title: DivisionRecorder+ and unmodified memory OT-I T cells

status: Public on Nov 01 2021

city: Amsterdam

first: Kaspar

last: Bresser

address: Plesmanlaan 125

department: Hematopoeisis

country: Netherlands

institute: Sanquin

data_processing:
Raw data were processed by Cell Ranger 3.1.0. Data for both experiments was obtained from replicate sequencing runs (experiment 1: run 5713 and 5744; experiment 2: run 6209 and 6335), replicative files from these replicate runs were pooled prior to processing
Resulting 10x files were combined into a Seurat object in the R environment, and hashtag assignment was performed using HTOdemux
Subsequent analysis was performed using the MetaCell package in the R environment.
Cells that could be ascribed to multiple samples or to no sample (inferred from the detection of multiple or no Hash tags), cells with a transcript (UMI) count lower than 1,500 and cells with a mitochondrial-gene fraction higher than 0.12 were excluded from downstream analysis.
Next, cells were further filtered based on gene counts, setting upper and lower thresholds separately for each sample-batch to control for differences in sequencing depth (gene-count-thresholds: Experiment 1 [1,200-3,000], experiment 2 batch 1 [800 -2,500], experiment 2 batch 2 [1,000-3,000]).
Clustering was performed using MetaCell
Genome_build: mm10-3.0.0
Supplementary_files_format_and_content: imm_genes.txt: Immune related genes used for analyses within the manuscript.
Supplementary_files_format_and_content: labeling_ratios.tsv: Normalized RFP over GFP ratios per MetaCell.
Supplementary_files_format_and_content: lfp_table.tsv: gene enrichment values (log2 transformed) for all MetaCells.
Supplementary_files_format_and_content: metacell_objects.tar: relevant output files generated by the MetaCell R package.
Supplementary_files_format_and_content: Metadata_table_DivRec.tsv: Table containing metadata on all cells profiled by scRNAseq.
Supplementary_files_format_and_content: seurat_object_all_exps.rds: Seurat object. All DivRec experiments combined.
Supplementary_files_format_and_content: seurat_object_Exp1.rds: Seurat object. First memory experiment.
Supplementary_files_format_and_content: Experiment1_10x_files.tar: 10x file output from CellRanger. First memory experiment.
Supplementary_files_format_and_content: Experiment2_Batch1_10x_files.tar: 10x file output from CellRanger. Second memory experiment, batch 1.
Supplementary_files_format_and_content: Experiment2_Batch2_10x_files.tar: 10x file output from CellRanger. Second memory experiment, batch 2.
Supplementary_files_format_and_content: seurat_object_Exp2-1.rds: Seurat object. Second memory experiment, batch 1.
Supplementary_files_format_and_content: seurat_object_Exp2-2.rds: Seurat object. Second memory experiment, batch 2.

source_name: Spleen

extract_protocol:
Transcriptomes of DivisionRecorder modified and unmodified OT-I memory T cells were obtained in two independent experiments, comprising 11 mice in total. Experiment 1 included 3 mice containing DR+ memory T cells (mouse 1-3), which were processed in a single batch. Experiment 2 included 4 mice containing DR+ memory T cells (mouse 4-7) and 4 mice containing unmodified memory T cells (mouse 8-11), which were processed in two separate batches (batch 1: mouse 4+5 and mouse 8+9, batch 2:  mouse 6+7 and mouse 10+11). Spleens of DivisionRecorder+ OT-I T cell recipient mice (n=7) or unmodified OT-I T cell recipient mice (n=4) were harvested >85 days post-infection. Splenocytes were stained with fluorochrome-conjugated antibodies directed against CD8, CD45.2 and Vβ5, to allow purification of transferred cells by FACS. DR+ cells were subsequently FACS purified based on their expression of RFP and GFP. Following the isolation of DRGFP and DRRFP memory T cells by FACS, obtained cell populations were barcode-labeled with distinct anti-mouse TotalSeq Hashtag antibodies, and pooled, with an equal number of cells from each mouse to form the total pool of cells for scRNA-sequencing. If the amount of sorted DRRFP cells was limited from a single sample, it was pooled together with another DRRFP sample to reduce cell loss during cell hashing. Single-cell RNA isolation and library preparation was performed according to the manufacturer’s protocol of the 10X Genomics Chromium Single Cell 3’ kit, and the cDNA library was sequenced on a NextSeqTM 550 Sequencing System (Illumina).
Library preperation was performed in according the manufacturer's protocol of the 10X Genomics Chromium Single Cell 3' kit (V3)

tag: strain

value: OT-I

tag: time point

value: >86 days post LM-OVA infection

value: CD8 T cells


title: DivisionRecorder+ memory OT-I T cells

type: SRA

library_source: transcriptomic

data_processing:
Raw data were processed by Cell Ranger 3.1.0. Data was obtained from two separate sequencing runs (run 5713 and 5744), replicative files from these two runs were pooled prior to processing
Resulting 10x files were combined into a Seurat object in the R environment, and hashtag assignment was performed using HTOdemux
Subsequent analysis was performed using the MetaCell package in the R environment.
Cells with less than 2000 total UMIs were dropped, hashtag doublets and negatives were removed, cells with more than 2000 genes were considered doublets and were removed.
Clustering was performed using MetaCell
Genome_build: mm10-3.0.0
Supplementary_files_format_and_content: imm_genes.txt: Immune related genes used for analyses within the manuscript.
Supplementary_files_format_and_content: labeling_ratios.tsv: Normalized RFP over GFP ratios per MetaCell.
Supplementary_files_format_and_content: lfp_table.tsv: gene enrichment values (log2 transformed) for all MetaCells.
Supplementary_files_format_and_content: metacell_objects.tar: relevant output files generated by the MetaCell R package.
Supplementary_files_format_and_content: Metadata_table_DivRec.tsv: Table containing metadata on all cells profiled by scRNAseq.
Supplementary_files_format_and_content: seurat_object_all_exps.rds: Seurat object. All DivRec experiments combined.
Supplementary_files_format_and_content: seurat_object_Exp1.rds: Seurat object. First memory experiment.
Supplementary_files_format_and_content: Experiment1_10x_files.tar: 10x file output from CellRanger. First memory experiment.
Supplementary_files_format_and_content: Experiment2_Batch1_10x_files.tar: 10x file output from CellRanger. Second memory experiment, batch 1.
Supplementary_files_format_and_content: Experiment2_Batch2_10x_files.tar: 10x file output from CellRanger. Second memory experiment, batch 2.
Supplementary_files_format_and_content: seurat_object_Exp2-1.rds: Seurat object. Second memory experiment, batch 1.
Supplementary_files_format_and_content: seurat_object_Exp2-2.rds: Seurat object. Second memory experiment, batch 2.

molecule: total RNA

organism: Mus musculus

extract_protocol:
Spleens were collected from 3 mice, homogenized to a single cell suspension, treated with NH4Cl to lyse erythrocytes, and DivisionRecorder+ OT-I T cells (CD8+CD45.2+GFP+) were isolated by FACS. RFP+ and RFP- T cells were separately sorted, stained with sample hashtags individually, and subsequently pooled into a single sample. Library preperation was performed in according the manufacturers protocol of the 10X genomics Chromium Single Cell 3' kit. Sequencing was performed on Next-Seq550 (Illumina)
Library preperation was performed in according the manufacturer's protocol of the 10X Genomics Chromium Single Cell 3' kit (V3)

value: 86 days post LM-OVA infection

tag: cell type


title: 2-Adipo-Late-rep2

status: Public on Dec 06 2021

type: RNA

city: Chicago

first: Matthew

last: Piron

state: IL

address: 900 E 57th St. KCBD 8230A

country: USA

institute: University of Chicago

description:
Subject2
SAMPLE 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with GenomeStudio software

label: biotin

organism: Homo sapiens

source_name: Adipose tissue biopsy

label_protocol: Biotinylated cRNA were prepared with Illumina prep kits

extract_protocol: Total RNA obtained from SubQ adipose biopsy under early or late eating protocols.

tag: Sex

value: Male

tag: mean age

value: 32 yr

tag: tissue

value: subcutaneous adipose tissue

tag: protocol

value: late eating


title: 1-Adipo-Late-rep1

description:
Subject1
SAMPLE 3

value: Female

value: 35 yr


title: 1-Adipo-Early-rep2

description:
Subject1
SAMPLE 2

tag: age

value: early eating


title: T24-S1

status: Public on Oct 22 2021

city: Guangzhou

first: Ming

last: Huang

address: Yanjiang West Road

country: China

institute: Sun Yat-sen Memorial Hospital

data_processing:
Base-calling: Base-calling using bcl2fastq2 v2.19.1 with -r 4 -p 16 -w 4  --barcode-mismatches 0
Data filtering : Adaptor contamination was remove from reads (the number of bases contaminated by the adaptor in reads is greater than 5bp. For pair-end sequencing, if one end is contaminated by the adaptor, the Reads at both ends are removed)；Remove low-quality reads (Reads with more than 50% of the total bases are bases with a mass value of Q ≤ 19 . For pair-end sequencing, if one pair is low-quality reads, the both reads will be removed)；Remove the reads with N rate greater than 5%  (For pair-end sequencing, if one pair contains more than 5% N, the both reads will be removed)
Read alignment: Fastq reads were mapped to genome using hisat2 v2.1.0 with default parameters
transcript assemble: Reads count of echo gene was calculated using htseq-count v0.6.1 with -t exon -f bam -s no -a 10
Genome_build: hg19(ftp://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.toplevel.fa.gz)
Supplementary_files_format_and_content: excel files include normalize values for each Sample

source_name: bladder cancer cell line T24

growth_protocol: T24 was cultured in RPMI-1640 (Gibco) supplemented with 10% FBS (Biological Industries) and 1% penicillin/streptomycin (Gibco). Cells were grown in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using Trizol reagent and was further purified using Qiagen RNeasy Mini Kit according to the manufactures’ instructions. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1 OD SiRNA was  diluted at a stocking solution of 125 μL in sterile DEPC-treated water, and cells were treated for 48h with 5 μL of SiRNA.

tag: cell line

value: bladder cancer cell line T24

tag: treatment

value: 0.04 OD Si-RNA-1


title: T24-NC

value: Negative control


title: 3-Adipo-Late-rep1

description:
Subject3
SAMPLE 12

value: 27 yr


title: 2-Adipo-Early-rep1

description:
Subject2
SAMPLE 4


title: 2-Adipo-Late-rep1

description:
Subject2
SAMPLE 5


title: 1-Adipo-Early-rep1

description:
Subject1
SAMPLE 1


title: Myeloid cells from young and aged mouse lungs

status: Public on Oct 20 2021

city: New Brunswick

first: Qi

last: Yang

state: NJ

address: 89 French St

institute: Rutgers RWJMS

data_processing:
Library was generated using chromium 5' gene expression kit (10x genomics)
Reference genome human (mm9) was used to read alignment and gene expression quantification using Cellranger v3.0.2 pipelines
The Cellranger pipelines include Cellranger mkfastq, Cellranger count, Cellranger Aggr, and Cellranger reanalyze pipelines.
These pipelines combine Chromium specific algorithms with RNA-seq aligner STAR.
Genome_build: mm9
Supplementary_files_format_and_content: mtx and tsv for processed data

source_name: Sorted myeloid cells from young and aged mouse lung

extract_protocol:
Myeloid cells from lungs of young and aged mice were sorted based on their surgace marker expressions. Total RNA extracted following the instructions of the 10X genomics kit
RNA seq libraries were prepared using the 5' single cell gene expression kit (10x genomics) according to the manufacturer's instructions.

treatment_protocol: Untreated CD45+ CD11b+ Gr1+ cells sorted from lungs of young (2-3 months old) and aged (20-22 months old) female mice. Cells from young mice were labeled with Biolegend TotalSeq-C0951 (Barcode sequence AACCTTTGCCACTGC), and cells from aged mice were labeled with Biolegend TotalSeq-C0952 (Barcode sequence GTCCGACTAATAGCT)

value: lung

value: myeloid cells

value: mixed sample (non-demultiplexed) representing young and aged

value: Untreated


title: T24-S2

value: 0.04 OD Si-RNA-2


title: CD45+ CD11b+ Gr1+ sorted cells from lungs of aged mice treated with Isotype control antibody

data_processing:
Library was generated using chromium 5' gene expression kit (10x genomics)
Reference genome mouse (mm9) was used to read alignment and gene expression quantification using Cellranger v3.0.2 pipelines
The Cellranger pipelines include Cellranger mkfastq, Cellranger count, Cellranger Aggr, and Cellranger reanalyze pipelines.
These pipelines combine Chromium specific algorithms with RNA-seq aligner STAR.
Genome_build: mm9
Supplementary_files_format_and_content: mtx and tsv for processed data

extract_protocol:
CD45+ CD11b+ Gr1+ (monocytes and neutrophils) cells from lungs of mice were sorted based on their surface marker expressions. Total RNA extracted following the instructions of the 10X genomics kit
RNA seq libraries were prepared using the 5' single cell gene expression kit (10x genomics) according to the manufacturer's instructions.

treatment_protocol: Aged female mice were treated with either Isotype or anti-IFNAR1 antibody for one day or one week (500ug/i.p. injection)

value: Lung myeloid cells (CD45+ CD11b+ Gr1+ cells)

value: Isotype control


title: CD45+ CD11b+ Gr1+ sorted cells from lungs of aged mice treated with anti-IFNAR1, 1 week

description: CD45+ CD11b+ Gr1+ sorted cells from lungs of aged mice treated with anti-IFNAR1 (4 injections, over the course of a week) and sacrificed the day after the last injection

source_name: CD45+ CD11b+ Gr1+ sorted cells from lungs of aged mice treated with 500ug anti-IFNAR1 i.p. 4 times over the course of a week and sacrificed the day after the last injection

value: Anti-IFNAR1, 4 i.p. doses


title: CD45+ CD11b+ Gr1+ sorted cells from lungs of aged mice treated with anti-IFNAR1, 1 day

description: CD45+ CD11b+ Gr1+ sorted cells from lungs of aged mice treated with anti-IFNAR1 once and sacrificed the next day

source_name: CD45+ CD11b+ Gr1+ sorted cells from lungs of aged mice treated with 500ug anti-IFNAR1 once i.p. and sacrificed the next day

value: Anti-IFNAR1, 1 i.p. dose


title: 293T_ORL_rep2_control

status: Public on Oct 15 2021

city: Wuhan

first: Yalun

last: Xie

state: Hubei

address: Ba Yi Road

institute: Wuhan University

data_processing:
Library strategy: m6A-ORL-Seq
Adapter seqeucnes were trimmed by using trim galore.
fastuniq is used to remove PCR duplication. Then use seqtk trimfq '-e 10' and '-b 10' remove random sequences added in library construction.
Clean reads were mapped to genome by using STAR; with parameter "--outFilterMultimapNmax 20 --outFilterMismatchNmax 10". Only the proper pair and uniquely mapped alignments was persisted for the downstream pipelines.
Aligned reads were used for peak calling and enriched regions comparing by exomePeak.
HOMER was used for peak annotation and detection of the sequence motif.
Genome_build: hg38
Supplementary_files_format_and_content: m6A peaks resulting from MeRIP-Seq (IP1/2) and m6A-ORL-Seq (total/mRNA1).

molecule: polyA RNA

source_name: HEK-293T cells

growth_protocol: HEK-293T cells were cultured in DMEM medium without sodium pyruvate (Dulbecco’s Modified Eagle Medium, HyClone) supplemented with 10% FBS (Cegrogen) and 1% penicillin/streptomycin (Genview). The cells were maintained at 37 °C under a humidified atmosphere containing 5% CO2.

extract_protocol: Chemical treated RNA was first subjected to end repair by T4 PNK, 3′-adapter ligation (3′ adapter, /5rApp/NNNNNNTGGAATTCTCGGGTGCCAAGG/3ddC/) followed by the 3′ adapter removing by 5′-deadenylase and RecJf digestion. After purification, SuperScript III was used to perform RT (RT primer, /ACACGACGCTCTTCCGATCT). After cDNA synthesis, 5′ adapter (5′ adapter, /5Phos/NNNNNNNNNNAGATCGGAAGAGCACACGTCTG/3ddC/) ligation were performed. After purification, qPCR was performed to evaluate the cycle numbers of each samples to avoid over-amplification. Library PCR amplification was performed using the NEB primers. The products were purified by NEBNext Sample Purification Beads or low melting point agarose gel and used for sequencing.

treatment_protocol: Total RNA was isolated from HEK-293T with TRIzol (Invitrogen) according to the manufacture’s protocol. The poly A+ RNA was isolated by subjecting total RNA to oligo(dT) enrichment using Dynabeads Oligo(dT)25 (NEB) and gDNA was removed by TURBO DNase (Invitrogen). Purified poly A+ RNA was fragmented using RNA fragmentation reagents (Ambion) at 70 °C for 8-15 min.  For MeRIP samples, fragmented RNA was reserved as MeRIP input sample, fragmented RNA was incubated with anti-m6A antibody and then eluted to get the MeRIP IP sample. For m6A-ORL samples, fragmented RNA was stepwise incubated with NO/O2, TDO, probe BA. A portion of biotinylated RNA (or untreated fragmented RNA) was reserved as m6A-ORL input sample, the left RNA was enriched by streptavidin-coated beads and then eluted by DTT to get m6A-ORL IP sample. All the input and IP samples were subjected to RNA-Seq.

value: Fragmented RNA was stepwise incubated with NO/O2, TDO, probe BA. A portion of biotinylated RNA was reserved as m6A-ORL input sample.

tag: sample type

value: input


title: 293T_MeRIP_rep1_treated

data_processing:
Adapter seqeucnes were trimmed by using trim galore.
fastuniq is used to remove PCR duplication. Then use seqtk trimfq '-e 10' and '-b 10' remove random sequences added in library construction.
Clean reads were mapped to genome by using STAR; with parameter "--outFilterMultimapNmax 20 --outFilterMismatchNmax 10". Only the proper pair and uniquely mapped alignments was persisted for the downstream pipelines.
Aligned reads were used for peak calling and enriched regions comparing by exomePeak.
HOMER was used for peak annotation and detection of the sequence motif.
Genome_build: hg38
Supplementary_files_format_and_content: m6A peaks resulting from MeRIP-Seq (IP1/2) and m6A-ORL-Seq (total/mRNA1).

value: Fragmented RNA was incubated with anti-m6A antibody and then eluted to get the MeRIP IP sample.

value: IP


title: Aged lung, biological replicate 3

description: Gene expression data from resected left lung lobe tissue from an old (20-22 months old) female C57BL/6 mouse.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 2.0 ST for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez-Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray mogene20stmmentrezgcdf R package (version 17.0.0).

source_name: resected left lung lobe tissue

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: Lungs from young (2-3 months old) or aged (20-22 months old) untreated female C57BL/6 mice

extract_protocol: RNA was purified from snap frozen lung tissue using TRIzol following the manufacturer's instructions.

value: female

value: Aged


title: Young lung, biological replicate 2

description: Gene expression data from resected left lung lobe tissue from a young (2-3 months old) female C57BL/6 mouse.

value: Young


title: Young lung, biological replicate 3


title: 28C_csp1_2

status: Public on Oct 10 2021

city: Parlier

first: Lindsey

last: Burbank

state: California

address: 9611 S Riverbend Ave

institute: USDA-ARS

data_processing:
Guppy, A neural network basecaller that converts Nanopore electronic raw signal from sequencer into bases.
Deepbinner, A signal-level demultiplexer for Oxford Nanopore reads.
Porechop, An adapter trimmer for Oxford Nanopore reads.
Minimap2, A pairwise reads aligner for genomic and spliced nucleotide sequences
Salmon, A transcript quantification tool for RNA-Seq data
Tximport, Imports transcript-level estimates and summarizes abundances, counts, and transcript lengths to the gene-level
DESeq2, Provides methods to test for differential gene expression based on the negative binomial distribution
Supplementary_files_format_and_content: tab-delimited text files including gene ID and transcipts per million (TPM) values for each sample.

organism: Xylella fastidiosa subsp. fastidiosa

source_name: In vitro bacteria culture

extract_protocol:
Bacteria cells were scraped off PD3 agar plates and flash frozen on dry ice. RNA was purified using Trizol reagent. Oxford Nanopore direct cDNA sequencing kit was was used with  250ng of rRNA depleted RNA for the construction of sequencing libraries.
Nanopre direct cDNA sequencing library

value: Stag's Leap

tag: genotype

tag: growth temperature

value: 7 days post inoculation


title: Aged lung, biological replicate 2

value: lung


title: 28C_csp1_1


title: Young lung, biological replicate 1


title: 293T_ORL_rep1_treated

value: Fragmented RNA was stepwise incubated with NO/O2, TDO, probe BA. The biotinylated RNA was enriched by streptavidin-coated beads and then eluted by DTT to get m6A-ORL IP sample.


title: 293T_ORL_rep1_control


title: Aged lung, biological replicate 1


title: 293T_MeRIP_control

value: Fragmented RNA was reserved as MeRIP input sample.


title: 293T_ORL_rep2_treated


title: 28C_WT_1

value: wild type


title: 28C_csp1_3


title: 28C_WT_2


title: Placenta Slc6a4-KO rep2 [S4]

status: Public on Oct 04 2021

city: Columbia

first: Cheryl

middle: S

last: Rosenfeld

state: MO

address: 1201 Rollins Street

department: BIOMEDICAL SCIENCES

institute: University of Missouri.edu

data_processing:
Illumina Casava1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to grcm38 whole genome using HISAT2 (v2.0.5).
The number of reads that aligned to each protein-coding gene were counted with the featureCount tool from Subread software suite (v2.0.1, Liao Y, Smyth GK, Shi W. Bioinformatics. 2014)
Genome_build: grcm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Placenta Slc6a4-KO

extract_protocol:
Placenta samples were collected, flash frozen in liquid nitrogen, and RNA was isolated using Qiagen AllPrep DNA/RNA/miRNA Universal Kit (Catalogue #80224; Qiagen, Germantown, MD). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: genotype/variation

value: embryo day 12.5

value: Placenta


title: Placenta WT rep2 [S3]

source_name: Placenta WT

value: Wild type


title: Placenta Slc6a4-KO rep3 [S6]


title: Placenta WT rep3 [S5]


title: E10 posterior trunk ChIP CTCF

status: Public on Oct 05 2021

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

country: Switzerland

institute: EPFL

description: ChIP

library_source: genomic

data_processing:
All scripts are available on https://github.com/lldelisle/scriptsForAmandioEtAl2021
TrueSeq adapters were removed from single-reads fastqs with cutadapt version 1.16 (Martin 2011 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -q 30 -m 15).
Filtered reads were mapped to the mouse genome mm10 with bowtie2 version 2.3.5 (Langmead et al. 2012 with default options). Only alignments with a mapping quality above 30 were kept (samtools version 1.9 Danecek et al. 2021).
Peak calling was run with a fixed fragment size of 200bp with macs2 callpeak version 2.1.1.20160309 (--call-summits --nomodel --extsize 200 -B).
Finally the coverage were normalized to the million unique tags.
Genome_build: mm10
Supplementary_files_format_and_content: bw: normalized coverage track
Supplementary_files_format_and_content: narrowPeak: narrowPeak from macs2

molecule: genomic DNA

source_name: Posterior embryonic trunk

extract_protocol:
For the posterior trunk sample, the portion corresponding to the tailbud, presomitic mesoderm, and 2-3 somite pairs, excluding as much as possible the region of the evaginating hindlimb buds, was micro-dissected from approximately thirty E9.75-E10 embryos. For the brain sample, a pool of six micro-dissected telencephalons from E12.5 embryos was used. CTCF ChIP-seq experiments were performed as described in (Rodríguez-Carballo et al 2017).
Libraries were prepared as described in Rodríguez-Carballo et al., 2017

tag: developmental stage

value: Posterior embryonic trunk

value: WT

tag: chip antibody

value: CTCF (Active Motif #61311)


title: Placenta Slc6a4-KO rep1 [S2]


title: 293T_MeRIP_rep2_treated

value: Fragmented RNA was incubated with anti-m6A antibody and then eluted to get the MeRIP IP sample.


title: Placenta WT rep1 [S1]


title: MB002_rep2

city: Shanghai

first: Yujie

last: Tang

address: 280 South Chongqing Road

department: Pathophysiology

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
RNA-seq data sets were mapped to the reference genome of human (GRCh38) using STAR v2.7
Aligned reads were assigned to genes using GENCODE annotations from (gencode.vM20.primary_assembly.annotation.gtf; downloaded in January 2019) and featureCounts (subread version 1.5.2)
The value of fragments per kilobase of transcript per million read pairs (FPKM) was computed by StringTie
Differentially expressed genes (DEGs) were calculated using DESeq2
Supplementary_files_format_and_content: Matrix table with raw gene counts and FPKM for every expressed gene and every sample

source_name: Group 3 subtype Medulloblastoma cell

growth_protocol: MB002 and HDMB03 were cultured in Tumor Stem Media (TSM) comprising DMEM/F12 (11330-032, Gibco), Neurobasal(-A) (10888-022, Gibco), B27(-A) (12587-010, Gibco), human EGF (20 ng/ml, 100-15, PeproTech, NJ, USA), human FGF-basic (20 ng/ml, 100-18B, PeproTech), human LIF (10 ng/ml, 300-05, PeproTech), 0.2% Heparin Solution (10 ng/ml, 07980, Stem Cell Technology), and 1×Antibiotic-Antimycotic (15240-062, Gibco).D425 and UW228 were cultrued in DMEM (BI-01-052-1ACS, Biological Industries) supplemented with 10% fetal bovine serum (FBS, F2442, Sigma)

extract_protocol:
Total RNA was extracted with TRIzol Reagent (Thermo Fisher Scientific, 15596-026) according to the manufacturers’ protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: JQ1, THZ1 or lentivirus treatment as previous description

value: untreated

value: Group 3 subtype Medulloblastoma cell


title: MB002_rep1


title: JKD6008 pSD-1::sRNA275 CRISPRi knock-down RNA-seq (3ug/ml vancomycin for 10 mins ) replicate 1

status: Public on Sep 14 2021

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

description: CRISPRi_275_vs_pSD_DESeq2.xls,  2021.03.16_MUTvsWT.DEseq2_combined_output.xlsx,  meta.xls  pSD275v_pSDv_DESeq2.xls

data_processing:
Trimming - BBTrim from BBTools
RNase III-CLASH: Merging paired reads: BBMerge from BBTools
RNase III-CLASH: Calling RNase III binding sites: pyCRAC (Webb et al Genome Biol 2014)
RNase III-CLASH: Calling RNA-RNA interactions: hyb (Travis et al Bioinformatics 2013)
dRNA-seq: Mapping, calling RNA 5' ends: ANNOgesic (Yu, Vogel, Forstner Gigascience, 2018)
Term-seq: Read mapping/alignment: bowtie2
Term-seq: 3' end mapping: bedtools genomecov
Term-seq: Statistical filtering: Custom R scripts inspired by Dar & Sorek Science 2016.
RNA-seq: Read mapping/alignment: bowtie2
RNA-seq: Statistical analysis: DESeq2 (Bioconductor)
Genome_build: NC_017341.1
Genome_build: NZ_LR027876.1
Supplementary_files_format_and_content: BEDGRAPH format, files contain mapped read depth representing RNase III-RNA interaction sites (binding sites)
Supplementary_files_format_and_content: BEDGRAPH, RNA 3' end depth (reverse complement read 5' ends)

organism: Staphylococcus aureus subsp. aureus str. JKD6009

source_name: whole bacterial cells

growth_protocol: Muller-Hinton media, grown at 37C to an OD600 of 3.0

extract_protocol:
Total RNA was extracted using a GTC Phenol extraction protocol (Tollervey and Mattaj, EMBO J 1987)
Total RNA-seq libraries were constructed by NovoGene.

treatment_protocol: 3ug/ml vancomycin for 10 mins at OD600 where indicated | 10ug/ml chloramphenicol was added to cultures with pSD-1 and derivatives

tag: growth media

value: Muller-hinton broth

tag: antibiotic

value: 3 ug/ml vancomcyin for 10min, chlorampenicol plasmid selection

value: pSD-1::sRNA275 sgRNA

tag: sequencing type

value: RNA-seq


title: JKD6009 dRNA-seq TEX- sample

extract_protocol:
Total RNA was extracted using a GTC Phenol extraction protocol (Tollervey and Mattaj, EMBO J 1987)
Libraries were contructed at Veritis Biotechnology, Germany using the protocl described by Sharma et al Nature 2010

value: Muller-Hinton broth

value: no antibiotic

value: dRNA-seq


title: JKD6009 dRNA-seq TEX+ sample


title: JKD6008 pSD-1::sRNA275 CRISPRi knock-down RNA-seq (3ug/ml vancomycin for 10 mins ) replicate 2


title: JKD6008 pSD-1::sRNA275 CRISPRi knock-down RNA-seq (no vancomycin ) replicate 2

value: chloramphenicol plasmid selection


title: Δrok rep2 - IPOD RNA-pol ChIP

status: Public on Oct 01 2021

city: Ann Arbor

first: Lydia

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr., MSRB 3 room 3315

department: Biological Chemistry

institute: University of Michigan

data_processing: Supplementary_files_format_and_content: For all summary/processed files, note that we provide one file per experimental condition, which represents a consolidation of all replicates for that condition, as described in the accompanying manuscript. Ipod_vs_inp.gr files – Raw IPOD occupancy traces prior to ChIP subtraction, given as a log_2 ratio of extracted to input. The .gr file extension refers to a simple graph type, where the first column indicates a genomic position and the second a corresponding signal chip_vs_inp.gr files – RNA polymerase occupancy given as a log_2 ratio of extracted to input V6rzlog10p.gr files – ChIP-subtracted IPODHR occupancy, z-scored and then used to calculate enrichment p values as described in the text. Tsv files – differential expression calling from sleuth

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Culture lysate

extract_protocol:
DNA samples: Frozen cell pellets were resuspended in 1x IPOD lysis buffer (10 mM Tris HCl, pH 8.0; 50 mM NaCl) containing 1x protease inhibitors (Roche Complete Mini, EDTA free) and 52.5 kU/mL of ready-lyse (Epicentre); 600 uL per pellet (stationary phase cells were diluted 10x prior to lysis due to the much higher biomass of those pellets). We incubated the resuspended pellet for 15 minutes at 30 C, and then placed it on ice. We then sonicated the cells using a Branson digital sonicator at 25% power, using three 10 second bursts with 10 second pauses between bursts. The cells were maintained in a wet ice bath throughout sonication. We then performed a calibrated DNA digestion to sub-200 bp fragments, by adding to the sonicated lysates 60 ug RNase A (Thermo Fisher), 6 uL DNase I (Fisher product #89835), 5.4 uL 100 mM MnCl2, and 4.5 uL 100 mM CaCl2, and then incubating on ice. While the appropriate digestion time must be calibrated for each particular sample type and batch of DNase, 30 minutes of digestion proved appropriate for all samples here. Reactions were quenched after completion by the addition of 50 uL 500 mM EDTA (pH 8.0), typically yielding 50-200 bp fragments. Samples were clarified by centrifugation for 10 minutes at 16,9000xg at 4 C. After clarification, the lysate was mixed with 1 volume of 100 mM Tris base and 2 volumes of 25:24:1 phenol:chloroform:isoamyl alcohol, vortexed, and then incubated for 10 minutes at room temperature. After incubation, the sample was spun at 21,130xg for two minutes at room temperature, allowing formation of a white disc at the aqueous-organic interface enriched for protein-DNA complexes. The complete aqueous phases were removed and discarded, and the remaining disc washed again with 350 microliters TE (10 mM Tris, pH 8.0; 1 mM EDTA), 350 microliters 100 mM Tris base, and 700 microliters 24:1 chloroform:isoamyl alcohol. The resulting mixture was vortexed vigorously, and again centrifuged for 2 minutes at 21,130xg. All liquid was again removed, and the wash was repeated using 700 microliters TE and 700 microliters 24:1 chloroform:isoamyl alcohol. After vortexing, centrifugation, and removal of the final wash (exactly as above), any residual liquid was removed by wicking with a laboratory wipe (if any substantial pools of liquid were present). Finally, the interface was resuspended in 500 microliters of elution buffer (described above), vortexed vigorously, and reverse crosslinked overnight at 65 C. After allowing the samples to cool to room temperature, we then added 100ug of RNase A (Thermo-Fisher), incubated 2 hours at 37 C, then added 200ug of proteinase K (Fermentas) and incubated an additional 2 hours at 50 C. DNA was then recovered via standard phenol-chloroform extraction and ethanol precipitation, following protocols from (Ausubel, 1998). We used Glycoblue (Ambion) as a co-precipitant, NaCl as a precipitating salt (due to the presence of SDS in our solution), and washed with ice-cold 95% ethanol to avoid loss of low molecular weight DNA. RNA: RNA was harvested using Qiagen RNAProtect. RNA was isolated, and rRNA depletion was performed according to the Illumina Ribo-Zero rRNA Removal Kit for Bacteria.
DNA samples: NEB Nebnext Ultra 2 DNA kit, but with a spin column replacing the first bead cleanup (see the accompanying paper for details).

tag: strain

value: {delta}rok

tag: media

value: Lysogeny broth (LB)

tag: time of harvest

value: logarithmic phase


title: JKD6008 pSD-1::sRNA275 CRISPRi knock-down RNA-seq (3ug/ml vancomycin for 10 mins ) replicate 3


title: JKD6008 pSD-1 empty vector control RNA-seq (3ug/ml vancomycin for 10mins) replicate 2


title: JKD6008 pSD-1 empty vector control RNA-seq (no vancomycin ) replicate 3


title: JKD6008 pSD-1 empty vector control RNA-seq (no vancomycin ) replicate 1


title: MB-6-E-Rep2

data_processing:
Alignments made using Illuminca web App: RNA-Seq Alignment using the STAR protocol
Diff. Expression data was generated using Illiumina webbased App: RNA-Seq Differential Expresion using DESq2
Genome_build: hg19
Supplementary_files_format_and_content: text file (tab-delimited)

extract_protocol:
RNA-solv via Omega Bio-tek RNA Kit II
Contact Uchicago genomics core http://fgf.uchicago.edu/index.php
mRNA directional

tag: gender

value: Female

value: 58 yr

tag: tissue

value: subcutaneous adipose tissue

tag: protocol

value: early eating


title: JKD6008 ∆sRNA275 (∆vigR) RNA-seq (3ug/ml vancomycin for 10mins) replicate 2

value: 3ug/ml vancomcyin for 10 mins

value: [delta]sRNA275 ([delta]vigR 3'UTR)


title: JKD6008 ∆sRNA275 (∆vigR) RNA-seq (3ug/ml vancomycin for 10mins) replicate 3


title: JKD6008 pSD-1::sRNA275 CRISPRi knock-down RNA-seq (no vancomycin ) replicate 3

value: Muller-hinton broth


title: JKD6008 WT RNA-seq (3ug/ml vancomycin for 10mins) replicate 3

value: WT


title: JKD6008 pSD-1 empty vector control RNA-seq (3ug/ml vancomycin for 10mins) replicate 1

value: 3 ug/ml vancomcyin for 10min, chlorampenicol plasmid selection


title: JKD6008 WT RNA-seq (3ug/ml vancomycin for 10mins) replicate 1

value: RNA-seq


title: JKD6008 WT RNA-seq (3ug/ml vancomycin for 10mins) replicate 2

value: Muller-Hinton broth


title: JKD6008 ∆sRNA275 (∆vigR) RNA-seq (3ug/ml vancomycin for 10mins) replicate 1


title: JKD6008 ∆sRNA275 (∆vigR) RNA-seq (no vancomycin) replicate 2

value: no antibiotic


title: JKD6008 pSD-1::sRNA275 CRISPRi knock-down RNA-seq (no vancomycin ) replicate 1

value: pSD-1::sRNA275 sgRNA


title: JKD6008 ∆sRNA275 (∆vigR) RNA-seq (no vancomycin) replicate 3


title: JKD6008 WT RNA-seq (no vancomycin) replicate 3


title: JKD6008 WT RNA-seq (no vancomycin) replicate 2


title: JKD6008 WT RNA-seq (no vancomycin) replicate 1


title: 203524200078_R06C01: AS

status: Public on Sep 01 2021

type: genomic

city: Basel

first: Juergen

last: Hench

state: BS

address: Schoenbeinstr. 40

department: Pathology

institute: University Hospital Basel

hyb_protocol: Illumina default

scan_protocol: Illumina default

data_processing:
Minfi (R 3.6.3), Conumee (R 3.6.3), www.epidip.org
The algorithm to process the data is our online tool (www.epidip.org), and the raw data are/were processed by this platform on an ad-hoc basis. EpiDiP is our free, publicly available unsupervised machine learning tool (UMAP-based) that cross-compares all submitted methylation datasets (450K/850K). The tool requires raw IDAT files only. All conclusions made in this study are based on UMAP results and copy number plots, also generated in EpiDiP. The employed R version (for minfi/conumee) is specified in the metadata. As a consequence, no normalized data are included.

label: Cy3, Cy5

source_name: tumor

label_protocol: Illumina default

extract_protocol: Promega FFPE DNA extraction kit for both FFPE and native samples

value: female

tag: tissue source

value: DNA FFPE

value: breast tumor

tag: tumor type

value: AS


title: JKD6008 pSD-1 empty vector control RNA-seq (3ug/ml vancomycin for 10mins) replicate 3

tag: genotype


title: JKD6008 pSD-1 empty vector control RNA-seq (no vancomycin ) replicate 2

value: chloramphenicol plasmid selection


title: Liver, Control, rep1

city: Muenster

first: Marcos

middle: J.

last: Araúzo-Bravo

address: Rogentstrasse

department: Cell and Developmental Biology

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description: replicate 1

data_processing:
The proprietary 10x Genomics CellRanger pipeline (v4.0.0) was used with default parameters except for the setting of expected cells (expect-cells 2500, 7500).
mkfastq command was used to demultiplex the data from the raw BCL sequencer images, given the supplied sample sheet with the utilized 10x barcodes to produce Standard fatq files and 10x specific metadata.
CellRanger was used to align read data to the reference genome provided by 10x Genomics (Mouse reference dataset refdata-gex-mm10-2020-A) using the aligner STAR.
Standard procedures for filtering, variable gene selection, dimension reduction and clustering were performed using the Scanpy toolkit version 1.6.0 (Wolf et al., 2018).
Cells with fewer than 200 detected genes were excluded. A gene was counted as expressed if it was detected in at least 3 cells. Genes with too many total counts (>20,000) were also removed.
For each cell we computed the fraction of counts in mitochondrial genes vs all genes and filtered out the cells with this fraction greater than 0.05.
The data matrix was total-count normalized (library-size corrected) to 10,000 reads per cell, so that counts became comparable among cells, and stabilized by computing the the natural logarithm of one plus the counts for each cell.
For feature selection we filtered the highly variable genes, remaining finally with a data matrix with 13,880 cells and 2,650 genes.
Each gene was scaled to unit variance and values exceeding standard deviation 10 were clipped.
For dimension reduction we used the the Principal Component Analysis (PCA) that reveals the main axes of variation and denoises the data, and the Uniform Manifold Approximation and Projection for Dimension Reduction (UMAP).
Genome_build: mm10 mouse
Supplementary_files_format_and_content: Sharma-adata_raw_x-10clusters.csv file includes counts values for each sample
The barcode-1-0 rows correspond with Control
The barcode-1-1 rows correspond with HNF4A

source_name: Control

growth_protocol:
8-12 weeks old male BALB/c mice for the experiments were obtained from the central animal facility of Hannover Medical School.
The experiments were performed according to the regulations of the Institutional Animal Care and Use Committee of the
Hannover Medical School, Germany (Protocol number: TVA 17/2658).
Liver fibrosis mouse models were established by either injecting 4µl/g 10% CCl4/olive oil into BALB/c mice,
twice a week for 8 weeks (fibrosis) and 16 weeks (cirrhosis), or fed with the DDC diet consistently for six weeks.
12-16 week old multidrug resistance 2 knockout mice (Mdr2-/-), a mouse ortholog of human MDR3
(also known as ATP binding cassette subfamily B member 4) on FVB background were used as a model of progressive familial intrahepatic cholestasis.
Mouse primary hepatocytes were isolated via liver perfusion with Liberase (Roche) and subsequently purified by Percoll density gradient centrifugation.
0.5 million-mouse hepatocytes were seeded per well of collagen-coated 12-well plates.
Four hours after seeding, the DMEM medium supplemented with 10% FBS was changed to hepatocyte culture medium (Lonza).
Primary human hepatocytes were purchased from Primacyt Cell Culture Technology Gmbh (Schwerin, Germany).

extract_protocol:
After liver perfusion and Percoll-density gradient centrifugation,
alive cells were enriched using dead cell removal kit (Miltenyi Biotec). Then the cell viability was confirmed by sort-lab of Hannover Medical School.
Library preparation for single cell mRNA-Seq analysis was performed according to the Chromium NextGEM Single Cell 3 Reagent Kits v3.1
User Guide (Manual Part Number CG000204 Rev B, 10x Genomics).
A twofold excess of cells was loaded to the 10x controller in the specified volume in order to reach a target number of
2500 cells (N2030-N2031) or 7500 cells (N2032-N2033) per sample. Fragment length distribution of generated cDNAs and libraries was monitored using
Bioanalyzer High Sensitivity DNA Assay (5067-4626, Agilent Technologies).
Quantification of libraries was performed by use of the ‘Qubit® dsDNA HS Assay Kit’ (Q32854, ThermoFisher Scientific).

treatment_protocol:
Liver biopsy specimens :
Liver biopsies were performed percutaneously under local anesthesia.
An approximately 5 mm portion of the needle biopsy was immediately preserved in Allprotect Tissue Reagent (QIAGEN) and then stored at -80° C.
The remaining cylinder was fixed in 4% neutral buffered formalin and embedded in paraffin wax.
RNA was isolated from cryo-conserved liver biopsy fragments as described recently.

tag: treatment

value: Control

value: liver


title: Ctrl_Gli1_P35_Prostate_scRNAseq

status: Public on Aug 27 2021

city: Duarte

first: Zijie

last: Sun

state: CA

address: 1500 E. Duarte Rd.

department: Cancer Biology

institute: City of Hope

data_processing:
The library purity and size was validated by capillary electrophoresis using 2,100 Bioanalyzer (Agilent Technologies)
The library quantity was measured fluorometrically using Qubit dsDNA HS Assay Kit from Invitrogen
The libraries were sequenced with a NovaSeq 6000 instrument (Illumina) to a depth of ~60-70k reads per cell. Raw sequencing data were processed using the 10x Genomics’ Cell Ranger pipeline (version 3.1.0) to generate FASTQ files and were aligned to the mm10 genome with an added mGFP sequence to generate gene expression counts
Genome_build: mm10 reference genome with added EGFP sequence
Supplementary_files_format_and_content: Txt file with counts for each cell corresponding to each gene

source_name: P35 Mouse Prostate

extract_protocol:
Prostate tissue was trimmed and dissociated to single cells using collagenase and TrypLE (Gibco)
The library was prepared using 10x Genomics Chromium Single Cell 3' Solution with v3 chemistry following manufacturer protocols (10x Genomics)

value: Prostate

value: Ar knockout in Gli1 expressing cells

tag: age


title: ARKO_Gli1_P35_Prostate_scRNAseq

tag: genotype/variation

value: Normal


title: JKD6008 ∆sRNA275 (∆vigR) RNA-seq (no vancomycin) replicate 1

value: [delta]sRNA275 ([delta]vigR 3'UTR)


title: Liver, HNF4A, rep1

description: replicate 1

value: HNF4A mRNA delivered


title: 203524200078_R05C01: AS


title: 916645

status: Public on Aug 24 2021

city: San Francisco

first: Denise

middle: M

last: Wolf

address: 2340 Sutter st

institute: University of California, San Francisco

hyb_protocol: Performed by Agendia Inc (Irvine, CA)

scan_protocol: Performed by Agendia Inc (Irvine, CA)

data_processing:
gnormalized signal (log2) data, as provided in the raw files on each patient, was extracted and aligned to the 75th quantile across arrays by Agendia. All values indicated for non-conformity, as indicated by the 'gIsFeatNonUnifOL' column in the raw files, are NA'd out. Probeset level data per array were mean-collapsed to the gene level, and genes common to the two platforms identified.  Expression data from the first ~900 I-SPY 2 patients distributed over the two platforms were combined into a single gene-level dataset over the set of common genes after batch-adjusting using ComBat [PMID:16632515].  The data matrix for this study constitutes 233 samples from this larger COMBAT-combined expression set.  Linear adjustment factors were derived from the larger ComBat operation, per platform, and can be used against these 233 samples for batch correcting on raw files.  The linear adjustment factors and updated probe annotation files per platform are provided.
The data matrix provided contains platform corrected, normalized expression values from two different platforms.  Data is collapsed on the gene level as was used in the analysis.

source_name: Breast cancer biopsy (pre-treatment)

label_protocol: Performed by Agendia Inc (Irvine, CA)

extract_protocol: Extraction, labeling, hybridization, and scanning are performed by Agendia Inc (Irvine, CA).  This company is referenced by the platforms used: GPL20078 and GPL16233.

value: breast cancer

tag: hr

tag: mp

tag: pcr

tag: arm

value: Control Arm


title: 890414


title: 973837

value: Ganitumab Arm


title: 932200


title: 800710


title: 803514


title: 885590


title: 906042


title: 845663


title: 749097


title: 962827


title: 627981


title: 819622


title: 782334


title: 794428


title: 581648


title: 709559


title: 672734


title: 766967


title: 615873


title: 602943


title: 511851


title: 527320


title: 520471


title: 507198


title: 614044


title: 517446


title: 677915


title: 580632


title: 477816


title: 489504


title: 405717


title: 491526


title: 495440


title: 433144


title: 579881


title: 460776


title: 373672


title: 327133


title: 367682


title: 395379


title: 349225


title: 318438


title: 282082


title: 299364


title: 273745


title: 239061


title: 264678


title: 248255


title: 238790


title: 181819


title: 202539


title: 151481


title: 255078


title: 198891


title: Pre-treatment Breast Cancer Biopsy 982086

city: Novato

first: Christina

last: Yau

address: 8001 Redwood Blvd

institute: Buck Institute of Age Research

hyb_protocol: Extraction, labeling, hybridization, and scanning are performed by Agendia Inc (Irvine, CA).

data_processing: gnormalized signal (log2) data, as provided in the raw files on each patient, was extracted and aligned to the 75th quantile across arrays by Agendia. All values indicated for non-conformity, as indicated by the 'gIsFeatNonUnifOL' column in the raw files, are NA'd out. Probeset level data per array were mean-collapsed to the gene level, and genes common to the two platforms identified.  Expression data from the first ~900 I-SPY 2 patients distributed over the two platforms were combined into a single gene-level dataset over the set of common genes after batch-adjusting using ComBat [PMID:16632515].  The data matrix for this study constitutes 127 samples from this larger COMBAT-combined expression set.  Linear adjustment factors were derived from the larger ComBat operation, per platform, and can be used against these 127 samples for batch correcting on raw files.  The linear adjustment factors and updated probe annotation files per platform are provided.

value: THP


title: 229144


title: 122795


title: Pre-treatment Breast Cancer Biopsy 981461

scan_protocol: Extraction, labeling, hybridization, and scanning are performed by Agendia Inc (Irvine, CA).


title: Pre-treatment Breast Cancer Biopsy 991818

label_protocol: Extraction, labeling, hybridization, and scanning are performed by Agendia Inc (Irvine, CA).


title: Pre-treatment Breast Cancer Biopsy 995480


title: Pre-treatment Breast Cancer Biopsy 999264


title: Pre-treatment Breast Cancer Biopsy 960029


title: Pre-treatment Breast Cancer Biopsy 953885


title: Pre-treatment Breast Cancer Biopsy 947398


title: 197942


title: Pre-treatment Breast Cancer Biopsy 982505


title: Pre-treatment Breast Cancer Biopsy 895653


title: Pre-treatment Breast Cancer Biopsy 981664


title: Pre-treatment Breast Cancer Biopsy 865416


title: Pre-treatment Breast Cancer Biopsy 831702


title: Pre-treatment Breast Cancer Biopsy 889721


title: Pre-treatment Breast Cancer Biopsy 845079


title: Pre-treatment Breast Cancer Biopsy 790397


title: Pre-treatment Breast Cancer Biopsy 786003


title: Pre-treatment Breast Cancer Biopsy 760011


title: Pre-treatment Breast Cancer Biopsy 831848


title: Pre-treatment Breast Cancer Biopsy 797499


title: Pre-treatment Breast Cancer Biopsy 721099


title: Pre-treatment Breast Cancer Biopsy 824350


title: Pre-treatment Breast Cancer Biopsy 767081


title: Pre-treatment Breast Cancer Biopsy 900959


title: Pre-treatment Breast Cancer Biopsy 799149


title: Pre-treatment Breast Cancer Biopsy 728149


title: Pre-treatment Breast Cancer Biopsy 795996


title: Pre-treatment Breast Cancer Biopsy 862244


title: Pre-treatment Breast Cancer Biopsy 825363


title: Pre-treatment Breast Cancer Biopsy 724293


title: Pre-treatment Breast Cancer Biopsy 738041


title: Pre-treatment Breast Cancer Biopsy 706418


title: Pre-treatment Breast Cancer Biopsy 685182


title: Pre-treatment Breast Cancer Biopsy 687288


title: Pre-treatment Breast Cancer Biopsy 896852


title: Pre-treatment Breast Cancer Biopsy 644609


title: Pre-treatment Breast Cancer Biopsy 649198


title: Pre-treatment Breast Cancer Biopsy 727255


title: Pre-treatment Breast Cancer Biopsy 705381


title: Pre-treatment Breast Cancer Biopsy 624777


title: Pre-treatment Breast Cancer Biopsy 618717


title: Pre-treatment Breast Cancer Biopsy 587691


title: Pre-treatment Breast Cancer Biopsy 536253


title: Pre-treatment Breast Cancer Biopsy 584561


title: Pre-treatment Breast Cancer Biopsy 598835


title: Pre-treatment Breast Cancer Biopsy 483667


title: Pre-treatment Breast Cancer Biopsy 604326


title: Pre-treatment Breast Cancer Biopsy 575457


title: Pre-treatment Breast Cancer Biopsy 494022


title: Pre-treatment Breast Cancer Biopsy 551795


title: Pre-treatment Breast Cancer Biopsy 535569


title: Pre-treatment Breast Cancer Biopsy 472799


title: Pre-treatment Breast Cancer Biopsy 491779


title: Pre-treatment Breast Cancer Biopsy 490805


title: Pre-treatment Breast Cancer Biopsy 503034


title: Pre-treatment Breast Cancer Biopsy 464547


title: Pre-treatment Breast Cancer Biopsy 527581


title: Pre-treatment Breast Cancer Biopsy 570685


title: Pre-treatment Breast Cancer Biopsy 410083


title: Pre-treatment Breast Cancer Biopsy 377460


title: Pre-treatment Breast Cancer Biopsy 453596


title: Pre-treatment Breast Cancer Biopsy 397505


title: Pre-treatment Breast Cancer Biopsy 474874


title: Pre-treatment Breast Cancer Biopsy 462605


title: Pre-treatment Breast Cancer Biopsy 507249


title: Pre-treatment Breast Cancer Biopsy 432114


title: Pre-treatment Breast Cancer Biopsy 396723


title: Pre-treatment Breast Cancer Biopsy 437162


title: Pre-treatment Breast Cancer Biopsy 413211


title: Pre-treatment Breast Cancer Biopsy 366120


title: Pre-treatment Breast Cancer Biopsy 324021


title: Pre-treatment Breast Cancer Biopsy 356431


title: Pre-treatment Breast Cancer Biopsy 311316


title: Pre-treatment Breast Cancer Biopsy 268937


title: Pre-treatment Breast Cancer Biopsy 296841


title: Pre-treatment Breast Cancer Biopsy 285339


title: Pre-treatment Breast Cancer Biopsy 273691


title: Pre-treatment Breast Cancer Biopsy 253531


title: Pre-treatment Breast Cancer Biopsy 254273


title: Pre-treatment Breast Cancer Biopsy 213913


title: Pre-treatment Breast Cancer Biopsy 235995


title: Pre-treatment Breast Cancer Biopsy 250274


title: Pre-treatment Breast Cancer Biopsy 204939


title: Pre-treatment Breast Cancer Biopsy 167271


title: Pre-treatment Breast Cancer Biopsy 220925


title: Pre-treatment Breast Cancer Biopsy 138425


title: Pre-treatment Breast Cancer Biopsy 208650


title: 362993


title: Pre-treatment Breast Cancer Biopsy 329941


title: Pre-treatment Breast Cancer Biopsy 131961


title: Pre-treatment Breast Cancer Biopsy 146033


title: Pre-treatment Breast Cancer Biopsy 125130


title: Pre-treatment Breast Cancer Biopsy 144302


title: Pre-treatment Breast Cancer Biopsy 203060


title: Pre-treatment Breast Cancer Biopsy 128051


title: 955035


title: Pre-treatment Breast Cancer Biopsy 122287


title: 950742


title: 966016


title: Pre-treatment Breast Cancer Biopsy 127791


title: 987728


title: 928170


title: 987914


title: 913527


title: 918979


title: 928446


title: 882538


title: 898618


title: 875089


title: 890372


title: 804979


title: 917762


title: 866660


title: 901705


title: 798604


title: 820807


title: 899692


title: 884011


title: 820348


title: 843554


title: 851488


title: 896621


title: 870077


title: 760901


title: 783764


title: 802308


title: 910188


title: 774840


title: 726940


title: 794128


title: 800447


title: 769972


title: 745633


title: 741535


title: 724384


title: 666147


title: 676630


title: 689452


title: 628823


title: 683457


title: 654021


title: 691753


title: 618860


title: 734997


title: 607843


title: 628788


title: 653927


title: 587604


title: 712785


title: 564701


title: 780272


title: 535779


title: 542392


title: 547892


title: 516834


title: 559021


title: 524170


title: 563681


title: 460642


title: 435279


title: 454808


title: 418593


title: 462582


title: 522140


title: 429220


title: 465008


title: 509012


title: 531988


title: 417474


title: 515281


title: 414844


title: 467686


title: 411950


title: 412772


title: 504838


title: 430441


title: 409288


title: 467622


title: 408692


title: 362150


title: 318407


title: 280375


title: 239910


title: 345483


title: 320538


title: 241705


title: 407539


title: 299962


title: 376676


title: 327917


title: 328160


title: 355942


title: 261304


title: 330134


title: 345460


title: 277888


title: 264305


title: 317131


title: 375342


title: 229328


title: 188700


title: 212307


title: 289420


title: 209967


title: 241998


title: 221686


title: 182346


title: 172366


title: 152090


title: 165925


title: 130580


title: 120422


title: 138027


title: 103939


title: 115987


title: 148357


title: 139973


title: 105286


title: 115638


title: 100899


title: Pre-treatment breast cancer biopsy  859699

value: TH Control


title: Pre-treatment breast cancer biopsy  797427


title: Pre-treatment breast cancer biopsy  889049


title: Pre-treatment breast cancer biopsy  809649


title: 296123


title: 145777


title: Pre-treatment breast cancer biopsy  596079


title: Pre-treatment breast cancer biopsy  726381


title: Pre-treatment breast cancer biopsy  725455


title: Pre-treatment breast cancer biopsy  573586


title: Pre-treatment breast cancer biopsy  442637


title: Pre-treatment breast cancer biopsy  720065


title: Pre-treatment breast cancer biopsy  742477


title: Pre-treatment breast cancer biopsy  627118


title: Pre-treatment breast cancer biopsy  402265


title: H3K4m3-ChIP H9 (primed) 7d+EZH2i rep3

status: Public on Aug 23 2021

city: Solna

first: Simon

middle: J

last: Elsässer

address: Tomtebodavägen 23A

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
Processing pipeline: minute processing pipeline (https://github.com/NBISweden/minute)
Pipeline manager: Snakemake v5.30.1
Demultiplexing and deduplication: Reads were demultiplexed using cutadapt v3.2 (Martin 2011) allowing only one mismatch per barcode. Deduplication was performed on aligned BAM files, marking duplicates using je-suite (v2.0.RC) using UMI and location of first mate. Resulting marked files were parsed and duplicate pairs were removed.
Mapping: bowtie2 (v2.3.5.1) with --fast parameter
Scaling: ChIP coverage tracks were generated from BAM files using deepTools (v3.5.0) bamCoverage. Quantitative scaling of the ChIP-Seq tracks amongst conditions within each pool was based on their Input-Normalized Mapped Read Count (INRC). INRC was calculated by dividing the number of unique hg38-mapped reads by the respective number of Input reads:  #mapped[ChIP] / #mapped[Input] . This essentially corrected for an uneven representation of barcodes in the Input and we could demonstrate that the INRC is proportional to the amount of epitope present in each condition.   Naïve-untreated condition pooled was chosen as the reference sample, which was scaled to 1x coverage (also termed Reads per Genome Coverage, RPGC). All other conditions were scaled relative to the reference using the ratio of INRCs multiplied by the scaling factor determined for 1x normalization of the reference: ( #mapped[ChIP] / #mapped[Input] ) / ( #mapped[ChIP_Reference] / #mapped[Input_Reference] ) * scaling factor.
Genome_build: hg38 (Homo_sapiens_UCSC_hg38.tar.gz - Illumina iGenomes: http://igenomes.illumina.com.s3-website-us-east-1.amazonaws.com/Homo_sapiens/UCSC/hg38/Homo_sapiens_UCSC_hg38.tar.gz )
Supplementary_files_format_and_content: bigWig files minute-scaled to Naïve-untreated condition. Naïve-untreated condition is scaled to a  reads-per-genome-coverage of one (1xRPGC, also referred to as ‘1x normalization’) using hg38 genome size 3095978588

source_name: H3K4m3-ChIP H9 (primed) 7d+EZH2i

growth_protocol: Primed H9 (Wicell; WA09) p28(11) were cultured in Nutristem hESC XF medium and passaged when they reached 70-80% confluency. Naive H9 p28(8) naive p7 were grown on high-density MEF plates using NaïveCult expansion media  supplemented with 10µM ROCKi.  Cells were passaged every four to five days. Both hESCs were cultured at 37°C, 5% O2 and 5% CO2.

extract_protocol:
During harvesting, mouse feeder removal microbeads (Milteny Biotech; 130-095-531) were used to reduce the amount of MEFs in the naive cell samples, according to the manufacturer's protocol. Primed cells were dissociated and centrifuged directly.Three replicates of 1e6 cells per condition were collected and pellets were flash frozen.
ChIP-seq libraries were prepared using the MINUTE-ChIP protocol as described in Kumar & Elsässer 2019; PMID: 3153304 and sequenced on the Illumina NextSeq 500 (Paired End) platform. Antibodies used : H2AUb Cell signalling 8240S; lot #6 , H3K27me3 Millipore 07-449; lot #3091919 , H3K4me3 Millipore 04-745; lot #3198414.

treatment_protocol: In addition to wildtype conditions, naïve and primed H9 cells where treated with 10 uM EZH2 inhibitor (EPZ-6438; BIOV2428-5) for 7 days, with daily media changes.

tag: background

value: H9 (female)

tag: cell type

value: Embryonic Stem Cell

tag: condition

value: primed

tag: antibody

tag: minute-pool

tag: supplementary file scaling

value: RPGC relative to naïve


title: H3K4m3-ChIP H9 (primed) 7d+EZH2i rep2


title: H3K4m3-ChIP H9 (primed) rep1

source_name: H3K4m3-ChIP H9 (primed)


title: H3K4m3-ChIP H9 (primed) 7d+EZH2i rep1


title: H3K4m3-ChIP H9 (primed) rep2


title: Pre-treatment breast cancer biopsy  382853


title: Pre-treatment breast cancer biopsy  375455


title: Pre-treatment breast cancer biopsy  335091


title: 567907

tag: tissue


title: Pre-treatment breast cancer biopsy  153880


title: Pre-treatment breast cancer biopsy  350331


title: Pre-treatment breast cancer biopsy  141782


title: H3K4m3-ChIP H9 (naïve) 7d+EZH2i rep1

source_name: H3K4m3-ChIP H9 (naïve) 7d+EZH2i

value: naive (t2iGoY)


title: Pre-treatment breast cancer biopsy  246134


title: H3K4m3-ChIP H9 (naïve) rep3

source_name: H3K4m3-ChIP H9 (naïve)

value: RPGC 1x genome coverage


title: 663144


title: H3K4m3-ChIP H9 (naïve) 7d+EZH2i rep3


title: Pre-treatment breast cancer biopsy  166412


title: H3K4m3-ChIP H9 (primed) rep3


title: H3K4m3-ChIP H9 (naïve) rep2


title: H3K27m3-ChIP H9 (primed) 7d+EZH2i rep3

source_name: H3K27m3-ChIP H9 (primed) 7d+EZH2i


title: H3K4m3-ChIP H9 (naïve) rep1


title: H3K27m3-ChIP H9 (primed) 7d+EZH2i rep1


title: H3K27m3-ChIP H9 (primed) rep3

source_name: H3K27m3-ChIP H9 (primed)


title: H3K4m3-ChIP H9 (naïve) 7d+EZH2i rep2


title: H3K27m3-ChIP H9 (primed) rep1


title: H3K27m3-ChIP H9 (naïve) 7d+EZH2i rep1

source_name: H3K27m3-ChIP H9 (naïve) 7d+EZH2i


title: H3K27m3-ChIP H9 (naïve) 7d+EZH2i rep2


title: H3K27m3-ChIP H9 (naïve) rep2

source_name: H3K27m3-ChIP H9 (naïve)


title: H3K27m3-ChIP H9 (naïve) rep3


title: H2Aub-ChIP H9 (primed) 7d+EZH2i rep2

source_name: H2Aub-ChIP H9 (primed) 7d+EZH2i


title: H2Aub-ChIP H9 (primed) 7d+EZH2i rep1


title: H2Aub-ChIP H9 (primed) rep3

source_name: H2Aub-ChIP H9 (primed)


title: H2Aub-ChIP H9 (primed) rep2


title: H2Aub-ChIP H9 (primed) rep1


title: H2Aub-ChIP H9 (naïve) 7d+EZH2i rep1

source_name: H2Aub-ChIP H9 (naïve) 7d+EZH2i


title: H2Aub-ChIP H9 (naïve) rep3

source_name: H2Aub-ChIP H9 (naïve)


title: H3K27m3-ChIP H9 (primed) 7d+EZH2i rep2


title: H2Aub-ChIP H9 (naïve) rep1


title: H3K27m3-ChIP H9 (primed) rep2


title: Antibody-derived tags from malignant pleural mesothelioma patient

status: Public on Aug 16 2021

city: Pittsburgh

first: Hatice

middle: Ulku

last: Osmanbeyoglu

state: Pennsylvania

address: 5607 Baum Blvd

department: Biomedical Informatics

institute: University of Pittsburgh

description:
mpm_barcodes.tsv.gz
mpm_features.tsv.gz
mpm_matrix.mtx.gz

data_processing:
Library strategy: CITE-seq
Raw sequence data were processed via CellRanger 3.0 (10X Genomics) and aligned to GRCh38 to generate UMI matrix for the downstream analysis.
Cell barcodes with fewer than 3 UMI counts in 1% of cells were removed.
Antibody counts for CITE-seq were counted using CITE-seq-count. Normalization and initial explanatory analysis of CITE-seq data were performed using the Seurat R package
Antibody-derived tags (ADTs) for each cell will be normalized using a centered log ratio (CLR) transformation across cells.
During quality control, we excluded cells with > 5000 and <300 expressed genes. Seurat “FindClusters” was applied to the first 50 principal components, with the resolution parameter set to 1. Cell labels were assigned using marker genes protein and gene expression levels.
Genome_build: GRCh38
Supplementary_files_format_and_content: CellRanger output files:  barcodes.tsv, features.tsv, matrix.mtx.

molecule: other

source_name: pleura

extract_protocol:
Pleural and peritoneal mesothelioma tumor tissues were treated with antibiotic rich media followed by mechanical digestion with blades followed by 5 minute incubation with 100uL of liberase at 80ug/uL at 37 degree celsius. Tissue is the passed over a 70 micron filter into RPMI media. Cells can be sorted by flow cytometry for CD45+ and CD45-EPCAM+ cells.
Treatment of cells with antibody tagged transcripts from biolegend's CITE-seq panel for 30 minutes. Chromium 5 prime single-cell RNA seq kit by 10x genomics is used for creation of samples and libraries.
CITE-seq with scRNAseq

tag: disease state

value: malignant mesotheliomas

value: pleura


title: Gene expression from malignant peritoneal mesothelioma patient

description:
mpem_barcodes.tsv.gz
mpem_features.tsv.gz
mpem_matrix.mtx.gz

data_processing:
Raw sequence data were processed via CellRanger 3.0 (10X Genomics) and aligned to GRCh38 to generate UMI matrix for the downstream analysis.
Cell barcodes with fewer than 3 UMI counts in 1% of cells were removed.
Antibody counts for CITE-seq were counted using CITE-seq-count. Normalization and initial explanatory analysis of CITE-seq data were performed using the Seurat R package
Antibody-derived tags (ADTs) for each cell will be normalized using a centered log ratio (CLR) transformation across cells.
During quality control, we excluded cells with > 5000 and <300 expressed genes. Seurat “FindClusters” was applied to the first 50 principal components, with the resolution parameter set to 1. Cell labels were assigned using marker genes protein and gene expression levels.
Genome_build: GRCh38
Supplementary_files_format_and_content: CellRanger output files:  barcodes.tsv, features.tsv, matrix.mtx.

source_name: peritoneum

value: peritoneum


title: H3K27m3-ChIP H9 (naïve) 7d+EZH2i rep3


title: Antibody-derived tags from malignant peritoneal mesothelioma patient


title: Gene expression from malignant pleural mesothelioma patient


title: Saline_Negative_660

status: Public on Aug 06 2021

city: South San Francisco

first: Jason

middle: Anthony

last: Vander Heiden

address: 1 DNA Way

department: Biological Research AI Development

institute: Genentech

data_processing:
Sequencing reads were filtered and aligned using HTSeqGenie against the mouse genome assembly GRCm38.
Genome_build: GRCm38
Supplementary_files_format_and_content: TSV count matrices

source_name: Triple- lung cells

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit.
Libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

value: Triple-

value: lung

value: Saline


title: Saline_Negative_661


title: Saline_Negative_663


title: Saline_EpCAM_658

source_name: EpCAM+ lung cells

value: EpCAM+


title: Saline_Negative_662


title: Saline_Negative_659


title: H2Aub-ChIP H9 (primed) 7d+EZH2i rep3


title: Saline_EpCAM_656


title: H3K27m3-ChIP H9 (naïve) rep1


title: H2Aub-ChIP H9 (naïve) 7d+EZH2i rep3


title: Saline_EpCAM_654


title: H2Aub-ChIP H9 (naïve) rep2


title: H2Aub-ChIP H9 (naïve) 7d+EZH2i rep2


title: Saline_EpCAM_657


title: Saline_CD45_647

source_name: CD45+ lung cells


title: Saline_CD45_648


title: Saline_CD31_653

source_name: CD31+ lung cells


title: Saline_CD45_644


title: Saline_CD45_646


title: Saline_CD45_645


title: Saline_CD31_651


title: Saline_CD31_652


title: Bleomycin_Negative_641

value: Bleomycin


title: Bleomycin_Negative_643


title: Saline_CD31_649


title: Saline_EpCAM_655


title: Bleomycin_EpCAM_635


title: Bleomycin_Negative_639


title: Bleomycin_Negative_640


title: Bleomycin_Negative_642


title: Bleomycin_Negative_638


title: Bleomycin_Negative_637


title: Bleomycin_EpCAM_634


title: Bleomycin_Negative_636


title: Bleomycin_EpCAM_631


title: Bleomycin_EpCAM_630


title: Bleomycin_EpCAM_632


title: Bleomycin_EpCAM_633


title: Bleomycin_CD45_618


title: Bleomycin_EpCAM_628


title: Bleomycin_CD45_619


title: Bleomycin_EpCAM_629


title: Bleomycin_CD45_617


title: Bleomycin_CD45_614


title: Bleomycin_CD45_616


title: Saline_CD31_650


title: Bleomycin_CD31_626


title: Bleomycin_CD45_612


title: Bleomycin_CD31_624


title: Bleomycin_CD31_625


title: Bleomycin_CD31_620


title: Bleomycin_CD31_623


title: Bleomycin_CD31_621


title: P_502626_T: 502626 tumor

status: Public on Jul 31 2021

city: Pyeongchang

first: Joonghoon

last: Park

state: Kangwon

address: Pyeongchang daero 1447

department: International Agricultural Technology

country: South Korea

institute: Seoul National University

data_processing:
Sequencing reads from cDNA were aligned with the NCBI human reference genome (hg19) by using GSNAP [31] and TopHat [32] with a 5% mismatch allowance.
To minimize mRNA splicing-caused misalignment, sequencing reads were also aligned to a custom human reference cDNA consisting of 161,250 mRNA sequences obtained from public databases (36,742 RefSeq, 73,671 UCSC, and 161,214 Ensembl).
In-frame fusion genes were identified by using GFP, and cross validated with defuse and FusionMap.
DEG analysis was performed by using GenePattern at Broad Institute.
Single nucleotide variances (SNVs) were identified after GSNAP alignment on the custom human reference cDNA.
Genome_build: hg19
Supplementary_files_format_and_content: excel, clinical information, mutation, fusion, and gene expression

source_name: Colon cancer

growth_protocol: Tumor tissues composed of more than 60% of tumor cells and less than 20% of necrotic cells or normal cells on histological assessment were included. Tumor tissues from patients who had a family history of colon cancer were excluded. In total, 150 tumor and 50 matched normal tissues were analyzed.

extract_protocol:
Total RNA was extracted by using the RNAiso Plus (Takara Bio, Japan). Extracted RNA was purified by using the RNeasy Mini Kit accompanied with the DNase I (Qiagen) treatment.
mRNA was enriched by using poly-T oligo-attached magnetic beads, followed by mRNA fragmentation by acoustic shearing. First-strand cDNA was synthesized by using reverse transcriptase and random hexamers, and second-strand cDNA by using DNA polymerase I and RNase H. cDNA was subject to adapter ligation, and then enriched with PCR to prepare cDNA library. cDNA libraries were sequenced on HiSeq 2000 (Illumina) to obtain around 100 million paired-end reads (2 x 101 bp).

value: Colon cancer

tag: location

value: SIGMOID

tag: gender

value: M

tag: Stage

value: III

tag: mms

value: MSS


title: Bleomycin_CD45_615

tag: treatment


title: P_11009_T: 11009 tumor

value: ASCENDING

tag: age


title: C_7505991_T: 7505991 tumor

value: TRANSVERSE


title: P_9108_T: 9108 tumor

value: F


title: P_506084_T: 506084 tumor


title: P_6258_T: 6258 tumor


title: 4245_T: 4245 tumor

value: II

value: MSI-H


title: C_3725_T: 3725 tumor


title: Bleomycin_CD45_613


title: P_11441_T: 11441 tumor


title: P_12038_T: 12038 tumor


title: P_11612_T: 11612 tumor


title: P_11214_T: 11214 tumor


title: P_10885_T: 10885 tumor


title: P_11154_T: 11154 tumor


title: P_10094_T: 10094 tumor


title: P_11139_T: 11139 tumor


title: Bleomycin_CD31_622


title: C_778_T: 778 tumor


title: C_500062_T: 500062 tumor


title: P_7405_T: 7405 tumor


title: P_12078_T: 12078 tumor


title: P_13022_T: 13022 tumor


title: C_3717_T: 3717 tumor

value: PROXIMAL SIGMOID


title: C_500163_T: 500163 tumor


title: C_3614_T: 3614 tumor


title: C_3539_T: 3539 tumor


title: C_1912_T: 1912 tumor


title: P_11233_T: 11233 tumor


title: C_2362_T: 2362 tumor


title: C_3369_T: 3369 tumor


title: C_2370_T: 2370 tumor


title: P_9201_T: 9201 tumor


title: C_3022_T: 3022 tumor


title: C_1800_T: 1800 tumor


title: P_500662_T: 500662 tumor

value: DESCENDING


title: P_501875_T: 501875 tumor


title: P_2313_T: 2313 tumor


title: P_13660_T: 13660 tumor


title: P_502839_T: 502839 tumor


title: P_12757_T: 12757 tumor


title: P_12404_T: 12404 tumor


title: P_500191_T: 500191 tumor


title: P_12207_T: 12207 tumor


title: P_11466_T: 11466 tumor


title: P_11210_T: 11210 tumor


title: P_11756_T: 11756 tumor


title: P_10779_T: 10779 tumor


title: C_581_T: 581 tumor


title: C_7506568_T: 7506568 tumor


title: C_3726_T: 3726 tumor


title: C_7506785_T: 7506785 tumor


title: C_749_T: 749 tumor

value: RECTOSIGMOID


title: C_3271_T: 3271 tumor


title: C_3649_T: 3649 tumor


title: C_2645_T: 2645 tumor


title: C_3692_T: 3692 tumor


title: C_2622_T: 2622 tumor


title: C_2279_T: 2279 tumor


title: C_2581_T: 2581 tumor


title: C_1963_T: 1963 tumor


title: P_7372_T: 7372 tumor

value: I


title: P_8292_T: 8292 tumor


title: P_12062_T: 12062 tumor


title: P_505907_T: 505907 tumor


title: P_5417_T: 5417 tumor


title: P_505820_T: 505820 tumor


title: P_505490_T: 505490 tumor


title: P_504723_T: 504723 tumor


title: P_504325_T: 504325 tumor


title: P_503981_T: 503981 tumor


title: P_505292_T: 505292 tumor


title: P_503667_T: 503667 tumor


title: P_70077_T: 70077 tumor


title: P_5626_T: 5626 tumor


title: P_500561_T: 500561 tumor


title: P_502872_T: 502872 tumor


title: P_12479_T: 12479 tumor


title: P_2593_T: 2593 tumor


title: P_1876_T: 1876 tumor


title: 70302_T: 70302 tumor


title: P_12433_T: 12433 tumor


title: P_10884_T: 10884 tumor


title: P_12449_T: 12449 tumor


title: P_503158_T: 503158 tumor


title: C_809_T: 809 tumor


title: P_11950_T: 11950 tumor


title: P_10160_T: 10160 tumor

value: CECUM


title: P_505056_T: 505056 tumor


title: P_12384_T: 12384 tumor


title: 70302_N: 70302 normal

source_name: Colon

value: Normal colon


title: 70297_N: 70297 normal


title: 70297_T: 70297 tumor


title: 505542_N: 505542 normal


title: 505542_T: 505542 tumor


title: 505395_N: 505395 normal


title: 505366_T: 505366 tumor


title: 505366_N: 505366 normal


title: 504874_T: 504874 tumor


title: 504874_N: 504874 normal


title: 504452_T: 504452 tumor

value: MSI-L


title: 504452_N: 504452 normal


title: C_3167_T: 3167 tumor

value: Colon cancer


title: 504355_N: 504355 normal


title: 503190_N: 503190 normal

value: SIGMOID


title: 504090_N: 504090 normal

value: M


title: 503190_T: 503190 tumor

value: III


title: 504355_T: 504355 tumor

value: MSS


title: 505395_T: 505395 tumor


title: 3427_T: 3427 tumor


title: 1836_T: 1836 tumor


title: 70075_N: 70075 normal

value: ASCENDING


title: 70075_T: 70075 tumor


title: 3360_T: 3360 tumor


title: 3042_T: 3042 tumor


title: 3034_N: 3034 normal


title: 3113_T: 3113 tumor


title: 3393_T: 3393 tumor


title: 3360_N: 3360 normal


title: 3292_T: 3292 tumor


title: 4054_T: 4054 tumor


title: 2026_T: 2026 tumor


title: 1429_T: 1429 tumor


title: 3292_N: 3292 normal


title: 3034_T: 3034 tumor


title: 3042_N: 3042 normal


title: 2586_N: 2586 normal


title: 2026_N: 2026 normal


title: 2586_T: 2586 tumor


title: 1429_N: 1429 normal


title: 504090_T: 504090 tumor


title: 13855_T: 13855 tumor


title: 13855_N: 13855 normal


title: 2743_T: 2743 tumor


title: 13837_T: 13837 tumor


title: 13837_N: 13837 normal


title: 11943_N: 11943 normal


title: 11943_T: 11943 tumor


title: 11821_T: 11821 tumor


title: PG8_54: 2369 tumor


title: PG8_53: 2099 tumor


title: PG8_52: 1792 tumor


title: PG8_50: 7506489 normal


title: 11821_N: 11821 normal


title: PG8_55: 3704 tumor


title: PG7_49: 7506291 normal


title: PG8_56: 7506479 tumor


title: PG8_51: 464 tumor


title: PG6_39: 2174 normal


title: PG6_38: 1789 normal


title: PG7_48: 7506155 normal


title: PG6_37: 1366 normal


title: PG7_47: 7003065 normal


title: PG6_36: 690 normal


title: PG7_44: 3211 normal


title: PG7_43: 3170 normal


title: PG6_42: 3031 normal


title: PG6_41: 2390 normal


title: PG5_34: 409 normal


title: PG5_32: 7506489 tumor


title: PG5_31: 7506291 tumor


title: PG5_35: 661 normal


title: PG5_30: 7506155 tumor


title: PG5_29: 7003065 tumor


title: PG4_25: 3170 tumor


title: PG6_40: 2700 normal


title: PG3_20: 1789 tumor


title: PG7_46: 3457 normal


title: PG3_18: 690 tumor


title: PG4_26: 3211 tumor


title: PG4_28: 3457 tumor


title: PG3_16: 409 tumor


title: PG3_21: 2174 tumor


title: PG4_23: 2700 tumor


title: PG2_8: 505024 normal


title: PG4_22: 2390 tumor


title: PG3_19: 1366 tumor


title: PG2_14: 506583 normal


title: PG2_12: 505677 normal


title: PG2_10: 505572 normal


title: PG3_17: 661 tumor


title: PG1_7: 505024 tumor


title: PG1_6: 504535 normal


title: PG1_5: 504535 tumor


title: PG2_11: 505677 tumor


title: PG2_13: 506583 tumor


title: PG1_4: 70422 normal


title: PG1_1: 12845 tumor


title: PG1_3: 70422 tumor


title: PG1_2: 12845 normal


title: JT_495_Bl6SpOv_scE3.5Blastocysts120x_CR_0_1perPFA_Gata6

status: Public on Jul 29 2021

city: Bethesda

first: Pedro

middle: P

last: Rocha

state: Maryland

address: 6 Center Drive Building 6B 2B220

department: NICHD

institute: National Institutes of Health

data_processing:
Library strategy: CUT&RUN
Mapping to genome using bowtie2 with the following options (-N 1 --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 -x). Reads that mapped to ENCODE mm10 blacklist regions were removed using Samtools (Li et al., 2009). Piccard (broadinstitute.github.io/picard/) was then used to identify non-duplicated reads. Duplicate reads were removed for libraries generated from blastocysts but kept for all others.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files

source_name: Blastocysts

growth_protocol: Cells were maintained at a density of 1 million cells per 10cm gelatinized plates at 37ºC x% O2, x% CO2 in 2i media (50% DMEM/F12, 50% Neurobasal, Penicillin-Streptomycin, GlutaMAX, 2-Mercaptoethanol, N2, B27, 0.3nM PD0325901, 0.1nM CHIR9902, and 2x105units/mL LIF).

extract_protocol:
Cells were harvested using accutase and 100,000 cells per replicate, per time point, were subjected to CUT&TAG and CUT&RUN. Blastocysts were fixed in 0.1% PFA and subjected to CUT&RUN by physically transferring the embryos into different CUT&RUN buffers under a dissection microscope.
DNA was issolated using phenol-chloroform extraction. For each sample, double stranded DNA (10µl), Template Preparation D Buffer (2µl), and Template Preparation D Enzyme (1µl) were combined and End Repair and A-tailing was performed in a Thermocycler with a heated lid (22ºC, 25 min; 55ºC, 20 min). Library Synthesis D Buffer (1µl) and Library Synthesis D Enzyme (1µl) were subsequently added, and library synthesis was performed (22ºC, 40min). Immediately after, Library Amplification D Buffer (25µl), Library Amplification D Enzyme (1µl), Nuclease-free water (4µl), and a unique Illumina-compatible indexed primer (5µl) were added. Library amplification was performed using the following cycling conditions: 72ºC for 3 min; 85ºC for 2 min; 98ºC for 2 min (denaturation); 4 cycles of 98ºC for 20 s, 67ºC for 20 s, 72ºC for 10 s (addition of indexes); 14 cycles of 98ºC for 20 s, 72ºC for 10 s (library amplification). Post-PCR clean-up was performed on amplified libraries with a SPRIselect bead 0.6X left/1x right double size selection then washed twice gently in 80% ethanol and eluted in 10-12µl 10 mM Tris pH 8.0. For CUT&TAG, DNA (20µl) was mixed with 5X Q5 reaction buffer (10µl), Q5 polymerase (0.5µl), dNTPs (1µl), nuclease free water (16µl), and an equimolar mixture of an universal i5 and a uniquely barcoded i7 primer (2.5µl) , using different barcodes for each sample. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72 °C for 5 min (gap filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 30 s; final extension at 72 °C for 1 min and hold at 8 °C.

treatment_protocol: Differentiation into primitive endoderm was induced in serum containing ESS media (Knockout DMEM, 15% FBS,1% GlutaMAX, 1% Penicillin-Streptomycin, 1% 2-Mercaptoethanol, 1% Sodium Pyruvate, 1% MEM NEAA, 2x105units/mL LIF) containing doxycycline (1ug/mL) for 2 to 12 hours. For time points greater than 12 hours, mES cells were induced in serum media containing doxycycline for 12 hours and switched to serum media in the absence of doxycycline for the remaining time. Blastocysts were collected from 4-5 weeks old C57BL/6N females six days after PMSG/HCG injections. Blastocysts were used right away to profile E3.5 embryos, after removing the zona pellucida using acid tyrode’s solution. E4.5 embryos were isolated seven days after PMSG/HCG injections, and only blastocysts without any zona pellucida were used. Embryos were manipulated in 1% agar-coated 4-well dishes (ThermoFisher scientific, Nunc 4-Well Dishes for IVF) throughout the protocol.

value: Blastocysts

tag: developmental stage

tag: strain

tag: transgene

value: Stem cells have TRE:GATA6-DSREd2

tag: assay

value: CUT&RUN


title: JT_517_Bl6SpOv_scE3.5Blastocysts160x_CR_0_1perPFA_Gata6

tag: cell type


title: PG2_9: 505572 tumor

value: F


title: PG4_24: 3031 tumor

value: II


title: JT_141_CR_IgG

source_name: Embryonic stem cell line

tag: cell line

value: Embryonic stem cells

tag: time point

value: 48 hour post doxycycline

value: IgG


title: JT_134_CR_H3K9me3_48hr_rep2

tag: antibody


title: DL_228_CT_H3K27ac_24h_rep1

data_processing:
Library strategy: CUT&TAG
Mapping to genome using bowtie2 with the following options (-N 1 --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 -x). Reads that mapped to ENCODE mm10 blacklist regions were removed using Samtools (Li et al., 2009). Piccard (broadinstitute.github.io/picard/) was then used to identify non-duplicated reads. Duplicate reads were removed for libraries generated from blastocysts but kept for all others.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files

value: 24 hour post doxycycline

value: CUT&TAG


title: DL_17_CR_H3K9me3_0h_rep1

value: 0 hour no doxycycline


title: DL_229_CT_H3K27ac_24h_rep2


title: JT_133_CR_H3K9me3_48hr_rep1


title: DL_234_CT_H3K27ac_48h_rep1


title: DL_225_CT_H3K27ac_16h_rep2

value: 16 hour post doxycycline


title: DL_224_CT_H3K27ac_16h_rep1


title: DL_221_CT_H3K27ac_8h_rep2

value: 8 hour post doxycycline


title: DL_235_CT_H3K27ac_48h_rep2


title: DL_220_CT_H3K27ac_8h_rep1


title: JT252_CR_H3K9me3_0h_rep2


title: DL_237_CT_H3K27me3_48h_rep2


title: DL_215b_CT_H3K27ac_0h_rep2


title: DL_214b_CT_H3K27ac_0h_rep1


title: DL_232_CT_H3K4me3_48h_rep1


title: E12.5 wild type distal forelimb capture Hi-C

status: Public on Jul 20 2021

data_processing:
CUT and RUN reads processing was done on the Duboule local Galaxy server (Afgan et al., 2016). First, adapters were removed using cutadapt version 1.6 (Martin, 2011) with the following parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC for R1 and -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT for R2.
They were then processed by using hicup version 6.1.0 with the bowtie2 version 2.2.6 (Langmead and Salzberg, 2012) and SAMtools version 1.2, with mm10 as reference genome and GATC as restriction enzyme recognition sequence.
The pairs were next converted from bam to tabulated files, with the position of the middle of the fragment to which hicup assigned the read, by using an ad hoc python script (script available at https://github.com/lldelisle/scriptsForBoltEtAl2021).
Only valid pairs with both MAPQ above 30 were kept.
Then, pairs with both mates in the capture region (mm10, chr2:72402000-77000000) were extracted and processed with cooler to obtain a balance matrix of the capture region with 5-kb bins.
Genome_build: mm10
Supplementary_files_format_and_content: pairs: contains every valid pair for each dataset in the juicebox format: Each line is a pair: <readname> <str1> <chr1> <pos1> <frag1>   <str2> <chr2> <pos2> <frag2> <mapq1> <mapq2> str = strand (0 for forward, anything else for reverse)
cool: contains the iced matrix in the capture region at 5kb resolution

source_name: distal forelimb

growth_protocol: Crosses were made between heterozygous adults. Animals were checked for vaginal plugs on the next morning, establishing the timepoint 0.5 embryonic days. Embryos were collected 12 days later.

extract_protocol:
The forelimbs of embryos were dissected and placed into PBS with 10% FCS and 8ul collagenase at 50mg/ml (Sigma C9697) at 37º for approximately 5min. Collagenase treated samples were cross-linked with 1% formaldehyde (ThermoFisher 28908) for 10 minutes at room temperature and stored at -80º until further processing as previously described (Yakushiji-Kaminatsui et al., 2018)
Following the Hi-C protocol, ligated DNA fragments were processed throught the Agilent SureSelectXT protocol to enrich for fragments coming from the probe region chr2:72240000-76840000 (mm9).
SureSelectXT

treatment_protocol: No treatment

tag: genotype

value: wild type

value: distal forelimb


title: E12.5 wild type proximal forelimb capture Hi-C

source_name: proximal forelimb

tag: tissue

value: proximal forelimb


title: DL_212b_CT_H3K4me3_0h_rep1


title: DL_217_CT_H3K27me3_0h_rep2


title: scRNA-seq of rescued Treg

status: Public on Jul 09 2021

city: New York

first: Michail

last: Schizas

address: 1275 York ave

institute: Memorial sloan Kettering

description:
cellxgene_counts.txt
cellxgene_norm_counts.txt

data_processing:
scRNA-seq data pre-processing and alignment: Cell Ranger v3.0
scRNA-seq imputation: MAGIC v0.1.1
scRNA-seq diffusion component and pseudotime analysis: Palantir v1.0.0
scRNA-seq clustering: PhenoGraph v1.5.7
scRNA-seq differential gene expression: Single-Cell Analysis in Python v1.7.2
scRNA-seq gene set module score calculation: Seurat v3.1.5
Genome_build: GRCm38

source_name: T cell

extract_protocol: 10X genomics Chromium Single Cell 3’ Library & Gel bead Kit V3

treatment_protocol: Male mice were treated with a single dose of 4-hydroxytamoxifen on postnatal day 14 and 8-10-week-old female mice were treated with diphtheria toxin 1, 3, 5, and 7 days prior to analysis.

value: Spleen and lymph node

value: T cell

value: 7 months

tag: fraction

value: mRNA


title: scRNA-seq of control Treg


title: E12.5 wild type distal forelimb, replicate 1 CR_HOXD13

description: CUT&RUN

data_processing:
Library strategy: CUT&RUN
CUT and RUN reads processing was done on the Duboule local Galaxy server (Afgan et al., 2016). Adapters and bad-quality bases were removed with Cutadapt version 1.16 (Martin, 2011). Reads were mapped to the mouse genome (mm10) using Bowtie2 (v2.3.4.1) (Langmead and Salzberg, 2012), (-I 0 -X 1000 –fr –dovetail –very-sensitive).
Reads with mapping quality below 30 or not properly paired were removed from the analysis. PCR duplicates were removed.
The output BAM file was converted to BED using bamtobed bedtools v2.18.2 (Quinlan, 2014).
The coverage was obtained as the output of MACS2 (v2.1.1.20160309) (Zhang et al., 2008) (--format BED --keep-dup all --bdg --nomodel --extsize 200 --shift 100).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig: coverage from macs2
narrowPeak: narrowPeak from macs2

extract_protocol:
The forelimbs of embryos were dissected and placed into PBS with 10% FCS and 8ul collagenase at 50mg/ml (Sigma C9697) at 37º for approximately 5min.
DNA isolated from the CUT&RUN protocol were prepared with KAPA HyperPrep reagents (07962347001) with 2.5ul of adaptors at 0.3uM and ligated for 1 hour at 20ºC. The DNA was amplified for fourteen cycles. Post-amplified DNA was cleaned and size selected using 1:1 ration of DNA:Ampure SPRI beads (A63881) followed by an additional 1:1 wash and size selection with HXB. HXB is equal parts 40% PEG8000 (Fisher FIBBP233) and 5M NaCl. The anti-CTCF  antibody is Active Motif 61311, and the anti-HOXD13 antibody is Abcam Ab19866.

value: wild-type

value: anti-HOXD13 (Abcam Ab19866)


title: DL_216b_CT_H3K27me3_0h_rep1

value: Embryonic stem cells

value: Stem cells have TRE:GATA6-DSREd2


title: DL_233_CT_H3K4me3_48h_rep2

value: 48 hour post doxycycline


title: DL_213b_CT_H3K4me3_0h_rep2


title: 205022240077_R02C01: BR_CA

status: Public on Jul 07 2021

source_name: tumor

value: female

tag: tissue source

value: DNA FFPE

value: breast tumor

tag: tumor type


title: 205022240077_R03C01: DNADEG

tag: gender

value: DNADEG


title: E12.5 wild-type distal forelimb ATAC-seq

data_processing:
ATAC-seq reads processing was done on the Duboule local Galaxy server (Afgan et al., 2016). Reads were mapped to the mouse genome (mm10) using Bowtie2 (v2.3.4.1) (Langmead and Salzberg, 2012), (-I 0 -X 2000 --fr --dovetail --very-sensitive-local).
Reads with mapping quality below 30, mapping to mitochondria, or not properly paired were removed from the analysis. PCR duplicates were filtered using Picard (v1.56.0).
BAM file was converted to BED with bedtools version 2.27. Peak calling was done using MACS2 (v2.1.0.20151222) callpeak (--nomodel --shift 100 --extsize 200 --call-summits --keep-dup all).
The coverage was done using the center of the Tn5 insertion and extended on both sides by 20 bp (script available at https://github.com/lldelisle/scriptsForBoltEtAl2021)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig: coverage centered on the Tn5 insertion (20bp extended both sides)
narrowPeak: narrowPeak from macs2

extract_protocol:
The forelimbs of embryos were dissected and placed into PBS with 10% FCS and 8ul collagenase at 50mg/ml (Sigma C9697) at 37º for approximately 5min. Cells were counted and 50,000 cells were isolated for processing with the Nextera Tn5 enzyme (Illumina FC-131-1096) as previously described (Buenrostro NatMeth 2013).
Tn5 treated DNA was amplified with Nextera Library primers using NEBNext library amplification master mix (NEB M0541).


title: 205022240077_R01C01: DNADEG


title: 205022240078_R06C01: BR_CA


title: 205022240078_R04C01: BR_CA


title: 205022240078_R07C01: BR_CA


title: 205022240078_R03C01: BR_CA


title: 205022240078_R02C01: BR_CA


title: 205022240078_R08C01: BR_CA


title: 205022240166_R03C01: -


title: DL_236_CT_H3K27me3_48h_rep1

value: CUT&TAG


title: 205022240078_R01C01: BR_CA


title: 205022240078_R05C01: BR_CA


title: 205022020133_R04C01: BR_CA


title: 205022240166_R07C01: BR_CA


title: 205022240166_R06C01: DNADEG


title: 205022030077_R05C01: -


title: 205022030077_R06C01: BR_FAD


title: 205022240166_R05C01: BR_CA


title: 205022240166_R04C01: BR_CA


title: 205022240166_R08C01: BR_CA


title: 204957740106_R02C01: DNADEG


title: 204949780066_R01C01: DNADEG


title: 204949780066_R06C01: BR_CA


title: 204949780066_R07C01: BR_CA


title: 204957740106_R01C01: BR_CA


title: 204957740066_R06C01: BR_CA


title: 204001300138_R08C01: BR_CA

value: DNA native


title: 205022240166_R02C01: BR_CA


title: 205022030077_R07C01: BR_CA


title: 204001350044_R02C01: BR_FAD


title: 205022030077_R04C01: -


title: 204972790085_R08C01: DNADEG


title: 203885690015_R04C01: DNADEG


title: 204949780066_R08C01: BR_CA


title: 204949780066_R05C01: DNADEG


title: 203927450088_R02C01: BR_FAD


title: 203927450088_R03C01: BR_FAD


title: 203930200142_R04C01: BR_FAD


title: 204957740066_R07C01: DNADEG


title: 204972790085_R07C01: BR_CA


title: 204026500042_R06C01: BR_CA


title: 203930200048_R07C01: BR_FAD


title: 203930200044_R01C01: BR_FAD


title: 204001300138_R07C01: BR_CA


title: 203930200142_R03C01: BR_FAD


title: 203946830053_R06C01: BR_FAD


title: 203930200142_R02C01: BR_FAD


title: 203253040182_R06C01: PHYT_BEN


title: 203259060045_R03C01: PHYT_BOR


title: 203923030139_R04C01: BR_FAD


title: 203253040191_R01C01: PHYT_BOR


title: 203293640041_R05C01: DLBCL

value: DLBCL


title: 204957740066_R08C01: BR_CA


title: 203930200142_R01C01: BR_FAD


title: 203824910109_R07C01: BR_FAD


title: 203257020148_R08C01: PHYT_NOS


title: 203836210043_R02C01: PHYT_BOR


title: 203253040191_R02C01: BR_FAD


title: 203885690015_R05C01: BR_FAD


title: 203271740040_R05C01: FA

value: FA


title: 203271740040_R06C01: benign PT

value: benign PT


title: 203836210043_R01C01: PHYT_BEN


title: 203885690015_R03C01: BR_FAD


title: 203244500079_R08C01: PHYT_BEN


title: 203259060045_R02C01: borderline PT

value: borderline PT


title: 203271740040_R03C01: benign PT


title: 203271740040_R07C01: benign PT


title: 203293640041_R02C01: PHYT_NOS


title: 203836210043_R07C01: benign or borderline PT

value: benign or borderline PT


title: 203293640041_R01C01: PHYT_BEN


title: 203836210043_R04C01: malignant PT

value: malignant PT


title: 203257020148_R06C01: PHYT_BOR


title: 203259600099_R08C01: PHYT_BEN


title: 203244490194_R08C01: PHYT_NOS


title: 203836210043_R03C01: benign PT


title: 203244490194_R07C01: PHYT_NOS


title: 203253040182_R08C01: malignant PT


title: 203257020148_R07C01: malignant PT


title: 203271740040_R01C01: malignant PT


title: 203271740040_R02C01: benign PT


title: 203293640041_R08C01: PHYT_MAL


title: 203946830053_R07C01: benign PT


title: 203808570131_R05C01: malignant PT


title: 203271740040_R08C01: PT NOS

value: PT NOS


title: 203293640041_R07C01: malignant PT


title: 203259600099_R05C01: benign PT


title: 203293640041_R03C01: benign PT


title: 203244490194_R06C01: borderline PT


title: 2055_Day7-FB

status: Public on Jun 25 2021

city: Stanford

first: Madeleine

last: Scott

address: 729 Lagunita Dr

institute: Stanford

description: ADT

data_processing:
Cellranger 3.1.0
Seurat 3.6.3 used for all downstream processing
Genome_build: Hg38
Supplementary_files_format_and_content: gene expression matrices (mtx)

source_name: PBMCs

extract_protocol:
PBMC isolation directly after blood sample collection
10x Single Cell 3' v3

value: PBMCs

tag: patient

tag: time (days)

tag: Sex

value: Female

tag: race

value: White

tag: ethnicity

value: Mediterranean, Jewish, Syrian, Southern European


title: 2055_Day42-FB

description: ADT

tag: age


title: 2055_Day28-FB

description: ADT


title: 203293640041_R06C01: malignant PT

data_processing:
Minfi (R 3.6.3), Conumee (R 3.6.3), www.epidip.org
The algorithm to process the data is our online tool (www.epidip.org), and the raw data are/were processed by this platform on an ad-hoc basis. EpiDiP is our free, publicly available unsupervised machine learning tool (UMAP-based) that cross-compares all submitted methylation datasets (450K/850K). The tool requires raw IDAT files only. All conclusions made in this study are based on UMAP results and copy number plots, also generated in EpiDiP. The employed R version (for minfi/conumee) is specified in the metadata. As a consequence, no normalized data are included.

value: female


title: 2055_Day2-FB

description: ADT


title: 2053_Day42-FB

description: ADT

value: Asian

value: Non-Hispanic


title: 203253040182_R07C01: malignant PT

value: DNA FFPE

value: breast tumor


title: 2053_Day7-FB

description: ADT


title: 203259600099_R06C01: malignant PT

value: DNA native


title: 203259600099_R07C01: borderline PT


title: 203259060045_R01C01: benign PT


title: 203259060045_R04C01: benign PT


title: 2055_Day22-FB

description: ADT


title: 2055_Day0-FB

description: ADT


title: 2055_Day21-FB

description: ADT


title: 2052_Day42-FB b

description: ADT

value: Male

value: South Asian


title: 2052_Day7-FB

description: ADT


title: 2053_Day22-FB

description: ADT


title: 2052_Day28-FB

description: ADT


title: 2053_Day21-FB

description: ADT


title: 2052_Day22-FB b

description: ADT


title: 2052_Day21-FB b

description: ADT


title: 2053_Day2-FB

description: ADT


title: 2053_Day28-FB

description: ADT


title: 2052_Day7-FB b

description: ADT


title: 2052_Day42-FB

description: ADT


title: 2052_Day28-FB b

description: ADT


title: 2051_Day0-FB

description: ADT

value: Armenian


title: 2052_Day22-FB

description: ADT


title: 2047_Day7-FB

description: ADT


title: 2052_Day21-FB

description: ADT


title: 2047_Day42-FB

description: ADT


title: 2051_Day7-FB

description: ADT


title: 2047_Day28-FB

description: ADT


title: 2051_Day42-FB

description: ADT


title: 2047_Day22-FB

description: ADT


title: 2047_Day21-FB

description: ADT


title: 2047_Day1-FB

description: ADT


title: 2051_Day28-FB

description: ADT


title: 2051_Day2-FB

description: ADT


title: 2049_Day1-FB

description: ADT

value: Chinese American


title: 2049_Day0-FB

description: ADT


title: 2055_Day28

description: RNA


title: 2051_Day1-FB

description: ADT


title: 2053_Day0-FB

description: ADT


title: 2055_Day21

description: RNA


title: 2053_Day7

description: RNA


title: 2047_Day2-FB

description: ADT


title: 2047_Day0-FB

description: ADT


title: 2055_Day7

description: RNA


title: 2053_Day0

description: RNA


title: 2055_Day42

description: RNA


title: 2052_Day7b

description: RNA


title: 2051_Day22-FB

description: ADT


title: 2051_Day21-FB

description: ADT


title: 2055_Day22

description: RNA


title: 2055_Day2

description: RNA


title: 2052_Day28

description: RNA


title: 2052_Day22

description: RNA


title: 2055_Day0

description: RNA


title: 2053_Day42

description: RNA


title: 2053_Day21

description: RNA


title: 2053_Day28

description: RNA


title: 2053_Day22

description: RNA


title: 2051_Day28

description: RNA


title: 2052_Day42b

description: RNA


title: 2051_Day22

description: RNA


title: 2051_Day21

description: RNA


title: 2052_Day7

description: RNA


title: 2053_Day2

description: RNA


title: 2052_Day42

description: RNA


title: 2052_Day21

description: RNA


title: 2049_Day28

description: RNA


title: 2052_Day2

description: RNA


title: 2052_Day0

description: RNA


title: 2049_Day21

description: RNA


title: 2051_Day42

description: RNA


title: 2052_Day21b

description: RNA


title: 2051_Day7

description: RNA


title: 2052_Day28b

description: RNA


title: 2051_Day2

description: RNA


title: 2051_Day1

description:
Sample contains a mix of day 1 2049 and 2051 cells
RNA


title: 2051_Day0

description: RNA


title: 2047_Day7

description: RNA


title: 2047_Day22

description: RNA


title: 2047_Day28

description: RNA


title: 2049_Day7

description: RNA


title: 2047_Day1

description: RNA


title: 2047_Day0

description: RNA


title: 2049_Day42

description: RNA


title: 2052_Day22b

description: RNA


title: 2049_Day22

description: RNA


title: 2049_Day1