTT] was added to each sample for reverse cross-linking at 65°C overnight.

value: Cell line (DIPG)

value: SF8628 (DIPG)

value: DMSO


title: striatum_YAC128_AON_A1906953


title: plasma, subject 8d91c4beT8

city: New York

first: Pushkala

value: No

value: Yes


title: DMSO_H3K27AC_2


title: DMSO_H3K27AC_1


title: plasma, subject 8e87fba2T1

value: Male

value: Somascan discovery platform v4


title: striatum_WT_aCSF_A1906947


title: MCF10A_H1047R_rep2_ATAC

data_processing:
All sequencing library reads were trimmed of adapters and assessed for quality using the Trim Galore! (version 0.4.0) Wrapper of Cutadapt and FastQC.
Trimmed reads were mapped to the human genome assembly hg38 using the BBTools (version 38.69) package and Burrows-Wheeler Aligner (version 0.7.17)
Quality filtering was performed on the mapped reads using SAMtools(26). Peaks of accessibility were called using Genrich (version 0.6.1)
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing genomic coordinates of called accessible regions

growth_protocol: All cell lines were grown in 5% CO2 at 37oC with 1% Pen Strep in respective media conditions. MCF-10A parental cell lines were purchased from American Type Culture Collection (ATCC). MCF-10A cell line knock-ins were previously generated as described in Gustin et al. Parental MCF-10A cell lines were cultured in DMEM/F12 (1:1) supplemented with 5% horse serum, 20 ng/ml epidermal growth factor (EGF), 10 µg/ml insulin (Roche), 0.5 µg/mL hydrocortisone (Sigma), and 100 ng/ml cholera toxin (Sigma). Knock-in cell lines were maintained in the same conditions except without EGF. Cells were grown to 80% confluence. Twenty-four hours prior to collection of RNA or nuclei, for RNA-seq or ATAC-seq respectively, all MCF-10A cells were transferred to an assay media of phenol red-free DMEM/F12 (1:1) supplemented with 1% charcoal-dextran stripped FBS (Fisher), 0.2 ng/ml EGF, 10 µg/ml insulin, 0.5 µg/mL hydrocortisone, and 100 ng/ml cholera toxin.

extract_protocol: Nuclei were isolated and ATAC-seq libraries were prepared using previously published methods from Barnett et al 2020 Mol Cell.

value: Breast Epithelium


title: striatum_WT_aCSF_A1906942


title: AZD5153_H3K27AC_2


title: U373 Control, Input, Rep 1

value: Glioblastoma


title: plasma, subject 8d91c4beT12

value: Female


title: striatum_YAC128_AON_A1906939


title: MCF10A_E545K_rep2_ATAC


title: AZD5153_H3K27AC_1


title: striatum_WT_aCSF_A1906938


title: MCF10A_E545K_rep1_ATAC


title: plasma, subject 8d72483bT1


title: plasma, subject 8d72483bT4


title: MCF10A_WT_rep2_ATAC


title: striatum_YAC128_AON_A1906921


title: MCF10A_WT_rep1_ATAC


title: striatum_YAC128_Scr_A1906952


title: plasma, subject 8d91c4beT21


title: striatum_YAC128_Scr_A1906919


title: striatum_YAC128_aCSF_A1906918


title: MCF10A_H1047R_rep3_RNA

data_processing:
All sequencing library reads were trimmed of adapters and assessed for quality using the Trim Galore! (version 0.4.0) Wrapper of Cutadapt and FastQC.
Trimmed reads were mapped to the human genome assembly hg38 using the Spliced Transcripts Alignment to a Reference (STAR) aligner (version 2.5.4b)
Mapped reads were sorted and filtered for mapping quality score over 30 using utilities within the SAMtools package (version 1.5)
Reads were counted to gene transcripts using featureCounts (version 2.0.0)
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

extract_protocol:
RNA was prepared from all cell lines using the Qiagen RNeasy kit
Libraries were prepared by the Vanderbilt Technologies for Advanced Genomics (VANTAGE) Core using the Illumina Ribo-Zero Plus rRNA Depletion Kit. Each library was sequenced on an Illumina NovaSeq, PE150, at a requested depth of 50 million reads.


title: plasma, subject 8d91c4beT20


title: plasma, subject 8c849dfbT1


title: plasma, subject 8c7a6694T4


title: MCF10A_H1047R_rep2_RNA


title: striatum_WT_aCSF_A1906916


title: MCF10A_H1047R_rep1_RNA


title: plasma, subject 8c7a6694T1


title: MCF10A_E545K_rep3_RNA


title: plasma, subject 8d91c4beT1


title: plasma, subject 8c7a6694T0


title: striatum_YAC128_Scr_A1906896


title: striatum_YAC128_AON_A1906893


title: MCF10A_E545K_rep2_RNA


title: plasma, subject 8b48500bT1


title: striatum_YAC128_aCSF_A1906924


title: plasma, subject 8aeb8455T1


title: MCF10A_E545K_rep1_RNA


title: striatum_YAC128_Scr_A1906885


title: plasma, subject 8c849dfbT12


title: MCF10A_WT_rep3_RNA


title: plasma, subject 8a75ea1fT8


title: plasma, subject 8a75ea1fT12


title: plasma, subject 8a75ea1fT1


title: striatum_YAC128_Scr_A1855510


title: striatum_YAC128_aCSF_A1855509


title: striatum_YAC128_Scr_A1855488


title: plasma, subject 8a75ea1fT0


title: Input plasmid library, rep 3

city: Tartu

first: Tiit

last: Örd

address: Riia 23b/2

department: Institute of Genomics

country: Estonia

institute: University of Tartu

description: MPRA plasmid DNA (input)

data_processing:
Reads were trimmed to retain 35 bp from the start of Read1 (expected to contain the 10-bp MPRA sequence barcode followed by 25 bp of constant flanking sequence). The reads were then mapped using Bowtie (version 1.3.0) to a synthetic genome consisting of 35 bp contigs (each of the possible 10-bp barcodes attached to 25 bp of constant sequence). In mapping, one nucleotide mismatch was allowed and any multimapping reads were discarded.
After mapping, the UMI read (12bp, the entire Read2) was used for UMI deduplication with UMI-tools (version 1.1.0) to filter out likely PCR duplicate reads.
After UMI deduplication, featureCounts from the Subread package was used to generate the raw count matrix.
Assembly: hg38
Supplementary files format and content: Tab-separated text file containing raw counts for all MPRA oligonucleotides (barcodes) in all libraries. Extra columns provide metadata for each MPRA oligo, such as the genetic variant position in the hg38 genome and the alleles tested.
Library strategy: MPRA RNA barcode amplicon

molecule: other

growth_protocol: HepG2 cells were maintained in Dulbecco's Modified Eagle Medium (DMEM; 4.5 g/l glucose; Gibco) supplemented with 10% fetal bovine serum and 1x penicillin-streptomycin. 6×10e6 cells per 10 cm plate  were transfected with 22 ug MPRA plasmid library using the Lipofectamine 3000 transfection reagent (Thermo Scientific) and Opti-MEM I reduced-serum medium (Thermo Scientific).

extract_protocol:
Total RNA was extracted from the cells using the RNeasy Midi Kit (Qiagen) according to the procedure described by the manufacturer. Poly(A)+ RNA was subsequently isolated using Dynabeads Oligo(dT)25 beads (Invitrogen), treated with DNase I (Thermo Scientific) and purified using the RNeasy Micro kit (Qiagen).
Poly(A)+ RNA  was reverse-transcribed with SuperScript III (Invitrogen) using primer specific to the MPRA reporter RNA. The RT primer incorporated a 12-nt UMI (unique molecular identifier). To generate the MPRA plasmid library 'input' NGS libraries, the MPRA plasmid library was used as template in an DNA synthesis reaction with Phusion Hot Start II High-Fidelity DNA Polymerase. The resulting products were used to prepare targeted (amplicon) NGS libraries to quantify the MPRA barcodes.

treatment_protocol: 9 h after transfection, the medium was replaced with regular growth medium (described above) with or without 2 ug/ml tunicamycin, and the cells were harvested 17 h later. To generate replicates, the transfection and treatment of cells were repeated on separate days (n=5).

tag: library type

value: MPRA plasmid DNA

tag: replicate

tag: library


title: Input plasmid library, rep 4

description: MPRA plasmid DNA (input)


title: plasma, subject 89e8a858T1

last: Jayaraman

address: 1 Gustave Levy Pl

institute: Icahn School of Medicine at Mount Sinai

tag: Sex

tag: age

tag: days since first sample


title: Clone_B Untreated S5

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

country: Italy

institute: OSR - San Raffaele Scientific Institute

data_processing:
Reads have been trimmed with Cutadapt for adapter sequences and quality and Aligned to the reference genome with hisat2
Bam files were counted against the Genecode V31 human GTF annoation of genes (exon and gene_name) using featureCounts
RPKM normalization was applied using rpkm function in edgeR R Package
Assembly: mm10
Supplementary files format and content: XLSX table with RPKM values of 40 samples for all genes in the GTF

source_name: Hela

growth_protocol: GFP-p65 knock-in mouse embryonic fibroblasts (MEFs) were kindly provided by M. Pasparakis. MEFs were derived from a single male embryo of a homozygous knock-in GFP-p65 expressing mouse model, using standard protocols (De Lorenzi et al., 2009) and immortalized by serial passaging following the “3T3 method” that typically involves 20-30 passages (Amand et al., 2016). Clones were generated from a freshly frozen vial of these MEFs, and aliquots of each clone were frozen and then used for few passages, to keep at a minimum the number of passages. The cells were cultured in phenol-red free DMEM supplemented with 10% FCS, 50 mM b-mercaptoethanol, 1x L-glutamine, 1x pen/strep, 1x sodium pyruvate and 1x non-essential amino acids. MEFs were subcultured every 2-3 days before they reached 100% confluency and kept at 37°C and 5% CO2. MEFs were harvested by 1x Trypsin solution and counted. Final concentration of 5 cells/ml was achieved by serial dilutions and 100 μl of the cell suspension per well were pipetted to a 96-well plate. The plate was screened for single colonies and selected colonies were then expanded.

extract_protocol:
1.5×10^5 MEFs were plated on a 6-well plate a day before the extraction. Total RNA was isolated using the NucleoSpin RNA II kit (Macherey-Nagel). The amount of RNA was determined using a NanoDrop spectrophotometer (Thermo Fisher Scientific).
SMART-Seq mRNA library prepartion following manufactures's intructions (TANAKA).

treatment_protocol: Where indicated the cells were stimulated with the final concentration of 10 ng/ml of recombinant human TNF-α protein (R&D Systems) or 100 ng/ml of recombinant human interleukin 1 beta (IL-1β, PeproTech).

value: Hela

value: Untreated


title: Clone_B Treated S5

value: TNF


title: striatum_WT_aCSF_A1855486

value: striatum


title: Clone_B Treated S4


title: Input plasmid library, rep 2

description: MPRA plasmid DNA (input)


title: plasma, subject 88c174e8T1

tag: patient classification at first sample

tag: covid-19 status

value: Negative

tag: instrument model


title: Clone_B Untreated S4

tag: cell line

tag: treatment


title: Input plasmid library, rep 1

description: MPRA plasmid DNA (input)


title: striatum_YAC128_AON_A1855466

tag: tissue

value: AON


title: plasma, subject 88e05bdeT1

value: Positive


title: striatum_YAC128_aCSF_A1906884

value: aCSF


title: plasma, subject 88924a03T12


title: striatum_YAC128_Scr_A1904917

value: Scr


title: MCF10A_WT_rep2_RNA

value: WT


title: HepG2, tunicamycin, rep 5

description: MPRA RNA readout

value: MPRA RNA

value: tunicamycin

value: e


title: MCF10A_WT_rep1_RNA

value: Breast Epithelium


title: Clone_B Untreated S3


title: striatum_YAC128_aCSF_A1855464


title: striatum_WT_aCSF_A1855445


title: plasma, subject 88924a03T1

value: No

value: Yes

value: Somascan discovery platform v4


title: HepG2, tunicamycin, rep 4

description: MPRA RNA readout

value: d


title: striatum_YAC128_AON_A1855455


title: Clone_B Treated S3

value: Hela


title: plasma, subject 887f501eT8

value: Male


title: Clone_B Treated S2

value: TNF


title: Clone_B Untreated S2

value: Untreated


title: HepG2, tunicamycin, rep 2

description: MPRA RNA readout

value: b


title: striatum_YAC128_aCSF_A1855442

value: striatum


title: plasma, subject 887f501eT4

value: Positive


title: HepG2, tunicamycin, rep 1

description: MPRA RNA readout

value: a


title: plasma, subject 887f501eT1


title: striatum_WT_aCSF_A1855434

value: WT

value: aCSF


title: plasma, subject 87f372cbT4


title: striatum_YAC128_aCSF_A1855433


title: Clone_B Treated S1


title: HepG2, control, rep 5

description: MPRA RNA readout

value: MPRA RNA

value: control


title: Clone_B Untreated S1


title: Clone_G Treated S5


title: HepG2, control, rep 4

description: MPRA RNA readout


title: T_100_rep4 [Sample_24171]

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
Demultiplexing was perfomed using bcl2fastq2 v2.20
Adapter trimming was performed using Trimmomatic v0.36 with following parameters ILLUMINACLIP:NexteraPE-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:25 MINLEN:36 CROP:48
Alignment was performed using bowtie2 v2.4.5 against the human reference genome mm10.
Duplicated reads were removed using picard "dedup" function and the transposase-induced offset was removed using the deeptools v3.5.2 "alignmentSieve" function.
Sorting and indexing of bam files was done using samtools v1.14
Peak calling was performed using MACS2 v2.2.7.1. on sample merged .bam file
Quantification of sequencing reads in unified peak regions was performed in R 4.1.0 using the "summarizeOverlaps" function implemented in the GenomicAlignments package v1.28.0.
Assembly: mm10
Supplementary files format and content: comma separated files include raw count table

source_name: spleen

extract_protocol: ATAC-seq - Paired End 50 on a NovaSeq6000 (SP v1.5 chemistry)

value: spleen

tag: cell number

value: Tcell

value: wt

tag: strain

value: C57BL/6J WT


title: plasma, subject 87f372cbT1

value: No

value: Yes

value: Somascan discovery platform v4


title: HepG2, control, rep 3

description: MPRA RNA readout

value: c


title: T_100_rep3 [Sample_24170]

tag: cell type

tag: genotype


title: HepG2, tunicamycin, rep 3

description: MPRA RNA readout

value: tunicamycin


title: Clone_G Untreated S5

value: Hela

value: Untreated


title: plasma, subject 87f372cbT0

tag: subject id

tag: blood sample id

value: Male

value: Positive


title: plasma, subject 87906852T1


title: HepG2, control, rep 2

description: MPRA RNA readout

tag: library type

tag: replicate

value: b


title: T_100_rep1 [Sample_24168]


title: plasma, subject 87549347T3

tag: Sex

value: Female


title: Clone_G Treated S4

value: TNF


title: HepG2, control, rep 1

description: MPRA RNA readout

value: MPRA RNA

value: control

value: a

tag: library


title: T_100_rep2 [Sample_24169]

value: spleen

value: Tcell

value: wt


title: Clone_G Untreated S4


title: RRBS_humanizedNeutrophils_TET2_2

city: London

first: Dominique

last: Bonnet

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
The Illumina adapter sequence is trimmed from reads using Trim Galore, and then a custom script is used to trim additional bases that are added during the library creation process to facilitate sequencing. Reads are mapped to the genome using Bismark and Bowtie 2 allowing for no mismatches and a seed substring length of 20.
Following alignment, PCR duplicates are removed using a custom analysis script. Each read has a randomized barcode and if more than one read has the same start and end coordinates and the same barcode, then all but one of the reads are discarded.
Alignment information of the remaining reads are stored in BAM files. Methylation at CpG sites is then extracted from the BAM files using Bismark and reported in bedGraph, coverage, and CpG report formats.
CpG reports from the Bismark alignment are processed with the methylKit R package, and only CpG sites covered with at least 10 reads are retained for the downstream analyses. The average methylation at each chromosome and at each annotated transcript are determined on a per-sample basis.
For the region-based analysis, the genome is tiled into 1 kilobase regions and significantly differentially methylated tiles are identified.
Assembly: GRCh38 human genome
Supplementary files format and content: Differentially methylated regions (DMR) and differentially methylated bases (DMB)

source_name: Human Neutrophils

extract_protocol: Cell pellet was sent to ActiveMotif for Reduced Representation Bisulfite Sequencing (RRBS)

value: Human Neutrophils

value: KO


title: B_100_rep4 [Sample_24167]

value: Bcell

value: C57BL/6J WT


title: Clone_G Treated S3

value: Hela


title: plasma, subject 86526fceT4

tag: age

tag: days since first sample

value: Yes

value: Somascan discovery platform v4


title: B_100_rep3 [Sample_24165]


title: plasma, subject 85d4973aT1

value: Male

tag: patient classification at first sample

tag: covid-19 status

value: Negative


title: RRBS_humanizedNeutrophils_TET2_1


title: RRBS_humanizedNeutrophils_WT_2

value: WT


title: Clone_G Untreated S3

tag: cell line

value: Untreated


title: B_100_rep2 [Sample_24164]


title: Clone_G Treated S2

tag: treatment

value: TNF


title: plasma, subject 857f0148T8

value: Positive

tag: instrument model


title: B_100_rep1 [Sample_24163]

tag: tissue

tag: cell number


title: plasma, subject 857f0148T4

value: No


title: RRBS_humanizedNeutrophils_WT_1

tag: cell type


title: Clone_G Untreated S2

tag: genotype


title: B_patch_rep5 [Sample_24162]

value: spleen

tag: strain


title: plasma, subject 857f0148T1

tag: subject id

tag: blood sample id


title: T_patch_rep5 [Sample_24161]

value: Tcell


title: Clone_G Treated S1


title: RNA_AKP_Day12_STAR-pos-to-pos_3

city: Utrecht

first: Maria

middle: Christine

last: Heinz

address: Heidelberglaan 100

department: Molecular Cancer Research

institute: University Medical Center Utrecht

description: STAR+ cells were collected from 12-day-old AKP organoids for bulk RNA-seq.

data_processing:
Reads were aligned with Hisat2 (version 2.0.4) with enabled alignment tailoring for transcript assemblers.
Reads per gene were counted with htseq-count script (Hisat2 software suite, strandness disabled, identification attribute set to gene_id).
Genes with no reads in any of the samples were excluded from analysis.
Differential gene expression was performed with DESeq2 package.
Significantly changing genes were called after Walt test followed by correction for multiple testing (Benjamini-Hochberg method).
Data visualisation was performed upon normalisation, log2 transformation, and noise-stabilisation using the rlogTransformation function of the DESeq2 package.
Assembly: hg38
Supplementary files format and content: txt files containing transcript counts (PCR duplicates have been removed)

source_name: AKP organoid

growth_protocol: Engineered human colorectal cancer organoids (APCKO/KO; KRASG12D/-; TP53KO/KO) were grown from single STAR+ cells for 5-12 days in Matrigel (Corning). Growth media was refreshed every 2-3 days. Growth media contained Advanced DMEM/F12 (Invitrogen), supplemented with 10 mM Hepes (Invitrogen), 1% GlutaMAX (Invitrogen), 1% Penicillin-Streptomycin (Lonza) as well as 1x B27 supplement (Invitrogen), 1.25 mM N-Acetyl-L-cysteine (Sigma-Aldrich), 10 mM Nicotinamide (Sigma-Aldrich), 500 nM A83-01 (Tocris), and 10 µM SB202190 (Gentaur).

extract_protocol:
RNA was extracted using the RNeasy Mini RNA extraction kit (Qiagen, Cat. No. 74106) according to the manufacturer’s instructions with DNaseI treatment.
Up to 73ng RNA per sample was used for the preparation of the RNA sequencing libraries using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (KAPA Biosystems). In short, oligo hybridisation and rRNA depletion, rRNA depletion cleanup, DNase digestion, DNase digestion cleanup, and RNA elution were performed according to protocol. Fragmentation and priming were performed at 94⁰C for 6:30 min. First strand synthesis, second strand synthesis, and A-tailing were performed according to protocol. For the adapter ligation, a 1.5μM stock was used (NextFlex DNA barcodes, Bioo Scientific). First and second post-ligation cleanup were performed according protocol. The library was amplified in 13 cycles and the subsequent cleanup was performed using a 0.8x bead-based cleanup. Library size was determined using the High Sensitivity DNA bioanalyzer (Agilent Technologies) and the library concentration was measured using the KAPA Library Quantification Kit (KAPA Biosystems). Sequencing was performed using an Illumina NextSeq 500, while 50‐bp paired‐end reads were generated.

treatment_protocol: Organoids were harvested with 1 mg/mL Dispase II (Life Technologies) and pelleted by  spinning at 500xg, 4 min, 4°C.  Organoids  were trypsinized to single cells using TrypsinEDTA (Sigma-Aldrich), trypsin activity was blocked with trypsin inhibitor (Sigma-Aldrich) at a 1:1 ratio, and single cells were pelleted by spinning at 500xg, 4min, 4°C. To visualise dead cells on FACS, 1.5 µM DRAQ7 (Cell Signaling Technologies) was added to growth medium containing 10 µM Y-27632 (Gentaur). On FACS, alive cells with STAR expression being positive (pos) or negative (neg) were collected duplicates or triplicates (10,000-20,000 cells each). Samples were pelleted and snap-frozen until processed further.

value: AKP organoid

value: Colorectal cancer

tag: time

value: Day 12

tag: star day 0

value: pos

tag: star day 5/12

tag: technical replicate


title: plasma, subject 8557d073T8

tag: Sex

tag: age

tag: days since first sample


title: Clone_G Untreated S1

tag: cell line


title: B_patch_rep4 [Sample_24160]

value: Bcell

value: wt

value: C57BL/6J WT


title: RNA_AKP_Day12_STAR-pos-to-pos_1


title: RNA_AKP_Day12_STAR-pos-to-pos_2


title: Clone_R Treated S5

value: Hela

tag: treatment


title: RNA_AKP_Day12_STAR-pos-to-neg_2

description: STAR- cells were collected from 12-day-old AKP organoids for bulk RNA-seq.

value: neg


title: Clone_R Untreated S5


title: plasma, subject 8557d073T1

value: Male

tag: patient classification at first sample

tag: covid-19 status

value: Yes

tag: instrument model

value: Somascan discovery platform v4


title: plasma, subject 84739e82T1

value: Negative


title: Clone_R Treated S4

value: TNF


title: T_patch_rep3 [Sample_24157]

tag: tissue

tag: cell number

tag: cell type


title: RNA_AKP_Day5_STAR-pos-to-pos_3

description: STAR+ cells were collected from 5-day-old AKP organoids for bulk RNA-seq.

value: Day 5


title: Clone_R Untreated S4

tag: genotype

value: Untreated


title: plasma, subject 8403a192T1

tag: subject id

tag: blood sample id

value: Positive


title: RNA_AKP_Day5_STAR-pos-to-pos_2

value: AKP organoid

tag: time

tag: star day 0


title: plasma, subject 83df1b39T12


title: Clone_R Treated S3


title: RNA_AKP_Day5_STAR-pos-to-pos_1

value: Colorectal cancer

tag: star day 5/12

tag: technical replicate


title: Clone_R Untreated S3


title: plasma, subject 83df1b39T1

tag: Sex

tag: age

value: No


title: Clone_R Treated S2

tag: cell line


title: RNA_AKP_Day5_STAR-pos-to-neg_3

description: STAR- cells were collected from 5-day-old AKP organoids for bulk RNA-seq.

value: pos


title: T_patch_rep1 [Sample_24154]

value: spleen

value: Tcell

tag: strain


title: plasma, subject 8557d073T4

tag: days since first sample

tag: patient classification at first sample


title: Clone_R Untreated S2

tag: treatment


title: plasma, subject 835b62b9T1

tag: covid-19 status

tag: instrument model


title: B_patch_rep3 [Sample_24158]

tag: tissue

tag: cell number

tag: cell type

value: Bcell

value: wt

value: C57BL/6J WT


title: B_patch_rep1 [Sample_24153]

tag: genotype


title: 5xFAD, septum, 5m, replicate 2

city: Daegu

first: Jaemyung

last: Jang

address: 61, Cheomdan-ro, Dong-gu

country: South Korea

institute: Korea Brain Research Institute

description: inDropTM

data_processing:
The previously published pipeline in Python available at [https://github.com/indrops/indrops] was used to read raw sequencing data under modified settings (Bowtie 1.2.3, m = 200, n = 1, l = 15, e = 1000) and align them to the Ensembl mouse reference genome (GRCm39 release 102) to obtain a cell-gene expression matrix.
Seurat package (version 4.3) (Butler et al., 2018;Stuart et al., 2019;Hao et al., 2021) in R environment (version 4.3.0) were used to filter cells, reduce dimensionality, cluster with Louvain, and project cells with UMAP. We removed cells with low quality (less than 1,000 reads and 500 UMI-filtered mapped read) and doublets using ScDblFinder package (Germain et al., 2021). The G2M phase score, S-phase score, UMI count, and mitochondrial gene proportion were regressed out using the SCTransform wrapper. cells were annotated using the top most significant upregulated cluster-specific genes. Microglia was isolated preferentially expressed markers of microglia or macrophages. The subset of microglia was processed though dimensionality reduction, Louvain clustering, and projection into UMAP.
Assembly: GRCm38 (release 102)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: septum

extract_protocol:
Mice were euthanized by carbon dioxide gas overdose, and the brains were rapidly dissected out. The hippocampus of 3-, 9-, and 12-month-old mice, the septum of 6-month-old mice, and the Hb of 3-, 9-, and 12-month-old were collected from 5xFAD mice and WT mice. The samples were cut into small pieces, placed in digestion media (Neurobasal media containing 1 mg/mL Collagenase type 1, 2, 4 (Worthington Biochemical Corp., United States) or papain (Worthington Biochemical Corp., United States), and 20 U/mL of DNaseⅠ (Sigma)), and incubated in a shaking incubator at 37 °C for 45 min. The digested tissues were mechanically dissociated and filtered through a 40 µm cell strainer. The single-cell suspension was centrifuged at 500 g for 15 min at 4°C and the resulting pellet was suspended in ice cold neurobasal media containing B27. This neurobasal media wash was repeated twice with two different spins at 100 g and 200 g centrifugation to remove dead cells and cellular debris. The single-cell suspension was finally suspended in an ice cold Hanks’ balanced salt solution with 0.04 % bovine serum albumin (A3294, Sigma-Aldrich, United States) at approximately 2 ⅹ 105 cells/mL cell population.
The single cells were profiled using inDropTM barcoded beads in a home-made microfluidic device connected to the Drop-seq apparatus in the Korea Brain Research Institute. Libraries from isolated single cells were generated according to the inDropTM Protocol with the following modifications (Zilionis et al., 2017). Amplified cDNAs were not fragmented, and cDNA cleanup and size selection were performed using SPRIselect beads (B23317, Beckman Coulter, United States). Amplified cDNAs and final libraries were assessed on an Agilent BioAnalyzer using the High Sensitivity DNA Kit (Agilent Technologies, United States). The libraries were pooled and sequenced on a NovaSeq 6000 system / a NextSeq500 system at two sequencer companies (Macrogen, Korea / LAS Science, Korea).

value: septum

value: 05 months-old


title: RNA_AKP_Day12_STAR-pos-to-neg_1

tag: time

value: Day 12

value: neg


title: RNA_AKP_Day5_STAR-pos-to-neg_1

tag: star day 0


title: plasma, subject 835b62b9T4

tag: subject id

tag: blood sample id

value: Male

value: Yes

value: Somascan discovery platform v4


title: B_patch_rep2 [Sample_24155]


title: RNA_AKP_Day5_STAR-pos-to-neg_2

value: Day 5

tag: star day 5/12

tag: technical replicate


title: Clone_R Treated S1

tag: cell line

value: Hela

value: TNF


title: plasma, subject 824c6f4fT4

tag: Sex

tag: age

value: Positive


title: T_patch_rep4 [Sample_24159]

tag: strain


title: T_patch_rep2 [Sample_24156]


title: 5xFAD, septum, 5m, replicate 1

description: inDropTM


title: RNA_AKPS_Day12_STAR-pos-to-pos_3

description: STAR+ cells derived from 12-day-old AKPS organoids were sorted and STAR+ cells were collected for bulk RNA-seq.

source_name: AKPS organoid

growth_protocol: Engineered human colorectal cancer organoids (APCKO/KO; KRASG12D/-; TP53KO/KO; SMAD4 KO/KO) were grown from single STAR+ or STAR- cells for 5-12 days in Matrigel (Corning). Growth media was refreshed every 2-3 days. Growth media contained Advanced DMEM/F12 (Invitrogen), supplemented with 10 mM Hepes (Invitrogen), 1% GlutaMAX (Invitrogen), 1% Penicillin-Streptomycin (Lonza) as well as 1x B27 supplement (Invitrogen), 1.25 mM N-Acetyl-L-cysteine (Sigma-Aldrich), 10 mM Nicotinamide (Sigma-Aldrich), 500 nM A83-01 (Tocris), and 10 µM SB202190 (Gentaur).

value: AKPS organoid

value: Colorectal cancer

value: pos


title: WT, septum, 5m, replicate 2

description: inDropTM

value: wild-type


title: plasma, subject 824c6f4fT1

tag: days since first sample

tag: patient classification at first sample

value: No


title: Clone_R Untreated S1

tag: treatment

value: Untreated


title: MCF10A_H1047R_rep1_ATAC

tag: tissue

value: Breast Epithelium


title: plasma, subject 80d7b257T0

tag: covid-19 status

tag: instrument model


title: Pool Treated S5

tag: genotype

value: Pool


title: RNA_AKPS_Day12_STAR-pos-to-pos_2

tag: cell type

tag: time

value: Day 12


title: plasma, subject 80c90ec1T1

tag: subject id

value: Female

value: Negative


title: 5xFAD, habenula, 3m, replicate 2

description: inDropTM

source_name: habenula

value: habenula

value: 03 months-old


title: RNA_AKPS_Day12_STAR-pos-to-pos_1

tag: star day 0


title: Pool Untreated S5


title: plasma, subject 80bfcac2T8

tag: blood sample id

value: Yes

value: Somascan discovery platform v4


title: Pool Treated S4

value: Hela

value: TNF


title: 5xFAD, habenula, 3m, replicate 1

description: inDropTM


title: plasma, subject 80bfcac2T13

value: Positive


title: WT, habenula, 1y, replicate 2

description: inDropTM

value: 12 months-old


title: RNA_AKPS_Day12_STAR-pos-to-neg_3

description: STAR+ cells derived from 12-day-old AKPS organoids were sorted and STAR- cells were collected for bulk RNA-seq.

value: AKPS organoid

value: Colorectal cancer

value: pos

tag: star day 5/12

value: neg

tag: technical replicate


title: Pool Untreated S4

tag: cell line

value: Untreated


title: WT, habenula, 1y, replicate 1

description: inDropTM

tag: age

value: wild-type


title: plasma, subject 80bfcac2T1

tag: Sex

value: No


title: Pool Treated S3

value: Pool


title: RNA_AKPS_Day12_STAR-pos-to-neg_2

value: Day 12


title: plasma, subject 80bfcac2T12

value: Female

tag: days since first sample


title: RNA_AKPS_Day12_STAR-pos-to-neg_1


title: RNA_AKPS_Day12_STAR-neg-to-pos_3

description: STAR- cells derived from 12-day-old AKPS organoids were sorted and STAR+ cells were collected for bulk RNA-seq.


title: WT, habenula, 9m

description: inDropTM

value: habenula

value: 09 months-old

tag: strain


title: RNA_AKPS_Day12_STAR-neg-to-pos_2


title: Pool Untreated S3

tag: treatment


title: WT, habenula, 3m

description: inDropTM

tag: tissue

value: 03 months-old


title: Pool Untreated S2

value: Hela


title: WT, septum, 5m, replicate 1

description: inDropTM

value: septum

value: 05 months-old


title: RNA_AKPS_Day12_STAR-neg-to-pos_1


title: WT, hippocampus, 9m, replicate 3

description: inDropTM

source_name: hippocampus

value: hippocampus


title: Pool Treated S2

value: TNF


title: RNA_AKPS_Day12_STAR-neg-to-neg_3

description: STAR- cells derived from 12-day-old AKPS organoids were sorted and STAR- cells were collected for bulk RNA-seq.

value: AKPS organoid

value: Colorectal cancer


title: plasma, subject 8090b21cT1

tag: patient classification at first sample

tag: covid-19 status

value: Positive

value: Yes

value: Somascan discovery platform v4


title: Pool Treated S1

tag: genotype


title: plasma, subject 808fce87T8

value: Male

tag: instrument model


title: RNA_AKPS_Day12_STAR-neg-to-neg_2

tag: cell type

tag: time

value: neg


title: plasma, subject 808fce87T4

tag: subject id

value: No


title: Pool Untreated S1

value: Pool

value: Untreated


title: WT, hippocampus, 1y, replicate 3

description: inDropTM

value: 12 months-old

value: wild-type


title: plasma, subject 808fce87T1

tag: blood sample id


title: plasma, subject 809e4ed7T1

value: Negative


title: plasma, subject 807d4f28T1

value: Female


title: RNA_AKPS_Day12_STAR-neg-to-neg_1

value: Day 12

tag: star day 0

tag: star day 5/12


title: PDO Day 61

city: Rome

first: Evelina

last: Miele

address: Piazza di Sant'Onofrio 4

department: Oncoematologia

institute: Ospedale Pediatrico Bambino Gesù

data_processing:
Chromium single-cell sequencing raw (FASTQ format) data have been pre-processed for the quantification of gene expression running Cell Ranger 6.1.2 (10X Genomics).
Assembly: GRCh38
Supplementary files format and content: Each sample, once processed using 10X pipeline (cellranger), generate three files (barcodes.tsv.gz.gz, genes.tsv.gz.gz, matrix.mtx.gz.gz)

source_name: PDO harvested at day 61

growth_protocol: Fresh surgically resected tumor samples were disgregated within 24 hours of surgical resection and culured in PDO medium in a 37°C, 5% CO2 incubator (see Methods section for further details)

extract_protocol:
Tumor pieces and PDOs were dissociated with Trypsin, centrifuged, then resuspended in 0.1% BSA in PBS and strained through a 30 µm filter. Cells were then centrifuged and resuspended in freezing medium consisting of PDOs medium supplemented with 10% Fetal Bovine Serum (Gibco, 10270106) and 10% DMSO and placed in cryovials (10X Genomics.com, 2021).
Transcriptome single-cell datasets have been generated using the Chromium Next GEM Single Cell 3´v3.1 (10X Genomics)

value: PDO harvested at day 61


title: RNA_AKPS_Day5_STAR-pos-to-pos_3

description: STAR+ cells derived from 5-day-old AKPS organoids were sorted and STAR+ cells were collected for bulk RNA-seq.

value: Day 5

value: pos

tag: technical replicate


title: PDO Day 28

source_name: PDO harvested at day 28

value: PDO harvested at day 28


title: WT, hippocampus, 3m, replicate 2

description: inDropTM

value: hippocampus

tag: age

value: 03 months-old


title: plasma, subject 8059c147T1

tag: Sex

value: Positive

value: Yes

value: Somascan discovery platform v4


title: RNA_AKPS_Day5_STAR-pos-to-pos_2

value: AKPS organoid

value: Colorectal cancer


title: WT, hippocampus, 9m, replicate 1

description: inDropTM

value: 09 months-old


title: plasma, subject 803c6747T4

tag: days since first sample

value: No


title: WT, hippocampus, 1y, replicate 1

description: inDropTM

value: 12 months-old

tag: strain

value: wild-type


title: Primary tumor #15

source_name: G3 MB fresh tissue

value: G3 MB fresh tissue


title: Unpolarized, rep3 [P3.Up]

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

data_processing:
genome build/assembly: grch38
Human data: Raw fastq was aligned to human reference genome GRCh38 with hisat2 v2.1.0 [1]. Gene wise counts were generated with featureCounts from the subread package v1.5.1 [2] for genes annotated by ensembl Homo_sapiens.GRCh38.101, counting the primary alignment in the case of multimapped reads.
Mouse data: Individual FASTQ files were trimmed for adapter sequences and filtered using fastp v0.20.0. Mouse reference genome GRCm38.p6 and gene annotation described by Gene Transfer Format (GTF) were downloaded from Ensembl release 99 (January 2020). Reads alignment was performed against the reference genome using HISAT2 v2.1.0. Gene expression values for genes were quantified using the featureCounts tool of the Subread package v1.5.0-p2 in unstranded mode.
Supplementary files format and content: human_featurecounts.txt
Supplementary files format and content: mouse_counts.csv

source_name: Bone Marrow

extract_protocol:
RNA was harvested using total RNA purifcation plus kit (Biotek Corp). 200 ng per sample was used for the construction of sequencing libraries.
RNA-Seq libraries were prepared using NEBNext Ultra II directional RNA library prep kit following manufacturer's instruction

treatment_protocol: Both mouse Ly6G+ neutrophils, and human CD34+, bone marrow cells were cultured with media and with cytokines IL-4 and/or G-CSF

value: Bone Marrow

value: Stem Cell


title: plasma, subject 803c6747T20

source_name: serum

value: Female


title: RNA_AKPS_Day5_STAR-pos-to-neg_3

description: STAR+ cells derived from 5-day-old AKPS organoids were sorted and STAR- cells were collected for bulk RNA-seq.

value: Day 5

value: pos

value: neg


title: IL-4+G-CSF, rep3 [P3.L4plusG]


title: WT, hippocampus, 3m, replicate 1

description: inDropTM

value: hippocampus

value: 03 months-old


title: RNA_AKPS_Day5_STAR-pos-to-neg_2


title: IL-4, rep3 [P3.L4]


title: plasma, subject 803c6747T1

value: Positive

value: Yes


title: Isotype

city: los angeles

first: Mandy

last: Cheng

state: CA

address: 615 Charles E Young Dr S

department: MIMG

institute: UCLA

data_processing:
*library strategy: CUT&Tag
fastq files were trimmed to remove low-quality reads and adapters using Cutadapt (version 2.3)
The reads were aligned to the reference mouse genome (mm10) with bowtie2 (version 2.2.9).
Peak calling was performed with MACS2 (version 2.1.1).
Peaks/regions identified as H3K27me3-bound (H3K27me3 CUT&Tag) were annotated using the annotatepeaks.pl function from the HOMER analysis package.
Supplementary files format and content: bigWig

source_name: Spleen

growth_protocol: StemCell Naïve CD4+ T cell magnetic isolation kit was used to sort the cells from spleens of mice.

extract_protocol:
Genomic DNA from nuclei isolated using
H3K27me3 CUT&Tag

treatment_protocol: Naïve CD4+ T cells were treated with platebound anti-CD3 and soluble anti-CD28 for 48 hours.

value: Spleen

tag: cell line

value: Primary

value: T cell

value: UTX TCD

tag: treatment

value: Anti-CD3/CD28 stimulation for 2 days


title: WT, hippocampus, 9m, replicate 2

description: inDropTM

tag: tissue

value: 09 months-old

value: wild-type


title: RNA_AKPS_Day5_STAR-pos-to-neg_1

value: AKPS organoid

value: Colorectal cancer


title: plasma, subject 7ff326e0T21

value: Male

tag: patient classification at first sample

tag: covid-19 status

value: No

value: Somascan discovery platform v4


title: WT, hippocampus, 1y, replicate 2

description: inDropTM

value: 12 months-old

tag: genotype


title: G-CSF, rep3 [P3.G]

value: Bone Marrow

tag: cell type

value: Stem Cell


title: RNA_AKPS_Day5_STAR-neg-to-pos_2

description: STAR- cells derived from 5-day-old AKPS organoids were sorted and STAR+ cells were collected for bulk RNA-seq.

tag: time

value: Day 5

value: neg

value: pos


title: H3K27me3_UTX TCD - 3

value: Spleen

value: Primary


title: Unpolarized, rep2 [P2.Up]


title: plasma, subject 7ff326e0T20

tag: subject id

value: Positive

value: Yes

tag: instrument model


title: H3K27me3_UTX TCD - 2

value: T cell

value: UTX TCD

value: Anti-CD3/CD28 stimulation for 2 days


title: IL-4+G-CSF, rep2 [P2.L4plusG]


title: plasma, subject 7ff326e0T12

tag: blood sample id


title: plasma, subject 7ff326e0T1


title: RNA_AKPS_Day5_STAR-neg-to-pos_1

value: AKPS organoid

value: Colorectal cancer

tag: star day 0

tag: star day 5/12


title: H3K27me3_UTX TCD - 1


title: ATAC_AKPS_Day12_STAR-pos-to-pos_3

description: STAR+ cells derived from 12-day-old AKPS organoids were sorted and STAR+ cells were collected for bulk ATAC-seq.

data_processing:
Reads were aligned with BWA mem.
PCR duplicates were removed with picard tools version 1.129.
Reads were further filtered for a quality score of >= 1 and for not mapping to the mitochondrial chromosome.
Accesible sites were identified in each sample with macs2 using a Q value of 0.001. A union of all identified peaks was used for subsequent analyses.
Differential site accessibility was performed with DESeq2 package.
Significantly accessible sites were called after Wald test followed by correction for multiple testing (Benjamini-Hochberg method).
Data visualisation was performed upon normalisation, log2 transformation, and noise-stabilisation using the rlogTransformation function of the DESeq2 package.
Assembly: hg19
Supplementary files format and content: Single txt file containing read counts per peak of all samples (PCR duplicates have been removed)

extract_protocol:
Cells were lysed and DNA was extracted after performing the transposition reaction with a Tn5 enzyme for 30 min at 37°C. Subsequently, the reaction was stopped through addition of 44 mM EDTA, 131 mM NaCl, 0.3 % SDS, and 600 µg/mL proteinase K. DNA was extracted using the Quiagen MinElute PCR Purification Kit. For further details, please refer to (Lindeboom et al., 2018).
Transposed DNA fragments were amplified using Custom Nextera PCR Primers 1 and 2 together with 10 µl DNA input. Subsequent clean-up was performed using reverse 0.65x SPRI beads (AMPure). An Illumina NextSeq 500 was used for sequencing of 50 bp paired-end reads. For further details, please refer to (Lindeboom et al., 2018).

treatment_protocol: Organoids were harvested with 1 mg/mL Dispase II (Life Technologies) and pelleted by  spinning at 500xg, 4 min, 4°C.  Organoids  were trypsinized to single cells using TrypsinEDTA (Sigma-Aldrich), trypsin activity was blocked with trypsin inhibitor (Sigma-Aldrich) at a 1:1 ratio, and single cells were pelleted by spinning at 500xg, 4min, 4°C. To visualise dead cells on FACS, 1.5 µM DRAQ7 (Cell Signaling Technologies) was added to growth medium containing 10 µM Y-27632 (Gentaur). On FACS, alive cells with STAR expression being positive (pos) or negative (neg) were collected duplicates or triplicates (10,000-20,000 cells each). Samples were pelleted and frozen in Recovery Cell Culture Freezing Medium (Gibco) prior to processing.

value: Day 12

tag: technical replicate


title: RNA_AKPS_Day5_STAR-pos-to-pos_1


title: plasma, subject 7f657e7bT1

description: See https://www.synapse.org/#!Synapse:syn35874390/ for full clinical data and associated metadata including detailed description for process workflow.

extract_protocol: Blood samples were collected in Serum Separation Tubes (SST) with a polymer gel for serum separation as previously described in Del Valle DM, Kim-Schulze S, Huang HH, et al. An inflammatory cytokine signature predicts COVID-19 severity and survival. Nat Med. 2020. Samples were centrifuged at 1200 g for 10 minutes at 20°C. After centrifugation, serum was pipetted to a 15 mL conical tube. Serum was then aliquoted into cryovials and stored at -80°C.

tag: Sex

value: Female

tag: age

value: Somascan discovery platform v4


title: H3K27me3_WT - 3

value: Wild Type


title: H3K27me3_WT - 2


title: ATAC_AKPS_Day12_STAR-pos-to-pos_2


title: H3K27me3_WT - 1


title: plasma, subject 7ef61ea8T1

tag: days since first sample

value: No


title: ATAC_AKPS_Day12_STAR-pos-to-pos_1


title: plasma, subject 7e1cecbdT1


title: ATAC_AKPS_Day12_STAR-pos-to-neg_3

description: STAR+ cells derived from 12-day-old AKPS organoids were sorted and STAR- cells were collected for bulk ATAC-seq.


title: IL-4, rep1 [P1.L4]

value: Bone Marrow

value: Stem Cell