title: Washout_ATACseq_SOX2-FKBP_Washout

description: treated with dTAG-13 for 2 hours, after which culture medium was refreshed without treatment

data_processing:
Fastq files were aligned to the mm10 reference genome using the bwa mem software version 0.7.17-r1188 with the `-M` argument.
Alignments were filtered to exclude low quality alignments with samtools version 1.10 using the command `samtools view -h -b -q 10`.
Duplicated alignments were removed using the `MarkDuplicates` command from Picard tools version 2.12.0 with the argument `REMOVE_DUPLICATES=true`.
Properly paired reads of primary alignments were converted to fragments with a +4/-5 shift of 5’ ends of positive and negative strand reads using a custom R script.
Bigwig files were build from the fragments files pooled by condition, by scaling coverage to the sum of length of the standard chromosomes using a custom R script.
Assembly: mm10
Supplementary files format and content: bigWig files
Supplementary files format and content: narrowPeak files
Supplementary files format and content: Tab-delimited text files containing raw counts with peaks as rows and samples as columns

extract_protocol:
Cells were harvested and washed 1X in cold PBS. 50,000 cells were counted and nuclei were lysed using 2x lysis buffer (1M Tris-HCl pH 7.5, 5M NaCl, 1M MgCl2, 10% IGEPAL). Cells were spun down incubated for 1h at 37°C in tagmentation buffer (20 mM   Tris(hydroxymethyl)aminomethane; 10 mM MgCl2, 20% dimethylformamide, brought at pH 7.6 with acetic acid) containing custom Tn5.
For amplification of the tagmented DNA, two rounds of PCR were used using KAPA kit amplification protocol and sequencing adapters were included during the PCRs for library preparation. Fragments smaller than 700 bp were purified using SPRI beads selection. Quality of the libraries was checked on a Bioanalyzer before sequencing.

treatment_protocol: For depletion treatment, the OCT4-, SOX2-, NANOG-FKBP cell lines were treated with a final concentration of 500 nM dTAG-13 or DMSO (NT, Not treated). For time course experiments, cells were seeded overnight and treated the next day, by inducing protein depletion at different time points and harvesting at the end of the time course. DMSO was added at the same time as the latest dTAG-13 treatment.


title: HMGB2_Cl13_d8_2

status: Public on Jul 24 2023

type: SRA

city: Irvine

first: Roberto

last: Tinoco

state: CA

address: 3444 McGaugh Hall

department: Molecular Biology and Biochemistry

country: USA

institute: University of California, Irvine

library_source: transcriptomic

data_processing:
Post-processing of the run to generate FASTQ files was performed at the Institute for Genomics and Bioinformatics (UCI IGB).
PcaHubert was used to identify any outlier samples, which were removed from further analysis.
The quality of the sequencing was first assessed using the fastQC tool (v0.11.9). Raw reads were then quality trimmed and filtered by a length of 20 bases using trimmomatic (v0.39). Trimmed reads were analyzed with the mouse Grcm38 reference genome using pseudo aligner Salmon (v1.2.1) and resulting quantification files were imported using R package tximport to get TPM values for all annotated mouse genes.
Differential analysis was done using R package DESeq2 (v1.22.2) with an FDR cut off of 0.05.

molecule: total RNA

organism: Mus musculus

source_name: Spleen

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). Total RNA was monitored for quality control using the Agilent Bioanalyzer Nano RNA chip and Nanodrop absorbance ratios for 260/280nm and 260/230nm.
Library construction was performed according to the Illumina TruSeq mRNA stranded protocol.
The input quantity for total RNA within the recommended range and mRNA was enriched using oligo dT magnetic beads. The enriched mRNA was chemically fragmented. First strand synthesis used random primers and reverse transcriptase to make cDNA. After second strand synthesis the ds cDNA was cleaned using AMPure XP beads and the cDNA was end repaired and then the 3’ ends were adenylated. Illumina barcoded adapters were ligated on the ends and the adapter ligated fragments were enriched by nine cycles of PCR. The resulting libraries were validated by qPCR and sized by Agilent Bioanalyzer DNA high sensitivity chip. The concentrations for the libraries were normalized and then multiplexed together. The multiplexed libraries were sequenced using paired end 100 cycles chemistry on the NovaSeq 6000.

tag: tissue

value: Spleen

tag: genotype

value: HMGB2 KO P14


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 5, DPI 21, tech rep 1

city: Galveston

first: Thomas

last: Geisbert

state: TX

address: 301 University Blvd

department: Microbiology and Immunology

institute: University of Texas Medical Branch

description: Processed data file col_name: nhp1407408_28_416

data_processing:
Sequencing quality of each sequenced sample was analyzed with fastQC (version 0.11.7).
Raw fastq files were trimmed with trimmomatic (version 0.36) with “LEADING” and “TRAILING” set to cut sequences below quality Phred score of 3 from the beginning or end of the read, respectively. Sequences below 15bp were automatically rejected.
STAR RNA-seq aligner (Dobin & Gingeras, 2015) version 2.5.3a was then used to create an index containing the cynomolgus macaque (Version 5.0), BDBV, and VSV genomes. Trimmed reads were aligned to these genomes using STAR.
The number of reads associated with each transcript was then counted with featureCounts (subread package version 1.6.2).
Genes with multiple possible transcripts were combined to get the number of reads per gene using DESeq2 (version 1.32.0). DESeq2 was used to normalize library sizes and measure differential expression between pre-infection and post infection samples.
Assembly: Macaca_fascicularis_5.0 (GCA_000364345.1)
Supplementary files format and content: bdbv_2019_30min_raw_counts.xlsx: total gene counts, pre-normalization by DESeg2

organism: Macaca fascicularis

source_name: Blood

growth_protocol: The BDBV used in this study, strain 200706291 (GenBank accession no. MK028856.1), was isolated from a fatal human case in western Uganda during the outbreak in 2007. The challenge stock of BDBV was propagated on Vero E6 cells twice.

extract_protocol:
At least three million PBMC were inactivated with Trizol LS buffer (Thermo Fisher Scientific) for isolation of RNA. RNA was isolated using Direct-zol RNA Miniprep purification kits (Zymo Research) following the directions of the manufacturer with the optional DNAse I treatment and subsequent wash steps. RNA was eluted in 30ul of DNase/RNase-free water.
An Illumina Ribo-Zero Stranded kit was used to deplete ribosomal RNA (rRNA) and construct cDNA libraries according to the protocol provided by the manufacturer. RNA was fragmented, converted to double-stranded cDNA, and adapters ligated to each strand. The resulting base-pair cDNA fragments were then amplified by PCR. Each library was prepared with a unique indexed adapter for multiplexing. Multiplexed libraries were subjected to paired-end 75 base pair sequencing using the Illumina NextSeq550 PE platform.

value: Blood

tag: cell type

value: PBMC

value: WT

tag: animal id

tag: animal id supp

value: Survivor 5

tag: Sex

value: female

tag: outcome

value: survived

tag: challenge

value: BDBV

tag: time (days post infection)

tag: treatment time

tag: treatment

value: VSV-BDBV-GP

tag: tech rep


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 5, DPI 15, tech rep 2

description: Processed data file col_name: nhp1407408_28_415


title: HMGB2_Cl13_d8_1


title: 510 MPO R848 6h donor F

city: London

first: Michael

last: Robson

address: Great Maze Pond

country: United Kingdom

institute: King's College London

description:
donor F
genes.readcount2.annot.xls
genes.FPKM.annot2.xls

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through in-house scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software, which is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure.  HTSeq was used to count the read numbers mapped of each gene.
RPKM of each gene was then calculated based on the length of the gene and reads count mapped to this gene. RPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time.
Supplementary files format and content: 2 excel files contain the read counts for all the samples and 2 excel files contain the FPKM data for all the samples.

organism: Homo sapiens

source_name: monocytes isolated from blood

growth_protocol: Peripheral blood mononuclear cells from healthy controls were isolated from blood anticoagulated with EDTA using Ficoll-Paque (GE Healthcare) density gradient centrifugation.  For experiments including TLR agonists, monocytes were then isolated by depletion of CD16+ cells followed by positive section for CD14+ cells with magnetic microbeads (Miltenyi Biotec). For experiments performed not including TLR agonists, cells were positively selected for CD14+, but not CD16 depleted. Cells were resuspended in RPMI (Sigma) with 10% AB serum* or FCS ** (Sigma) and 1% Pen-Strep (Sigma) and plated as 500ml at 1x106 cells/ml in 48 well plates. *Without TLR agonists. ** With TLR agonists.

extract_protocol:
At 6 hours (experiments with TLR agonists) or 24 hours (experiments without TLR agonists) RNA was purified using Monarch total RNA miniprep kit (New England BioLabs Inc.) according to manufacturer’s instructions.
Library preparation and sequencing was performed by Novogene Bioinformatics Technology (Beijing, PR China). Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor- ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated. The read depth was 30 million reads per sample.

treatment_protocol: Where indicated, LPS (25ng/ml, Escherichia coli R515; Enzo Life Sciences, UK – catalogue number ALX-581-007-L002) or R848 (5mg/ml, Invivogen) was added.  250 mg/ml of human control, anti-PR3 or anti-MPO IgG was added and plates incubated at 37°C for the time indicated.

value: monocytes

tag: group (control, mpo, pr3)

value: MPO

tag: treatment (none, lps, r848)

tag: time (6h, 24h)


title: 509 MPO R848 6h donor F


title: Washout_ATACseq_SOX2-FKBP_2H

city: Amsterdam

first: Elzo

last: de Wit

state: Noord-Holland

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

description: treated with dTAG-13 for 2 hours

library_source: genomic

molecule: genomic DNA

source_name: Embryo

growth_protocol: Mouse Embryonic Stem Cells (ESCs) cell lines were cultured on 0.1% gelatin-coated plates in serum-free DMEM/F12 (Gibco) and Neurobasal (Gibco) medium (1:1) supplemented with N-2 (Gibco), B-27 (Gibco), BSA (0.05%, Gibco), 10*4U of Leukemia Inhibitory Factor/LIF (Millipore), MEK inhibitor PD0325901 (1 µM, Selleckchem), GSK3-β inhibitor CHIR99021 (3 µM, Cayman Chemical) and 1-Thioglycerol (1.5x10-4 M, SigmaAldrich). The cell lines were passaged every 2 days in daily culture.

value: Embryo

tag: cell line

value: Embryonic Stem Cell

tag: time


title: 514 MPO R848 6h donor F


title: Washout_ATACseq_SOX2-FKBP_DMSO

description: control treated with DMSO for 2 hours, after which culture medium was refreshed without treatment

tag: tissue

value: DMSO


title: WT_Cl13_d8_3

tag: genotype

value: WT P14


title: DAR-KO_ATACseq_SOX2-FKBP_C13

description: Knock-out of Klf2 downstream DAR

tag: cell type

value: NT


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 5, DPI 12, tech rep 2

description: Processed data file col_name: nhp1407408_21_413

tag: animal id


title: WT_Cl13_d8_1

value: Spleen


title: WT_Cl13_d8_2


title: 507 control R848 6h donor F

value: control


title: HMGB2_Arm_d8_2

value: HMGB2 KO P14


title: 508 control R848 6h donor F


title: 505 control R848 6h donor F


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 5, DPI 12, tech rep 1

description: Processed data file col_name: nhp1407408_15_414

value: Blood

value: PBMC

tag: animal id supp


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 5, DPI 9, tech rep 2

description: Processed data file col_name: nhp1407408_15_413

value: WT

value: Survivor 5

tag: Sex


title: WT_Arm_d8_3


title: 504 control R848 6h donor F


title: HMGB2_Arm_d8_1


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 5, DPI 9, tech rep 1

description: Processed data file col_name: nhp1407408_12_418

value: female

tag: outcome

value: survived


title: Overexpression_ATACseq_SOX2-FKBP_TAD_dTAG

description: SOX2 TAD-domain overexpression plasmid


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 5, DPI 7, tech rep 2

description: Processed data file col_name: nhp1407408_12_417

tag: challenge

value: BDBV

value: VSV-BDBV-GP


title: 503 control R848 6h donor F

value: monocytes


title: 506 control R848 6h donor F


title: WT_Arm_d8_2


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 5, DPI 7, tech rep 1

description: Processed data file col_name: nhp1407408_01_414

tag: time (days post infection)


title: Overexpression_ATACseq_SOX2-FKBP_HMG_dTAG

description: SOX2 HMG-domain overexpression plasmid

value: Embryo


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 5, DPI 15, tech rep 1

description: Processed data file col_name: nhp1407408_21_414

tag: treatment time


title: Overexpression_ATACseq_SOX2-FKBP_HMG_DMSO

description: SOX2 HMG-domain overexpression plasmid

value: Embryonic Stem Cell

tag: treatment


title: 502 control R848 6h donor F


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 5, DPI 5, tech rep 1

description: Processed data file col_name: nhp1407408_01_413

tag: tech rep


title: DAR-KO_ATACseq_SOX2-FKBP_C10

description: Knock-out of Klf2 downstream DAR


title: Overexpression_ATACseq_SOX2-FKBP_eGFP_dTAG

description: eGFP overexpression plasmid


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 5, DPI 1, tech rep 2

description: Processed data file col_name: nhp1407408_00_416


title: 424 PR3 LPS 6h donor F

description:
donor F
genes.readcount.annot.xls
genes.FPKM.annot.xls

tag: group (control, mpo, pr3)

value: LPS


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 5, DPI 1, tech rep 1

description: Processed data file col_name: nhp1407408_00_415


title: WT_Arm_d8_1

value: WT P14


title: Overexpression_ATACseq_SOX2-FKBP_TAD_DMSO

description: SOX2 TAD-domain overexpression plasmid

value: DMSO


title: 423 PR3 LPS 6h donor F

tag: treatment (none, lps, r848)


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 5, DPI 0, tech rep 2

description: Processed data file col_name: nhp1407408_09_414


title: 501 control R848 6h donor F

tag: time (6h, 24h)


title: 422 PR3 LPS 6h donor F


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 5, DPI 0, tech rep 1

description: Processed data file col_name: nhp1407408_09_413


title: 421 PR3 LPS 6h donor F


title: Overexpression_ATACseq_SOX2-FKBP_Full_DMSO

description: Full-length SOX2 overexpression plasmid

tag: cell line


title: Overexpression_ATACseq_SOX2-FKBP_Full_dTAG

description: Full-length SOX2 overexpression plasmid

tag: time


title: Peritoneal macrophages, LPS and CPZ, 4h, rep3 [S3_2]

city: Shanghai

first: Zehua

last: Zhang

state: --- Select One ---

address: No. 150 Jimo Road

country: China

institute: Tongji University School of Medicine

data_processing:
The raw data was handled by Skewer and data quality was checked by FastQC v0.11.2. The read length was 2×150 bp. Clean reads were aligned to the Mouse genome hg38 using STAR. StringTie. The expression of the transcript was calculated by FPKM (Fragments Per Kilobase of exon model per Million mapped reads) using Perl. Differentially expression transcripts were determined using the MA-plot-based method with Random Sampling (MARS) model in the DEGseq package between different time points (12 hpt vs. 0 hpt, 36 hpt vs. 0 hpt, 72 hpt vs. 0 hpt). Generally, in MARS model, M = log2C1 - log2C2, and A = (log2C1 + log2C2)/2 (C1 and C2 denote the counts of reads mapped to a specific gene obtained from two samples).
The thresholds for determining DETs are P < 0.05 and absolute fold change ≥ 2. Then DETs were chosen for function and signaling pathway enrichment analysis using GO and KEGG database. The significantly enriched pathways were determined when P < 0.05 and at least two affiliated genes were included. PPI analysis of differentially expressed genes was based on the STRING database, which known and predicted Protein-Protein Interactions. And the network was established according to the known interaction of the selected reference specie.
In the GO analysis bar graph, the x-axis represents -log10(p-value), and the y-axis represents the significantly enriched GO terms. In the network graph of the top 20 GO terms and their relationships, the ratio of overlapping genes to unique genes between the terms is greater than or equal to 20%, and the node size represents the total number of candidate genes belonging to the GO term, and the color represents -log10(p-value).
In the enrichment of diseases, the x-axis represents the names of significantly enriched diseases, and the y-axis represents -log10(p-value).
In the enrichment of Reactome pathways, the x-axis represents the names of significantly enriched Reactome pathways, and the y-axis represents -log10(p-value). Each point of the volcano graph represents a gene, and the abscissa represents the value of log2FC, and set ∣log2FC∣≥1 as a significantly different gene, where ≥1 points represent genes that are significantly upregulated in the experimental group G2 compared to the control group G1, ≤- The point of 1 indicates the genes that are significantly down-regulated in the experimental group G2 compared to the control group G1; the ordinate indicates -log10(P-Value), when P-Value≤0.05, it is considered as a significantly different gene. Therefore, in the volcano map, the purple points on the left represent the genes that are significantly down-regulated in the experimental group G2 compared to the control group G1, the blue points on the right represent the genes that are significantly up-regulated in the experimental group G2 compared to the control group G1, and the gray points represent non-significant differences Gene.
Assembly: hg38
Supplementary files format and content: Expression data for all samples exists at gene_sample_FPKM_with_symbol.

source_name: Peritoneal macrophages

extract_protocol:
Total RNA was isolated from each sample using the RNAmini kit (Qiagen, Germany). RNA quality was examined by gel electrophoresis and with Qubit (Thermo, Waltham, MA, USA). For RNA sequencing, RNA samples from three biological replicates every group were separated into three independent pools, each comprised of three distinct samples, at equal amounts.
Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA), and sequencing was carried out using the Illumina Novaseq 6000 instrument by the commercial service of Genergy Biotechnology Co. Ltd. (Shanghai, China).

value: Peritoneal macrophages

value: LPS and CPZ, 4h


title: Peritoneal macrophages, LPS and EtOH, 4h, rep3 [S3_1]

value: LPS and EtOH, 4h


title: Peritoneal macrophages, LPS and CPZ, 4h, rep2 [S2_2]


title: Peritoneal macrophages, LPS and CPZ, 4h, rep1 [S1_2]


title: Timeseries_ATACseq_NANOG-FKBP_24H_Rep3

tag: tissue

value: NANOG-FKBP


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 2, DPI 28, tech rep 2

description: Processed data file col_name: nhp1312511_09_416

value: Blood

value: PBMC

tag: genotype

value: Survivor 2

value: male


title: Peritoneal macrophages, LPS and EtOH, 4h, rep2 [S2_1]

tag: cell type


title: Timeseries_ATACseq_NANOG-FKBP_24H_Rep2


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 2, DPI 21, tech rep 2

description: Processed data file col_name: nhp1312511_07_414

value: WT

tag: animal id

value: survived


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 2, DPI 28, tech rep 1

description: Processed data file col_name: nhp1312511_09_415

tag: animal id supp

value: BDBV

value: VSV-BDBV-GP


title: Overexpression_ATACseq_SOX2-FKBP_eGFP_DMSO

description: eGFP overexpression plasmid

value: Embryo


title: Timeseries_ATACseq_NANOG-FKBP_6H_Rep3

value: Embryonic Stem Cell


title: Timeseries_ATACseq_NANOG-FKBP_24H_Rep1


title: Peritoneal macrophages, LPS, 4h, rep2 [control_2]

value: LPS, 4h


title: Peritoneal macrophages, LPS, 4h, rep3 [control_3]


title: 416 MPO LPS 6h donor F

value: monocytes

value: MPO

value: LPS


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 2, DPI 21, tech rep 1

description: Processed data file col_name: nhp1312511_07_413

tag: Sex


title: Timeseries_ATACseq_NANOG-FKBP_6H_Rep2


title: 417 PR3 LPS 6h donor F


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 2, DPI 15, tech rep 2

description: Processed data file col_name: nhp1312511_05_414

tag: outcome


title: 415 MPO LPS 6h donor F


title: Peritoneal macrophages, LPS, 4h, rep1 [control_1]

value: Peritoneal macrophages


title: Timeseries_ATACseq_NANOG-FKBP_6H_Rep1


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 2, DPI 15, tech rep 1

description: Processed data file col_name: nhp1312511_05_413

tag: challenge


title: 414 MPO LPS 6h donor F


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 2, DPI 12, tech rep 2

description: Processed data file col_name: nhp1312511_28_418

tag: time (days post infection)


title: DAR-KO_ATACseq_SOX2-FKBP_C5

description: Knock-out of Klf2 downstream DAR

value: NT


title: Peritoneal macrophages, LPS and EtOH, 4h, rep1 [S1_1]

value: LPS and EtOH, 4h


title: Timeseries_ATACseq_NANOG-FKBP_2H_Rep3

value: NANOG-FKBP


title: 413 MPO LPS 6h donor F


title: NC2

city: Hefei

first: Ke

last: Gong

address: 193 Tunxi Road, Baohe District

institute: Hefei University of Technology

description: liver from Nogo KO mice

data_processing:
CLC Genomics Workbench v11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM 38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 lengh fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: MM10
Supplementary files format and content: tab-delimitedtext lies include RPKM values for each Sample

source_name: liver

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNAwas usedkx the construction of sequencing libraries
RNA libraries for RNA-seq were prepared usingSMARTER mRNA-Seq Library Prep Kit Ulcwing manufacturer's protocols.

value: liver

value: Nogo-/-

value: normal chow


title: NC4

description: liver from Nogo KO mice


title: NC1

description: liver from Nogo KO mice


title: 419 PR3 LPS 6h donor F


title: 420 PR3 LPS 6h donor F


title: Timeseries_ATACseq_NANOG-FKBP_2H_Rep2


title: 412 MPO LPS 6h donor F


title: CC11

description: liver from wild type mice

value: WT


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 2, DPI 9, tech rep 2

description: Processed data file col_name: nhp1312511_21_418

value: Blood

value: PBMC

value: Survivor 2

value: male

value: survived

tag: treatment time


title: 411 MPO LPS 6h donor F


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 2, DPI 9, tech rep 1

description: Processed data file col_name: nhp1312511_21_417

value: BDBV

tag: treatment

value: VSV-BDBV-GP


title: Timeseries_ATACseq_NANOG-FKBP_NT_Rep2

value: Embryo

value: Embryonic Stem Cell


title: 410 MPO LPS 6h donor F

value: monocytes

value: MPO

value: LPS


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 2, DPI 7, tech rep 2

description: Processed data file col_name: nhp1312511_15_416

tag: tech rep


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 2, DPI 12, tech rep 1

description: Processed data file col_name: nhp1312511_28_417


title: CC4

description: liver from wild type mice


title: Timeseries_ATACseq_NANOG-FKBP_NT_Rep1

value: NANOG-FKBP

value: NT


title: CC2

description: liver from wild type mice

value: liver


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 2, DPI 5, tech rep 1

description: Processed data file col_name: nhp1312511_12_413


title: 406 control LPS 6h donor F

tag: group (control, mpo, pr3)

value: control


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 2, DPI 7, tech rep 1

description: Processed data file col_name: nhp1312511_15_415

value: WT


title: Timeseries_ATACseq_OCT4-FKBP_2H_Rep2


title: 405 control LPS 6h donor F

description:
donor F
genes.readcount.annot.xls
genes.FPKM.annot.xls

tag: treatment (none, lps, r848)


title: 407 control LPS 6h donor F

tag: time (6h, 24h)


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 2, DPI 1, tech rep 1

description: Processed data file col_name: nhp1312511_01_415

value: Blood


title: Timeseries_ATACseq_OCT4-FKBP_24H_Rep2

tag: cell line


title: Timeseries_ATACseq_OCT4-FKBP_24H_Rep1

tag: time


title: 404 control LPS 6h donor F


title: Timeseries_ATACseq_OCT4-FKBP_6H_Rep2

tag: tissue


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 2, DPI 0, tech rep 2

description: Processed data file col_name: nhp1312511_00_418

value: PBMC

tag: genotype


title: 409 MPO LPS 6h donor F

tag: cell type


title: Transgene-free F/R/C+CP-derived iMPCs

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
CellRanger v7.0.0 used for demultiplexing + read mapping + barcode assignment + UMI counting
Seurat v4.2.1 used for quality control + normalization + dimensionality reduction + clustering + integration
RNA Velocity: STARSolo was used to generate gene-level, spliced, and unspliced counts and preprocessed with scater. Velocities were calculated using scvelo in the velociraptor package, using 50 neighbors
Assembly: GRCm39
Supplementary files format and content: Filtered count matrices from CellRanger

source_name: induced myogenic progenitors

extract_protocol:
Transgene-free iMPC clones were trypsinized from the cell culture plate, resuspended in PBS after filtering out myofibers, and used for 10X platform.
Chromium Next GEM Single cell 3’ v3.1 protocol was used according to the manufacturer’s instruction. Shortly, a Gel Bead-In Emulsions (GEM) was generated by loading cells in chromium Next GEM chip G targeting ~5,000 cells in recovery. GEM then was incubated in a thermal cycler and cleaned with Dynabeads followed by cDNA amplification. Amplified cDNA was used for fragmentation followed by end repair and A-tailing. Next, adaptor ligation and index PCR were performed using single index plate T set A and double size selection was carried out using AMPure XP (Beckman Coulter, Cat. #A63881).

value: induced myogenic progenitors

value: chemically reprogrammed myogenic cells

value: Cultured in F/R/C+CP containing media, generated by 4x transfection with synthetic MyoD-mRNA (iMPC medium+B18R); in presence of F/R/C+CP


title: Timeseries_ATACseq_NANOG-FKBP_2H_Rep1


title: Transgene-free F/R/C-derived iMPCs

description: 10x Genomics

value: Cultured in F/R/C containing media, generated by 4x transfection with synthetic MyoD-mRNA (iMPC medium+B18R); in presence of F/R/C


title: Timeseries_ATACseq_OCT4-FKBP_6H_Rep1


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 2, DPI 0, tech rep 1

description: Processed data file col_name: nhp1312511_00_417

tag: animal id

value: Survivor 2

value: male

value: survived

value: BDBV

value: VSV-BDBV-GP


title: 408 control LPS 6h donor F

value: monocytes

value: LPS


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 2, DPI 5, tech rep 2

description: Processed data file col_name: nhp1312511_12_414

tag: animal id supp


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 2, DPI 1, tech rep 2

description: Processed data file col_name: nhp1312511_01_416

tag: Sex


title: 403 control LPS 6h donor F


title: 402 control LPS 6h donor F


title: Timeseries_ATACseq_OCT4-FKBP_NT_Rep2

value: Embryo

value: Embryonic Stem Cell

value: NT


title: 401 control LPS 6h donor F

value: control


title: 24week_wt_45_2

city: Palo Alto

first: Jayakrishnan (Jk)

last: Gopakumar

address: 240 Pasteur Dr Rm 4600

institute: Stanford

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
24 week mRNA-derived cDNA

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv, features.tsv, matrix.mtx

molecule: polyA RNA

source_name: atheromas

extract_protocol:
Following weeks of atherogenic diet, aortic roots, aortic arches, and aortas were harvested and made into a single-cell suspension. CD45.1 and CD45.2 cells were sorted from each condition, and scRNAseq was performed on the sorted cells separately.
GEM generation & barcoding, post GEM–RT cleanup & cDNA amplification, and 3’ gene expression library construction as described in Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (https://support.10xgenomics.com/single-cell-gene-expression/index/doc/user-guide-chromium-single-cell-3-reagent-kits-user-guide-v31-chemistry-dual-index-with-feature-barcoding-technology-for-cell-surface-protein)
10X scRNAseq
Illumina NovaSeq PE150

tag: timepoint

value: 24 week

value: WT

value: atheromas

value: Sorted immune cells from atheromas


title: Timeseries_ATACseq_OCT4-FKBP_NT_Rep1


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 4, DPI 28, tech rep 2

description: Processed data file col_name: nhp1207278_09_414

value: Blood

value: PBMC

value: Survivor 4

value: female

tag: outcome

tag: challenge


title: Timeseries_ATACseq_SOX2-FKBP_24H_Rep2


title: 324 PR3 LPS 6h donor E

description:
donor E
genes.readcount.annot.xls
genes.FPKM.annot.xls


title: Timeseries_ATACseq_SOX2-FKBP_24H_Rep1


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 4, DPI 28, tech rep 1

description: Processed data file col_name: nhp1207278_09_413

value: survived

tag: time (days post infection)

tag: treatment time


title: 24week_tet2_f_45_2

value: Tet2 KO


title: Timeseries_ATACseq_OCT4-FKBP_2H_Rep1

tag: treatment


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 4, DPI 21, tech rep 2

description: Processed data file col_name: nhp1207278_07_418

value: BDBV

value: VSV-BDBV-GP

tag: tech rep


title: Timeseries_ATACseq_SOX2-FKBP_6H_Rep2


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 4, DPI 21, tech rep 1

description: Processed data file col_name: nhp1207278_07_417


title: 322 PR3 LPS 6h donor E

value: monocytes

tag: group (control, mpo, pr3)

tag: treatment (none, lps, r848)

value: LPS


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 4, DPI 15, tech rep 2

description: Processed data file col_name: nhp1207278_05_414


title: 24week_dnmt3a_45_2

value: Dnmt3a KO


title: 321 PR3 LPS 6h donor E

tag: time (6h, 24h)


title: Timeseries_ATACseq_SOX2-FKBP_2H_Rep2

value: Embryo

tag: cell line

value: Embryonic Stem Cell

tag: time


title: Timeseries_ATACseq_SOX2-FKBP_6H_Rep1

tag: tissue

tag: genotype


title: 24week_dnmt3a_45_1

value: 24 week

tag: cell type


title: 320 PR3 LPS 6h donor E


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 4, DPI 12, tech rep 2

description: Processed data file col_name: nhp1207278_28_416

value: WT

tag: animal id

tag: animal id supp


title: 30week_wt_45_1

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
30 week mRNA-derived cDNA

tag: timepoint

value: 30 week

value: atheromas


title: Timeseries_ATACseq_SOX2-FKBP_2H_Rep1


title: Timeseries_ATACseq_SOX2-FKBP_1H_Rep2


title: 24week_wt_45_1

value: Sorted immune cells from atheromas


title: 319 PR3 LPS 6h donor E


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 4, DPI 12, tech rep 1

description: Processed data file col_name: nhp1207278_28_415

value: Blood

value: PBMC

tag: Sex

tag: outcome


title: 30week_tet2_45_2


title: 317 PR3 LPS 6h donor E


title: 30week_tet2_45_1


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 4, DPI 9, tech rep 1

description: Processed data file col_name: nhp1207278_21_413

value: Survivor 4

value: female

tag: challenge

tag: time (days post infection)


title: 24week_wt_f_45_2


title: 30week_dnmt3a_45_2


title: Timeseries_ATACseq_SOX2-FKBP_0.5H_Rep2

tag: treatment


title: 323 PR3 LPS 6h donor E


title: 316 MPO LPS 6h donor E

value: MPO


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 4, DPI 7, tech rep 2

description: Processed data file col_name: nhp1207278_15_414

value: survived

value: BDBV

tag: treatment time

tag: tech rep


title: 315 MPO LPS 6h donor E

value: monocytes

tag: group (control, mpo, pr3)

tag: treatment (none, lps, r848)


title: 314 MPO LPS 6h donor E

value: LPS

tag: time (6h, 24h)


title: Timeseries_ATACseq_SOX2-FKBP_NT_Rep2

tag: cell line

value: NT

tag: time


title: 313 MPO LPS 6h donor E


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 4, DPI 7, tech rep 1

description: Processed data file col_name: nhp1207278_15_413

tag: tissue

tag: genotype

value: VSV-BDBV-GP


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 4, DPI 15, tech rep 1

description: Processed data file col_name: nhp1207278_05_413

tag: cell type

tag: animal id


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 4, DPI 5, tech rep 2

description: Processed data file col_name: nhp1207278_12_418

tag: animal id supp


title: Timeseries_ATACseq_SOX2-FKBP_NT_Rep1

value: Embryo

value: Embryonic Stem Cell


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 4, DPI 5, tech rep 1

description: Processed data file col_name: nhp1207278_12_417

value: WT

tag: Sex


title: JH133wt_corpus_hp

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

institute: ETH ZURICH / University of Zurich

data_processing:
Rna-seq reads were aligned with STAR-aligner using the genome build Ensembl Mus musculus GRCm39 Release 106
Gene expression values were computed with the function featureCounts from the R package Rsubread.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited .txt files include 5 columns, ensemble transcripts identifier, transcript length, effective transcript length, estimated counts and transcripts per million.

source_name: Gastric corpus

growth_protocol: Stomachs of 8-10 week-old mice were harvested, opened along the greater curvature and washed in ice-cold DPBS . Mucus and muscle/serosa layer were removed under a stereomicroscope using forceps; antrum and corpus were separated with a large safety margin, and both tissues were cut into 2-5 mm² sized pieces. Pieces were dissociated in 43.4 mM sucrose, 54.9 mM d-sorbitol in DPBS by 5-10 rounds of vigorous pipetting and washing, followed by incubation in 10 mM EDTA at 4°C for 1h 20 min (rolling shaker). After one more washing step in 43.4 mM sucrose, 54.9 mM d-sorbitol, glands were extracted by placing tissue pieces under a glass slide and applying enough pressure to release individual glands; glands were collected in DMEM, pushed through a 40 m filter, counted, collected by centrifuging and mixed with Matrigel, seeded into 24 well plates (50 l per well) and cultivated at 37°C in ADMEM medium (Advanced DMEM/F12 + 10mM Pen/strep) supplemented with wnt-conditioned medium, R-spondin1, N-acetylcysteine, EGF, FGF, Noggin, [Leu15]-Gastrin I, N2, B27, HEPES, Glutamax, Y27632 (10M; only on the seeding day; exclude thereafter).

extract_protocol:
RNA was extracted using the Quiagen RNeasy Mini Kit following manufacturer’s protocol. Extracted RNA was prepared for sequencing using the Illumina Truseq mRNA Library assay following manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For seeding in 2D, 7-day-old 3D organoids were dissociated in cold DMEM by vigorous pipetting. Organoid fragments were resuspended in TrypLE and incubated at 37°C for 10 min. Single cell suspensions were washed, centrifuged, counted and seeded at 15’000 cells/well into rat tail collagen-coated wells in 2D culture medium (which is identical to 3D medium, but lacks Wnt-conditioned medium, R-spondin, Pen/Strep, FGF, Noggin and N-acetylcysteine; contains 10% FCS, and 1 M TGF- inhibitor); cells receive fresh medium after 2 days in culture, and are infected with H. pylori after 3 days in culture. Bacterial numbers were determined by measuring the optical density at 600 nm, and bacteria were added to cells at an MOI of 50 for 6 h, unless otherwise specified. The H. pylori strains used in this study were G27, PMSS1  and PMSS1RFP. Organoid cells were treated with the NF-B inhibitor BAY 11-7082, and the Cdck1 inhibitor XL413 at 0.2 M final concentration. -ADP-heptose was added at 0.5M final concentration for six hours.

value: Gastric corpus

value: Epithelial cells

value: Helicobacter pylori infection


title: Timeseries_TTchemseq_SOX2-FKBP_6H_Rep2

description:
nascent RNA
Timeseries_TTchemseq_SOX2-FKBP_6H_fwd.bw
Timeseries_TTchemseq_SOX2-FKBP_6H_rev.bw

data_processing:
Fastq files were aligned to the mm10 reference genome using the bwa mem software version 0.7.17-r1188 with the `-M` argument.
Alignments were filtered to exclude low quality alignments with samtools version 1.10 using the command `samtools view -h -b -q 10`.
Duplicated alignments were removed using the `MarkDuplicates` command from Picard tools version 2.12.0 with the argument `REMOVE_DUPLICATES=true`.
Alignments were separated by strand with a custom script based on Gregerson et al. (2020)
Strandwise bigWig tracks were generated using the GenomicRanges R package and scaled to 1x genome coverage
Assembly: mm10
Supplementary files format and content: bigWig files
Supplementary files format and content: Tab-delimited text file containing raw counts with transcribed untis as rows and samples as columns
Supplementary files format and content: Tab-delimited text file describing one transcribed unit per row. Columns indicate chromsome, start, end, strand, feature identifier, feature annotation, matching refseq id, gene symbol and transcript range.
Library strategy: TTchem-seq

extract_protocol: Libraries for TTchemseq were prepared following a published protocol(Gregersen et al., 2020). Cells  were labeled with 2mM 4SU for 10 minutes. Total RNA was isolated and  fragmented. The 4SU-biotin labeled RNA was enriched using  streptavidin coated MicroBeads. Libraries were prepared using KAPA  RNA HyperPrep kits (Roche) using dual indexing adapters.

treatment_protocol: SOX2-FKBP  cells were seeded and the day after treated with 500 nM of dTAG-13  (0.5hpd, 1hpd, 2hpd, 6hpd) or DMSO as control.


title: 312 MPO LPS 6h donor E


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 4, DPI 1, tech rep 2

description: Processed data file col_name: nhp1207278_01_416

value: Blood

tag: outcome


title: Timeseries_ATACseq_SOX2-FKBP_1H_Rep1


title: 318 PR3 LPS 6h donor E


title: JH133wt_corpus_con

value: CTRL


title: 311 MPO LPS 6h donor E


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 4, DPI 9, tech rep 2

description: Processed data file col_name: nhp1207278_21_414

value: PBMC

value: Survivor 4

tag: challenge


title: Timeseries_TTchemseq_SOX2-FKBP_2H_Rep2

description:
nascent RNA
Timeseries_TTchemseq_SOX2-FKBP_2H_fwd.bw
Timeseries_TTchemseq_SOX2-FKBP_2H_rev.bw


title: Timeseries_TTchemseq_SOX2-FKBP_6H_Rep1


title: 310 MPO LPS 6h donor E

description:
donor E
genes.readcount.annot.xls
genes.FPKM.annot.xls

value: MPO


title: Timeseries_TTchemseq_SOX2-FKBP_2H_Rep1


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 4, DPI 1, tech rep 1

description: Processed data file col_name: nhp1207278_01_415

value: female

value: survived

tag: time (days post infection)


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 4, DPI 0, tech rep 2

description: Processed data file col_name: nhp1207278_00_418

value: BDBV

tag: treatment


title: Timeseries_ATACseq_SOX2-FKBP_0.5H_Rep1


title: 30week_dnmt3a_45_1

tag: timepoint

value: 30 week

value: atheromas

value: Sorted immune cells from atheromas


title: Timeseries_TTchemseq_SOX2-FKBP_1H_Rep2

description:
nascent RNA
Timeseries_TTchemseq_SOX2-FKBP_1H_fwd.bw
Timeseries_TTchemseq_SOX2-FKBP_1H_rev.bw

value: Embryo


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 4, DPI 0, tech rep 1

description: Processed data file col_name: nhp1207278_00_417

tag: treatment time

value: VSV-BDBV-GP

tag: tech rep


title: JH133apc_corpus_hp

value: APC min


title: JH133wt_antrum_hp

source_name: Gastric antrum

value: Gastric antrum

value: WT


title: 308 control LPS 6h donor E

value: monocytes

tag: group (control, mpo, pr3)

value: control

tag: treatment (none, lps, r848)

value: LPS


title: Timeseries_TTchemseq_SOX2-FKBP_1H_Rep1

tag: cell line

value: Embryonic Stem Cell


title: Single-cell RNA-seq of PC44

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

description:
10x Genomics
SCAF1933

data_processing:
Data was processed using the 10x Genomics CellRanger pipeline to demultiplex reads and then align those reads to the GRCh38 reference genome.
Gene barcode matricies were generated using the CellRanger pipeline from 10x Genomics aligned against GRCh38.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

growth_protocol: Organoids were grown in 3D in Matrigel and culture media.

extract_protocol:
Dispase was added to the culture for two hours. Organoids were pelleted by centriguation and dissociated in TrypLE plus Dnase-I for 20 minutes. Cells were passed through a 30-micron cell strainer and washed.
Single cells were counted and loaded onto the 10x Genomics Chromium platform. RNA-seq libraries were prepared using the 3' v3.0 chemistry. Single cell libraries were sequenced on either an Illumina NextSeq 500/550 instrument.

tag: cancer type

value: prostate cancer


title: 307 control LPS 6h donor E

tag: time (6h, 24h)


title: JH133apc_antrum_hp

tag: tissue

value: Epithelial cells

tag: genotype

value: Helicobacter pylori infection


title: 309 MPO LPS 6h donor E

tag: cell type

value: MPO


title: JH133apc_corpus_con

value: Gastric corpus

value: CTRL


title: Timeseries_TTchemseq_SOX2-FKBP_0.5H_Rep2

description:
nascent RNA
Timeseries_TTchemseq_SOX2-FKBP_0.5H_fwd.bw
Timeseries_TTchemseq_SOX2-FKBP_0.5H_rev.bw

tag: time


title: Timeseries_TTchemseq_SOX2-FKBP_0.5H_Rep1


title: JH133apc_antrum_con


title: 306 control LPS 6h donor E


title: Single-cell RNA-seq of LuCaP 145.2, tagged, 3 weeks of growth

description:
10x Genomics
SCAF1424

source_name: LuCaP 145.2

value: LuCaP 145.2

value: Cell-tagged, 3 weeks


title: 305 control LPS 6h donor E


title: Single-cell RNA-seq of LuCaP 145.2, tagged, 2 days of growth

description:
10x Genomics
SCAF1385

value: Cell-tagged, 2 days


title: Timeseries_TTchemseq_SOX2-FKBP_NT_Rep2

description:
nascent RNA
Timeseries_TTchemseq_SOX2-FKBP_NT_fwd.bw
Timeseries_TTchemseq_SOX2-FKBP_NT_rev.bw

value: Embryo

value: NT


title: 304 control LPS 6h donor E


title: Timeseries_TTchemseq_SOX2-FKBP_NT_Rep1


title: Single-cell RNA-seq of LuCaP 145.2, untagged, 3 weeks of growth

description:
10x Genomics
SCAF1425

value: Untagged, 3 weeks


title: Single-cell RNA-seq of PC35-2, tagged, 4 weeks of growth

description:
10x Genomics
SCAF1512

value: Cell-tagged, 4 weeks


title: JH133wt_antrum_con

value: Gastric antrum

value: WT


title: JH132wt_corpus_hp


title: PDC-RNA-10-1-3

city: Houston

first: Yulin

last: Dai

address: 7000 fannin, suite 600

department: School of Biomedical Informatics

institute: University of Texas health science center at Houston

data_processing:
Raw reads (fastq files) were aligned to mouse reference (mm10) using STAR aligner (version 2.6) with default settings, read count files were generated
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text for gene read count, sample information, and gene annotation

source_name: murine pancreatic ducts

extract_protocol:
RNA was isolated from cultured ducts using RNeasy extraction kit
RNA libraries were prepared for sequencing using the standard Illumina protocols

treatment_protocol: Eight week old transgenic mice were given tamoxifen and euthanized at day 4 for ex vivo culture analysis.

value: murine pancreatic ducts

tag: strain

value: Hnf1b:CreERT2; LSL-KrasG12V

value: tamoxifen


title: Single-cell RNA-seq of PC35-2, tagged, 1 week of growth

description:
10x Genomics
SCAF1427

value: prostate cancer

value: Cell-tagged, 1 week


title: 303 control LPS 6h donor E

value: monocytes

value: control

value: LPS


title: JH132wt_corpus_con

value: Gastric corpus

value: Epithelial cells

value: CTRL


title: JH132wt_antrum_hp

value: Helicobacter pylori infection


title: 302 control LPS 6h donor E


title: 301 control LPS 6h donor E


title: PDC-RNA-10-1-2


title: PDC-RNA-10-1-1


title: Single-cell RNA-seq of PC35-2, untagged, 4 weeks of growth

description:
10x Genomics
SCAF1513

value: Untagged, 4 weeks


title: Single-cell RNA-seq of PC35-1, tagged, 4 weeks of growth

description:
10x Genomics
SCAF1510


title: JH132apc_corpus_hp

value: APC min


title: 224 PR3 LPS 6h donor D

description:
donor D
genes.readcount.annot.xls
genes.FPKM.annot.xls


title: JH132apc_corpus_con


title: PDC-RNA-0-1_3


title: Single-cell RNA-seq of PC35-1, untagged, 4 weeks of growth

description:
10x Genomics
SCAF1511


title: Single-cell RNA-seq of PC35-1, tagged, 1 week of growth

description:
10x Genomics
SCAF1426


title: 223 PR3 LPS 6h donor D


title: JH132apc_antrum_hp


title: PDC-RNA-0-1_2


title: Single-cell ATAC-seq of PC35-2

description:
SCAF1988
10x Genomics

data_processing:
Data was processed using the 10x Genomics CellRanger scatac pipeline to demultiplex reads and then align those reads to the GRCh38 reference genome.
Peaks were called from scATAC fragments using CellRanger
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Dispase was added to the culture for two hours. Organoids were pelleted by centriguation and dissociated in TrypLE plus Dnase-I for 20 minutes. Cells were passed through a 30-micron cell strainer and washed.
Single cells were counted and resuspended in ATAC lysis buffer and incubated for 5 minutes. Nuclei were pelleted and resuspended in nuclei buffer. Single nuclei libraries were sequenced on either an Illumina NextSeq 500/550 instrument.


title: 222 PR3 LPS 6h donor D


title: PDC-RNA-0-1_1


title: JH132apc_antrum_con


title: 221 PR3 LPS 6h donor D


title: JH131wt_corpus_hp


title: Single-cell ATAC-seq of PC35-1

description:
SCAF1987
10x Genomics


title: JH132wt_antrum_con


title: JH131wt_corpus_con


title: 220 PR3 LPS 6h donor D


title: 219 PR3 LPS 6h donor D


title: JH131wt_antrum_hp


title: liver, 5000 vitD, rep6

city: Krakow

first: Tomasz

last: Szmatoła

state: Małopolskie

address: Mickiewicza 21

department: OMEI

country: Poland

institute: University of Agriculture in Krakow

data_processing:
Data was checked for quality with FastQC software
Then, data was filtered with Flexbar software to remove reads under 36 bp, adapters and low quality reads (<20 phread quality)
Filtered reads were mapped to Rattus Norvegicus 7.2 genome with the use of STAR software
HTSeq-count was used to calculate which read lies in anotation threshold of the Ensembl database version 109.
DESeq2 was used to calculate differentially expressed genes.
Assembly: Rattus Norvegicus 7.2
Supplementary files format and content: counts

organism: Rattus norvegicus

extract_protocol:
RNA was isolated using Total RNA Mini  kit ( A&A Biotechnology, Poland), according to the manufacturer protocol
Libraries were constructed using QuantSeq 3' mRNA-Seq Library Prep Kit FWD (Lexogen, Austaria), according to the manufacturer protocol.
3' UTR mRNA-seq (Lexogen)

value: liver

tag: age

value: adult (about one year old)

tag: Sex

value: female

value: 5000 vitD


title: liver, 5000 vitD, rep4


title: liver, 5000 vitD, rep5


title: liver, 5000 vitD, rep3


title: 218 PR3 LPS 6h donor D


title: JH131apc_corpus_hp


title: 217 PR3 LPS 6h donor D


title: 216 MPO LPS 6h donor D

value: MPO


title: liver, 5000 vitD, rep1


title: Human CAR T cells, TOX2OE, input nine

city: Philadelphia

first: Sierra

middle: Marie

last: Collins

state: PA

address: 3400 Civic Center Blvd. Rm 9-164 SCTR BLDG 421/CD

department: Perelman School of Medicine

institute: University of Pennsylvania

description: Human CAR T cells, TOX2OE, input

data_processing:
ChIPseq reads were trimmed of adapter contamination using Cutadapt
Trimmed sequence reads were mapped to GRC37/hg19 using bowtie2
Mitochondrial reads were removed
PCR duplicates were removed with Picard
Peaks were called with MACS2, using input files as background
bedGraph files showing all ChIP-seq signal
Peaks called with MACS2 and annotated with Homer
hg19

growth_protocol: CD4+ and CD8+ human T cells isolated from healthy donor PBMCs using the EasySep Human T Cell Isolation Kit (Stemcell), activated with CD3/CD28 beads, infected with CAR19 lentivirus and shRNA or OE virus, cultured for 14 days with IL-2

extract_protocol:
ChIP-seq: Nuclei were isolated and lysed, chromatin was sonicated to ~200bp fragments, chromatin was immunoprecipitated with an antibody against TOX2, DNA was purified using ethanol precipitation
ChIP libraries for ChIP-seq were prepared using the NEBNext Ultra II DDNA Library Prep Kit for Illumina, following manufacturer's protocols.

value: T cells


title: Human CAR T cells, shControl, TOX2-IP two

description: Human CAR T cells, shControl, TOX2-IP

value: WT


title: Human CAR T cells, TOX2OE, TOX2-IP ten

description: Human CAR T cells, TOX2OE, TOX2-IP


title: JH131apc_corpus_con


title: liver, 5000 vitD, rep2


title: Human CAR T cells, shTOX X569_TOXKD_CD8

description: Human CAR T cells, shTOX

data_processing:
Sequence reads were mapped to GRC37/hg19 using STAR
Reads for each gene with RefSeq annotations were counted using htseq-counts or featureCounts
Counts were normalized and significant differences calculated with DESeq2
Raw counts generated by htseq-counts or featureCounts
Normalized counts generated by DESeq2
hg19

extract_protocol:
RNA-seq: RNA was harvested using RNA Clean-and-Concentrator kit (Zymo Research). 36-690 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the NEBNext Ultra II Directional Library Prep Kit  with the NEBNext Poly(A) mRNA Magnetic Isolation Module, following manufacturer's protocols.

value: shTOX


title: Human CAR T cells, shControl, input one

description: Human CAR T cells, shControl, input


title: 214 MPO LPS 6h donor D

value: monocytes


title: 215 MPO LPS 6h donor D


title: liver, 1000 vitD, rep6

value: 1000 vitD


title: JH131apc_antrum_hp

value: Gastric antrum


title: Human CAR T cells, shControl X569_NT_CD8

description: Human CAR T cells, shControl

value: control


title: JH131apc_antrum_con

value: Epithelial cells


title: liver, 1000 vitD, rep5


title: Human CAR T cells, shTOX X561_TOXKD_CD8

description: Human CAR T cells, shTOX


title: liver, 1000 vitD, rep4


title: JH131wt_antrum_con

value: CTRL


title: day3, sample7, rep2 [scATAC-Seq]

city: Saint Louis

first: Samantha

last: Morris

state: Missouri

address: 660 S Euclid Ave

institute: Washington University School of Medicine

description: 10x Genomics

library_source: genomic single cell

data_processing:
Single-cell barcoded bam files were generated using CellRanger ATAC (https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac)
lineage barcodes were processed using our in house pipeline (https://github.com/morris-lab/newCloneCalling)
Assembly: mm10
Supplementary files format and content: H5 files for single-cell peak accessibility matrices

source_name: reprogrammed MEFs

extract_protocol:
FACS sorting
10x Genomics scATAC-seq library prep, with modifications to capture CellTags

value: reprogrammed MEFs


title: Human CAR T cells, shControl X561_NT_CD8

description: Human CAR T cells, shControl


title: 213 MPO LPS 6h donor D

value: LPS


title: liver, 1000 vitD, rep3


title: liver, 1000 vitD, rep2


title: day3, sample5, rep2 [scATAC-Seq]

description: 10x Genomics


title: 211 MPO LPS 6h donor D


title: day3, sample6, rep2 [scATAC-Seq]

description: 10x Genomics


title: 210 MPO LPS 6h donor D


title: Human CAR T cells, shControl X502_NT_CD8

description: Human CAR T cells, shControl


title: liver, 1000 vitD, rep1


title: Human CAR T cells, shTOX X502_TOXKD_CD8

description: Human CAR T cells, shTOX


title: 209 MPO LPS 6h donor D


title: 208 control LPS 6h donor D


title: liver, 0 vitD, rep5

value: 0 vitD


title: 207 control LPS 6h donor D


title: day3, sample2, rep2 [scATAC-Seq]

description: 10x Genomics


title: day3, sample3, rep2 [scATAC-Seq]

description: 10x Genomics


title: Human CAR T cells, shTOX X561_TOXKD_CD4

description: Human CAR T cells, shTOX


title: liver, 0 vitD, rep6

value: liver


title: liver, 0vitD, rep4

value: adult (about one year old)


title: 212 MPO LPS 6h donor D


title: day3, sample1, rep2 [scATAC-Seq]

description: 10x Genomics


title: 206 control LPS 6h donor D


title: Human CAR T cells, shControl X561_NT_CD4

description: Human CAR T cells, shControl


title: day3, sample4, rep2 [scATAC-Seq]

description: 10x Genomics


title: day3, sample6, rep1 [scATAC-Seq]

description: 10x Genomics


title: liver, 0 vitD, rep2

value: female


title: liver, 0 vitD, rep3


title: Human CAR T cells, shTOX X502_TOXKD_CD4

description: Human CAR T cells, shTOX


title: 205 control LPS 6h donor D


title: day3, sample5, rep1 [scATAC-Seq]

description: 10x Genomics


title: Human CAR T cells, shTOX X569_TOXKD_CD4

description: Human CAR T cells, shTOX


title: Human CAR T cells, shControl X569_NT_CD4

description: Human CAR T cells, shControl


title: 204 control LPS 6h donor D


title: day3, sample4, rep1 [scATAC-Seq]

description: 10x Genomics


title: liver, 0 vitD, rep1


title: Human IMR90 fibroblasts, FLAG-TOX2-OE Tox2-B

description: Human IMR90 fibroblasts, FLAG-TOX2-OE

growth_protocol: IMR90 human embryonic lung fibroblasts, cultured in DMEM with 10% FBS and 1% Penn/Strep, at 5% CO2

value: fibroblast


title: 203 control LPS 6h donor D


title: day3, sample3, rep1 [scATAC-Seq]

description: 10x Genomics


title: 201 control LPS 6h donor D


title: Human IMR90 fibroblasts, FLAG-TOX2-OE Tox2-A

description: Human IMR90 fibroblasts, FLAG-TOX2-OE


title: Human IMR90 fibroblasts, FLAG-OE Empty_B

description: Human IMR90 fibroblasts, FLAG-OE

value: FLAG


title: day3, sample2, rep1 [scATAC-Seq]

description: 10x Genomics


title: day3, sample1, rep1 [scATAC-Seq]

description: 10x Genomics


title: Controlplasma-D-cfMCC-SEQ

city: Washington

first: Anton

last: Wellstein

state: DC

address: 3970 Reservoir Road, N.W.,

department: Oncology

institute: Georgetown University

data_processing:
Paired-end FASTQ files were trimmed using TrimGalore (V 0.6.6) with parameters “--paired -q 20 --clip_R1 10 --clip_R2 10 --three_prime_clip_R1 10 --three_prime_clip_R2 10 --retain_unpaired -r1 20 -r2 20” (https://github.com/FelixKrueger/TrimGalore).
Trimmed paired-end FASTQ reads were mapped to the human genome  (GRCh37/hg19 build) using Bismark (V 0.22.3) with parameters “--non-directional” (Kreuger et al. 2011), then converted to BAM files using SAMtools (V 1.12) (Li et al., 2009). BAM files were sorted and indexed using Samtools (V1.12).
Reads were stripped from non-CpG nucleotides and converted to BETA and PAT files using wgbstools (V 0.1.0) (Loyfer and Kaplan, 2022).
Assembly: hg19
Supplementary files format and content: BETA, PAT, and index files were generated using wgbstools bam2pat (https://github.com/nloyfer/wgbs_tools) with default parameters
Library strategy: MCC-seq (MethylC-capture sequencing)

source_name: Plasma

extract_protocol:
Circulating cell-free DNA was extracted from 4 mL human serum or plasma, using the QIAamp Circulating Nucleic Acid kit (Qiagen, Cat. No. 55114) according to the manufacturer’s instructions. Cell-free DNA was quantified via Qubit fluorometer using the dsDNA Assay Qubit fluorometer Kits (ThermoFisher Scientific, Cat. No. Q32853 and Q10212 respectively). As a quality control, fragment size distribution of isolated cfDNA was verified based on analysis using a 2100 Bioanalyzer TapeStation using either a High Sensitivity DNA Assay or DNA 1000 Assay (Agilent Technologies, Santa Cruz, CA, USA) dependent on concentration determined via either Qubit dsDNA BR or HS Assay. Additional purification using Beckman Coulter beads was implemented to remove high-molecular weight DNA reflective of cell-lysis and leukocyte contamination (Agencourt AMPure cat#A63880) (Maggi et al. 2018).
Cell-free DNA from serum was subject to bisulfite conversion using the Zymo EZ DNA Methylation Gold kit  (#D5005 Zymo Research, Irvine, CA). Whole Genome Bisulfite Sequencing libraries were generated using the Zymo Research Pico Methyl-Seq Library Prep Kit (#D5455 Zymo Research, Irvine, CA). WGBS libraries were quantified using KAPA Library Quantification Kits for Illumina Platforms (Kapa Biosystems; Wilmington, MA) and then pooled to meet the required 1ug DNA input necessary for targeted enrichment. Hybridization capture was carried out according to the SeqCap Epi Enrichment System protocol (Roche NimbleGen, Inc.; Pleasanton, CA) using xGen Universal Blocker-TS Mix (Integrated DNA Technologies, USA) as the blocking reagent and SeqCap Epi CpGiant probe pools (human) or SeqCap Epi Developer probe pools (mouse samples). MethylC-Capture Sequencing (MCC-seq) libraries were assessed using Qubit Fluorometer (ThermoFisher) and Agilent Bioanalyzer DNA 1000 assays (Agilent Technologies, Inc., USA). MCC-seq libraries with inclusion of 15-20% spike-in PhiX Control v3 library (Illumina; San Diego, CA) were clustered on a Illumina Novaseq 6000 S4 flow cell followed by 150-bp paired-end sequencing.

value: Plasma

value: Control


title: Human IMR90 fibroblasts, FLAG-OE Empty-A

description: Human IMR90 fibroblasts, FLAG-OE


title: Human CAR T cells, TOX2OE 578-TOX2OE-CD8

description: Human CAR T cells, TOX2OE


title: lymph node S144 scRNAseq BCR enrichted

city: Leiden

first: Cornelis

last: van Bergen

address: Albinusdreef 2

department: Hematology

institute: Leiden University Medical Center

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 using GRCh38-3.0.0 (K1B_GEX) and vdj_GRCh38_alts_ensembl-3.1.0 (K1B_BCR) as references
K1B_GEX Tab-separated values files and matrix files
K1B_BCR comma separated cellranger output files
Supplementary files format and content: all_contig_annotations.csv
Supplementary files format and content: SeuratObject.rds
Supplementary files format and content: BCR_subclones.xls
Supplementary files format and content: all_contig.fasta

source_name: lymph node

growth_protocol: Frozen cells were thawed, stained with CD19 and CD10, and purified by FACSariaII device prior to submission for 10X Genomics Chromium processing

extract_protocol: Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics).

value: lymph node

value: B cell

value: fresh


title: lymph node S144 scRNAseq full transcriptome

description: 10x Genomics


title: Controlplasma-C-cfMCC-SEQ


title: day 21, sample6, rep2 [scATAC-Seq]

description: 10x Genomics


title: Human CAR T cells, shControl X502_NT_CD4

description: Human CAR T cells, shControl


title: Human CAR T cells, empty OE 578-control-CD8

description: Human CAR T cells, empty OE


title: day 21, sample5, rep2 [scATAC-Seq]

description: 10x Genomics


title: Ctrl_refed_3_1_b2

city: Munich

first: Mauricio

last: Berriel Diaz

state: Bavaria

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Cancer

country: Germany

institute: Helmholtz Center Munich

data_processing:
Downstream analysis was performed using a combination of programs including STAR, HTseq, Cufflink and our wrapped scripts. Alignments were parsed using Tophat program and differential expressions were determined through DESeq2/edgeR. GO and KEGG enrichment were implemented by the ClusterProfiler. Gene fusion and difference of alternative splicing event were detected by Star-fusion and rMATS software
Assembly: mm10
Supplementary files format and content: a single tab-delimited text file include read counts  for each Sample

source_name: Liver

growth_protocol: Male mice were maintained on a 12/12 h light/dark cycle and were fed a regular chow diet until the age of 8 weeks.

extract_protocol:
RNA was harvested with Trizol, loaded to EconoSpin columns (Epoch) and washed with RPE buffer (QIAGEN)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: At 8 weeks of age the expression of hepatic Prox1 (K556R) was induced via Cre recombination, mice were then fed a high-fat (45%)/high-fructose (20%) diet for 18 weeks.

value: Liver

tag: repeat

value: refed

tag: batch


title: Ctrl_fast_4_1_b2

tag: treatment

value: fasted


title: Ctrl_refd_1_1_b2


title: Ctrl_refed_2_1_b2


title: Human CAR T cells, TOX2OE 561-TOX2OE-CD8

description: Human CAR T cells, TOX2OE


title: day 21, sample4, rep2 [scATAC-Seq]

description: 10x Genomics


title: Controlserum-D-cfMCC-SEQ

source_name: Serum

value: Serum


title: Ctrl_fast_3_1_b2


title: Human CAR T cells, empty OE 561-control-CD8

description: Human CAR T cells, empty OE

value: control


title: Controlserum-C-cfMCC-SEQ


title: day 21, sample3, rep2 [scATAC-Seq]

description: 10x Genomics

value: reprogrammed MEFs


title: day 21, sample2, rep2 [scATAC-Seq]

description: 10x Genomics


title: Ctrl_fast_2_1_b2


title: Controlserum-B-cfMCC-SEQ


title: Ctrl_fast_1_1_b2


title: Human CAR T cells, TOX2OE 528-TOX2OE-CD8

description: Human CAR T cells, TOX2OE


title: Controlplasma-B-cfMCC-SEQ


title: Controlserum-A-cfMCC-SEQ


title: day 21, sample1, rep2 [scATAC-Seq]

description: 10x Genomics


title: day 21, sample6, rep1 [scATAC-Seq]

description: 10x Genomics


title: Human CAR T cells, TOX2OE 578-TOX2OE-CD4

description: Human CAR T cells, TOX2OE


title: Cre_refed_4_1_b2


title: Cre_refed_3_1_b2


title: Controlplasma-A-cfMCC-SEQ


title: Human CAR T cells, empty OE 578-control-CD4

description: Human CAR T cells, empty OE


title: day 21, sample5, rep1 [scATAC-Seq]

description: 10x Genomics


title: Cre_refed_2_1_b2


title: BuffyCoat-C-MCC-SEQ

data_processing:
Library strategy: MCC-seq (MethylC-capture sequencing)
Paired-end FASTQ files were trimmed using TrimGalore (V 0.6.6) with parameters “--paired -q 20 --clip_R1 10 --clip_R2 10 --three_prime_clip_R1 10 --three_prime_clip_R2 10 --retain_unpaired -r1 20 -r2 20” (https://github.com/FelixKrueger/TrimGalore).
Trimmed paired-end FASTQ reads were mapped to the human genome  (GRCh37/hg19 build) using Bismark (V 0.22.3) with parameters “--non-directional” (Kreuger et al. 2011), then converted to BAM files using SAMtools (V 1.12) (Li et al., 2009). BAM files were sorted and indexed using Samtools (V1.12).
Reads were stripped from non-CpG nucleotides and converted to BETA and PAT files using wgbstools (V 0.1.0) (Loyfer and Kaplan, 2022).
Assembly: hg19
Supplementary files format and content: BETA, PAT, and index files were generated using wgbstools bam2pat (https://github.com/nloyfer/wgbs_tools) with default parameters
Supplementary files format and content: blocks file (bed) was generated using wgbstools segment, and then compressed and indexed using tabix (samtools)

extract_protocol:
Genomic DNA from tissues was extracted with DNeasy Blood and Tissue Kit (Qiagen; Germantown, MD) following the manufacturer’s instructions and quantified via Qubit fluorometer dsDNA BR Assay Kit (ThermoFisher Scientific, Cat. No. Q32853). Extracted DNA was stored at  -20°C for bisulfite conversion and MCC-seq library preparation.
Genomic DNA was fragmented via sonification using a Covaris M220 instrument to the recommended target 150-200 base pairs and subject to bisulfite conversion using the Zymo EZ DNA Methylation Gold kit  (#D5005 Zymo Research, Irvine, CA). Whole Genome Bisulfite Sequencing libraries were generated using the Zymo Research Pico Methyl-Seq Library Prep Kit (#D5455 Zymo Research, Irvine, CA). WGBS libraries were quantified using KAPA Library Quantification Kits for Illumina Platforms (Kapa Biosystems; Wilmington, MA) and then pooled to meet the required 1ug DNA input necessary for targeted enrichment. Hybridization capture was carried out according to the SeqCap Epi Enrichment System protocol (Roche NimbleGen, Inc.; Pleasanton, CA) using xGen Universal Blocker-TS Mix (Integrated DNA Technologies, USA) as the blocking reagent and SeqCap Epi CpGiant probe pools (human) or SeqCap Epi Developer probe pools (mouse samples). MethylC-Capture Sequencing (MCC-seq) libraries were assessed using Qubit Fluorometer (ThermoFisher) and Agilent Bioanalyzer DNA 1000 assays (Agilent Technologies, Inc., USA). MCC-seq libraries with inclusion of 15-20% spike-in PhiX Control v3 library (Illumina; San Diego, CA) were clustered on a Illumina Novaseq 6000 S4 flow cell followed by 150-bp paired-end sequencing.

treatment_protocol: Cryopreserved passage 1 human liver sinusoidal endothelial cells (LSEC) isolated from single donor healthy whole human livers were purchased from Novabiosis (SKU#6500). Purity was determined by FACS analysis for the % positive of cell surface markers CD146, CD31, vWF, and CD105. Cryopreserved passage 2 human coronary artery (HCAEC SKU#C-14022), cardiac microvascular (HCMEC SKU#C-14029), and pulmonary artery (HPAEC SKU#C-14024) were isolated from single donor healthy human tissues purchased from PromoCell. All endothelial cell populations were CD31 positive and Dil-Ac-LDL uptake positive.

value: Blood

value: lymphocyte


title: BuffyCoat-D-MCC-SEQ


title: day 21, sample4, rep1 [scATAC-Seq]

description: 10x Genomics


title: Cre_refed_1_1_b2


title: Human CAR T cells, empty OE 561-control-CD4

description: Human CAR T cells, empty OE


title: Human CAR T cells, TOX2OE 561-TOX2OE-CD4

description: Human CAR T cells, TOX2OE


title: BuffyCoat-B-MCC-SEQ


title: day 21, sample3, rep1 [scATAC-Seq]

description: 10x Genomics


title: day 21, sample2, rep1 [scATAC-Seq]

description: 10x Genomics


title: Cre_fast_3_1_b2


title: Human CAR T cells, TOX2OE 528-TOX2OE-CD4

description: Human CAR T cells, TOX2OE


title: Human CAR T cells, empty OE 528-control-CD4

description: Human CAR T cells, empty OE


title: BuffyCoat-E-MCC-SEQ


title: Liver-Sinusoidal-Endothelium-A-MCC-SEQ

value: endothelial


title: Cre_fast_2_1_b2


title: Human CAR T cells, empty OE 528-control-CD8

description: Human CAR T cells, empty OE


title: day 21, sample1, rep1 [scATAC-Seq]

description: 10x Genomics


title: Liver-Sinusoidal-Endothelium-B-MCC-SEQ


title: day 12, sample2, rep2 [scATAC-Seq]

description: 10x Genomics


title: Cre_fast_1_1_b2


title: Ctrl_refed_2_1_b1


title: Cardiopulmonary-Endothelium-HCMEC-A-MCC-SEQ

source_name: Heart

value: Heart


title: Human CAR T cells, shControl ND566_NT_CD8

description: Human CAR T cells, shControl


title: day 12, sample2, rep1 [scATAC-Seq]

description: 10x Genomics


title: Human CAR T cells, shTOX2 ND502_TOX2KD_CD8

description: Human CAR T cells, shTOX2


title: Ctrl_refed_3_1_b1


title: Ctrl_refed_1_1_b1


title: day 12, sample1, rep1 [scATAC-Seq]

description: 10x Genomics


title: Ctrl_fast_4_1_b1


title: day 5 replicate 2, sample 4, scRNA-seq

description: 10x Genomics

data_processing:
Single-cell barcoded bam files were generated using CellRanger (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
lineage barcodes were processed using our in house pipeline (https://github.com/morris-lab/newCloneCalling)
Assembly: mm10
Supplementary files format and content: H5 files for single-cell gene expression matrices

source_name: adult mouse bone marrow

extract_protocol:
FACS sorting
10x Genomics scRNA-seq library prep, with modifications to capture CellTags

value: LSK cells

value: adult mouse bone marrow

value: 8 week

tag: differentiation day

value: day 5


title: Ctrl_fast_3_1_b1


title: day 5 replicate 2, sample 3, scRNA-seq

description: 10x Genomics


title: Human CAR T cells, shTOX2 ND365_TOX2KD_CD8

description: Human CAR T cells, shTOX2


title: Cardiopulmonary-Endothelium-HCAEC-B-MCC-SEQ


title: Human CAR T cells, shControl ND365_NT_CD8

description: Human CAR T cells, shControl


title: Cardiopulmonary-Endothelium-HCAEC-A-MCC-SEQ


title: day 12, sample1, rep2 [scATAC-Seq]

description: 10x Genomics


title: Ctrl_fast_2_1_b1


title: day 5 replicate 2, sample 2, scRNA-seq

description: 10x Genomics


title: RT115_3-cfMCC-SEQ

data_processing:
Library strategy: MCC-seq (MethylC-capture sequencing)
Paired-end FASTQ files were trimmed using TrimGalore (V 0.6.6) with parameters “--paired -q 20 --clip_R1 10 --clip_R2 10 --three_prime_clip_R1 10 --three_prime_clip_R2 10 --retain_unpaired -r1 20 -r2 20” (https://github.com/FelixKrueger/TrimGalore).
Trimmed paired-end FASTQ reads were mapped to the human genome  (GRCh37/hg19 build) using Bismark (V 0.22.3) with parameters “--non-directional” (Kreuger et al. 2011), then converted to BAM files using SAMtools (V 1.12) (Li et al., 2009). BAM files were sorted and indexed using Samtools (V1.12).
Reads were stripped from non-CpG nucleotides and converted to BETA and PAT files using wgbstools (V 0.1.0) (Loyfer and Kaplan, 2022).
Assembly: hg19
Supplementary files format and content: BETA, PAT, and index files were generated using wgbstools bam2pat (https://github.com/nloyfer/wgbs_tools) with default parameters

extract_protocol:
Circulating cell-free DNA was extracted from 4 mL human serum, using the QIAamp Circulating Nucleic Acid kit (Qiagen, Cat. No. 55114) according to the manufacturer’s instructions. Cell-free DNA was quantified via Qubit fluorometer using the dsDNA Assay Qubit fluorometer Kits (ThermoFisher Scientific, Cat. No. Q32853 and Q10212 respectively). As a quality control, fragment size distribution of isolated cfDNA was verified based on analysis using a 2100 Bioanalyzer TapeStation using either a High Sensitivity DNA Assay or DNA 1000 Assay (Agilent Technologies, Santa Cruz, CA, USA) dependent on concentration determined via either Qubit dsDNA BR or HS Assay. Additional purification using Beckman Coulter beads was implemented to remove high-molecular weight DNA reflective of cell-lysis and leukocyte contamination (Agencourt AMPure cat#A63880) (Maggi et al. 2018).
Cell-free DNA from serum was subject to bisulfite conversion using the Zymo EZ DNA Methylation Gold kit  (#D5005 Zymo Research, Irvine, CA). Whole Genome Bisulfite Sequencing libraries were generated using the Zymo Research Pico Methyl-Seq Library Prep Kit (#D5455 Zymo Research, Irvine, CA). WGBS libraries were quantified using KAPA Library Quantification Kits for Illumina Platforms (Kapa Biosystems; Wilmington, MA) and then pooled to meet the required 1ug DNA input necessary for targeted enrichment. Hybridization capture was carried out according to the SeqCap Epi Enrichment System protocol (Roche NimbleGen, Inc.; Pleasanton, CA) using xGen Universal Blocker-TS Mix (Integrated DNA Technologies, USA) as the blocking reagent and SeqCap Epi CpGiant probe pools (human) or SeqCap Epi Developer probe pools (mouse samples). MethylC-Capture Sequencing (MCC-seq) libraries were assessed using Qubit Fluorometer (ThermoFisher) and Agilent Bioanalyzer DNA 1000 assays (Agilent Technologies, Inc., USA). MCC-seq libraries with inclusion of 15-20% spike-in PhiX Control v3 library (Illumina; San Diego, CA) were clustered on a Illumina Novaseq 6000 S4 flow cell followed by 150-bp paired-end sequencing.

treatment_protocol: Breast cancer patients undergoing adjuvant radiation-therapy were enrolled and provided signed informed consent in this IRB approved study at Medstar Georgetown University Hospital (IRB protocol # 2013-0049). Serial serum samples were collected from 15 patients at Baseline (before radiation treatment), End-of-Treatment (EOT; 30 minutes after the last radiation treatment), and Recovery (one month after cessation of radiation treatment). For serum isolation, peripheral blood (~8-12 ml) was collected in red-top venous puncture tubes and allowed to clot at room temperature for 30 minutes before centrifugation at 1500 x g for 20 min at 4ºC to separate the serum fraction. The serum was aliquoted in 0.5 mL fractions to avoid multiple freeze-thaw cycles and stored at −80ºC until use.

value: Recovery


title: Human CAR T cells, shControl ND317_NT_CD8

description: Human CAR T cells, shControl


title: Human CAR T cells, shControl ND502_NT_CD8

description: Human CAR T cells, shControl


title: Cardiopulmonary-Endothelium-HCAEC-C-MCC-SEQ


title: Human CAR T cells, shTOX2 ND317_TOX2KD_CD8

description: Human CAR T cells, shTOX2


title: Cre_refed_3_1_b1


title: Human CAR T cells, shTOX2 ND566_TOX2KD_CD4

description: Human CAR T cells, shTOX2


title: RT115_1-cfMCC-SEQ

value: Baseline


title: day 5 replicate 1, sample 3, scRNA-seq

description: 10x Genomics


title: day 5 replicate 1, sample 4, scRNA-seq

description: 10x Genomics


title: Cre_refed_2_1_b1


title: Cre_refed_4_1_b1


title: day 5 replicate 1, sample 2, scRNA-seq

description: 10x Genomics


title: Cre_refed_1_1_b1


title: Human CAR T cells, shControl ND566_NT_CD4

description: Human CAR T cells, shControl


title: Human CAR T cells, shTOX2 ND566_TOX2KD_CD8

description: Human CAR T cells, shTOX2


title: day 5 replicate 1, sample 1, scRNA-seq

description: 10x Genomics


title: day 5 replicate 2, sample 1, scRNA-seq

description: 10x Genomics


title: Cre_fast_4_1_b1


title: RT115_2-cfMCC-SEQ

value: Radiation


title: day 2.5, scRNA-seq

description: 10x Genomics

value: day 2.5


title: RT114_1-cfMCC-SEQ


title: Cardiopulmonary-Endothelium-HPAEC-A-MCC-SEQ

source_name: Lungs

value: Lungs


title: Human CAR T cells, shControl ND365_NT_CD4

description: Human CAR T cells, shControl


title: RT114_3-cfMCC-SEQ


title: RT113_3-cfMCC-SEQ


title: day 14 kd control

description: 10x Genomics

source_name: Mouse E13.5

value: Mouse E13.5

tag: time point

value: day 14


title: Human CAR T cells, shTOX2 ND317_TOX2KD_CD4

description: Human CAR T cells, shTOX2


title: RT113_2-cfMCC-SEQ

value: Serum


title: Cre_fast_3_1_b1

value: Liver

value: fasted


title: RT113_1-cfMCC-SEQ


title: Cre_fast_2_1_b1


title: day 14, zfp281 kd

description: 10x Genomics

value: reprogrammed MEFs


title: Cre_fast_1_1_b1


title: RT114_2-cfMCC-SEQ


title: day 14, oe control

description: 10x Genomics


title: Human CAR T cells, shControl ND502_NT_CD4

description: Human CAR T cells, shControl

value: control


title: Human CAR T cells, shTOX2 ND502_TOX2KD_CD4

description: Human CAR T cells, shTOX2


title: RT112_3-cfMCC-SEQ


title: Human CAR T cells, shControl ND317_NT_CD4

description: Human CAR T cells, shControl


title: Human CAR T cells, shTET2 518_TET2KD_CD8

description: Human CAR T cells, shTET2


title: day 14, zfp281 oe

description: 10x Genomics


title: day 21, sample4, rep2

description: 10x Genomics

value: day 21


title: RT112_2-cfMCC-SEQ


title: RT112_1-cfMCC-SEQ


title: Human CAR T cells, shControl 518_NT_CD8

description: Human CAR T cells, shControl


title: Human CAR T cells, shTET2 502_TET2KD_CD8

description: Human CAR T cells, shTET2


title: day 21, sample3, rep2

description: 10x Genomics


title: RT111_3-cfMCC-SEQ


title: Cre_refed_2_b2

growth_protocol: Male mice were maintained on a 12/12 h light/dark cycle and were fed a regular chow diet.

treatment_protocol: At 8 weeks of age the expression of hepatic Prox1 (K556R) was induced via Cre recombination, liver samples were collected 11 weeks later.

value: refed


title: Cre_refed_3_b2


title: Ctrl_refed_1_b2


title: Human CAR T cells, shTET2 307_TET2KD_CD8

description: Human CAR T cells, shTET2


title: day 21, sample2, rep2

description: 10x Genomics


title: Human CAR T cells, shControl 502_NT_CD8

description: Human CAR T cells, shControl


title: RT111_2-cfMCC-SEQ


title: Cre_fast_1_b2


title: RT111_1-cfMCC-SEQ


title: Ctrl_fast_1_b2


title: Human CAR T cells, shControl 307_NT_CD8

description: Human CAR T cells, shControl


title: day 21, sample4, rep1

description: 10x Genomics


title: RT110_2-cfMCC-SEQ


title: RT110_3-cfMCC-SEQ


title: Ctrl_fast_1_1_b1


title: Cre_refed_1_b2


title: Human CAR T cells, shTET2 518_TET2KD_CD4

description: Human CAR T cells, shTET2


title: Cre_refed_1_b1


title: Cre_refed_2_b1


title: day 21, sample1, rep1

description: 10x Genomics


title: day 21, sample2, rep1

description: 10x Genomics


title: RT110_1-cfMCC-SEQ


title: Human CAR T cells, shControl 518_NT_CD4

description: Human CAR T cells, shControl


title: BuffyCoat-A-MCC-SEQ

source_name: Blood

value: Blood

value: lymphocyte


title: Human CAR T cells, shTET2 502_TET2KD_CD4

description: Human CAR T cells, shTET2


title: day 21, sample1, rep2

description: 10x Genomics


title: RT109_3-cfMCC-SEQ


title: RT109_2-cfMCC-SEQ


title: Ctrl_refed_3_b1


title: Human CAR T cells, shControl 502_NT_CD4

description: Human CAR T cells, shControl


title: Ctrl_refed_2_b1


title: day 12, sample2, rep2

description: 10x Genomics

value: day 12


title: Human CAR T cells, shTET2 307_TET2KD_CD4

description: Human CAR T cells, shTET2


title: RT108_3-cfMCC-SEQ

value: Recovery


title: RT109_1-cfMCC-SEQ

value: Baseline


title: Cre_fast_4_b1


title: MOLM13 Venetoclax resistant cells untreated [RU2]

city: Mumbai

first: Syed

last: Hasan

state: Maharashtra

address: Sector 22 Kharghar Navi Mumbai

country: India

institute: Advanced Centre for Treatment Research and Education in Cancer (ACTREC)

description: vst_normalised_matrix.xlsx, Column H, RU2

data_processing:
Once the cluster generation is completed, the clustered flow cell is loaded on Illumina HiSeq X instrument to generate 167 million, 150bp paired end reads per sample. Image analysis, base calling, and quality check was performed with Illumina data analysis pipeline RTA v1.18.64. RNAseq reads were provided in compressed Sanger FASTQ format.
Raw reads were available as fastq files. The quality of the Illumina sequenced paired-end fastq files were assessed using Fastqc (v0.11.4). Furthermore, Trimmomatic (v0.32) was used to remove adapters and improve average read phred quality. It is achieved using 3 parameters of the software: firstly, adapter removal via ILLUMINACLIP and TruSeq3-PE-2 as illumina adapter reference, secondly HEADCROP of bad quality 10bp of each of the read and lastly sliding window with average phred quality 15 in each 10bp window. The mean length, GC content and number of reads were found to be 151, 52.5% and 87203261 respectively in the paired-end fastq file. Post QC there is an average loss of 42.38% reads. Average read length is around 100 and 50229865 total reads in each of the paired end fastq file.
Since there are multiple conditions (PU, PT, RU and RT), it is recommended to use variance Stabilizing Transformation (VST) based normalisation. This function calculates a VST from the fitted dispersion-mean relations and then transforms the count data (normalized by division by the size factors or normalization factors), yielding a matrix of values which are now approximately homoskedastic (having constant variance along the range of mean values). The transformation also normalizes with respect to library size.https://rdrr.io/bioc/DESeq2/man/varianceStabilizingTransformation.html
Quantification of reads:FeatureCounts (Subread v1.6.2) was used to quantify the mapped reads for genomic regions present in the GRch38 annotated file including chromosomal coordinates of features. The downstream analysis of the quantified read matrix is done using DeSeq.
Assembly: GRCh38 human reference
Supplementary files format and content: vst_normalised

extract_protocol:
One µg of total RNA was isolated from paired Venetoclax sensitive and resistant MOLM13 cells with and without XL102 treatment, followed by DNAse I and silica-membrane purification (RNeasy kit, Qiagen, Germany). and diluted to 100 ng/µl. The quality of total RNA was confirmed by Bioanalyzer. Samples with RNA integrity numbers ≥8 were selected for RNA library preparation in an ISO/IEC 17025-accredited protocol (TruSeq RNA library preparation kit v2, Illumina, San Diego, CA).
After enrichment of mRNA by oligo dT magnetic beads and fragmentation, cDNA synthesis was performed in duplicate for each sample, followed by adapter ligation and PCR amplification. The obtained libraries were pooled and diluted to final optimal loading concentration before cluster amplification on the Illumina flow cell.

value: peripheral blood

value: MOLM13 Ven R

value: Acute myeloid leukemia


title: day 12, sample1, rep1

description: 10x Genomics

value: Mouse E13.5


title: RT108_2-cfMCC-SEQ

value: Radiation


title: MOLM13 Venetoclax resistant cells untreated [RU1]

description: vst_normalised_matrix.xlsx, Column G, RU1


title: Ctrl_refed_4_b1


title: day 12, sample2, rep1

description: 10x Genomics


title: day 21, sample3, rep1

description: 10x Genomics


title: MOLM13 Venetoclax resistant cells treated with CDK7 inhibitor [RT1]

description: vst_normalised_matrix.xlsx, Column I, RT1

value: CDK7 Inhibitor


title: Cre_fast_2_b1

value: Liver


title: RT107_3-cfMCC-SEQ

value: Serum


title: day 3, sample4, rep2

description: 10x Genomics

value: reprogrammed MEFs

value: day 3


title: Cre_fast_1_b1

value: fasted


title: RT108_1-cfMCC-SEQ


title: MOLM13 Venetoclax resistant cells treated with CDK7 inhibitor [RT2]

description: vst_normalised_matrix.xlsx, Column J, RT2


title: Ctrl_refed_1_b1

value: refed


title: Human CAR T cells, shControl 307_NT_CD4

description: Human CAR T cells, shControl

value: control


title: day 12, sample1, rep2

description: 10x Genomics


title: RT107_2-cfMCC-SEQ


title: day 3, sample3, rep2

description: 10x Genomics


title: MOLM13 parental Venetoclax sensitive cells untreated [PU1]

description: vst_normalised_matrix.xlsx, Column C, PU1

value: MOLM13 Ven S


title: Ctrl_fast_4_b1


title: Ctrl_fast_3_b1


title: day 3, sample2, rep2

description: 10x Genomics


title: day 3, sample1, rep2

description: 10x Genomics


title: RT107_1-cfMCC-SEQ


title: Cre_fast_3_b1


title: MOLM13 parental Venetoclax sensitive cells treated with CDK7 inhibitor [PT2]

description: vst_normalised_matrix.xlsx, Column F, PT2


title: RT106_2-cfMCC-SEQ


title: day 3, sample4, rep1

description: 10x Genomics


title: MOLM13 parental Venetoclax sensitive cells treated with CDK7 inhibitor [PT1]

description: vst_normalised_matrix.xlsx, Column E, PT1


title: Ctrl_fast_1_b1


title: RT106_3-cfMCC-SEQ


title: day 3, sample3, rep1

description: 10x Genomics


title: TNF-α-stimulated endothelial cells derived exosomes rep3

city: Fuzhou

first: Pengli

last: Zhu

address: 134Dongjie St, Gulou District

institute: Fujian Provincial Hospital

data_processing:
Raw sequencing data was firstly filtered by fastx_toolkit (version: 0.0.13.2) (parameters： -i {input} -q 20 -p 80 -Q 33 -o {output})fordiscarding the low-quality reads and adaptor sequences were trimmed by cutadapt(version: 1.15).(parameters:-f fastq -e 1.00 --overlap=5 -m 25 --discard-untrimmed --quality-base 33 -a {adaptor} -o {output})
Clean Reads were further treated with UMI_soft (in-house) to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter（Default Parameter developed by Wuhan Seqhealth Co., Ltd.）
The de-duplicated consensus sequences from each sample were mapped to the reference genome of GRCh38, using bowtie (version: 1.1.2) with default parameters.(parameters:-c -j -l 18 -r 20 -m -v -u -q）
The package of mirdeep2 (version:2.0.0.8) was used for mapping the reads to the known primary-miRNA in the database of miRBase and predicting the novel miRNA.(parameters:quantifier_v1.pl -g 0 -p {input.species_hairpin} -m {input.species_mature} -r {input.mapped_fa} -a {params.out_dir} > {params.log} 2>&1)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: HUVEC, TNF-alpha-stimulated

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were cultured inendothelial cell medium (ECM, Science, 1001).

extract_protocol:
The supernatants of cells were collected and Exosomes extracted using ultracentrifugation.Total RNA was extracted using SeraMir Exosome RNA Column Purification Kit TRIzol Reagent (systembio, cat#RA805A-1）. Three microlitre total RNA was used for the construction of sequencing libraries.
Three microlitre total RNA was used as input for miRNA library preparation by using KC-DigitalTM QIAseq miRNA Library Kit for Illumina® (Catalog NO. 331505, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

treatment_protocol: When the cells reached 60-70% confluency, the exosome-depleted medium with or without TNF-α was replaced, followed by incubation for 24 hours in medium .

value: HUVEC, TNF-alpha-stimulated

value: TNF-alpha-stimulated


title: RT106_1-cfMCC-SEQ

value: Baseline


title: day 3, sample2, rep1

description: 10x Genomics


title: RT105_3-cfMCC-SEQ

value: Recovery


title: TNF-α-stimulated endothelial cells derived exosomes rep2


title: MEL_Myb

city: Montpellier cedex 5

first: Eric

last: Soler

address: 1919 route de Mende

country: France

institute: IGMM

data_processing:
Raw reads were subjected to quality control and adapter trimming using Trimgalore (version 0.6.6)
Trimmed reads were then aligned to the reference genome (mm9) using STAR aligner (version  2.7.9a)
Aligned reads were converted from SAM to BAM format, sorted, and indexed using Samtools (version 1.11)
Duplicate reads were removed using Picard tool (version 2.17.11)
Peak calling was performed using the HOMER (version 4.10.3)
bigWig files were generated using deepTools (version 3.4.2)
Assembly: mm9
Library strategy: CUT&RUN

source_name: MEL

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were bound to BioMag Plus Concanavalin A-coated beads (Bangs Laboratories), permeabilized with digitonin and incubate with pA-Mnase, activated by CaCl2
Libraries were prepared with the MicroPlex Library Preparation kit v3 (Diagenode) and purified with Agencourt SPRIselect beads (Beckman Coulter)

value: MEL

value: Mouse Erythroleukemia cells

tag: cutnrun antibody

value: Myb ( Abcam, #ab45150)


title: MEL_IgRab


title: TNF-α-stimulated endothelial cells derived exosomes rep1


title: day 3, sample1, rep1

description: 10x Genomics

value: Mouse E13.5


title: MOLM13 parental Venetoclax sensitive cells untreated [PU2]

description: vst_normalised_matrix.xlsx, Column D, PU2

value: peripheral blood

value: Acute myeloid leukemia


title: RT105_2-cfMCC-SEQ

value: Serum

value: Radiation


title: RT105_1-cfMCC-SEQ


title: cultured PP_CD11c+MHCII+SIRPa+ cells + Co1 peptide_scRNAseq

city: Jeonju-si, Jeollabuk-do,

first: Saehae

last: Kim

address: 567 Baekje-daero, Deokjin-gu,

department: Molecular biology

country: South Korea

institute: Jeonbuk National University

description: 10x Genomics

data_processing:
cellranger-6.1.2 --> Rv3.6.2, Seurat V3.1.3 --> R v3.6.2, ML Method
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Peyer's patch in terminal ileum

extract_protocol:
PPs were harvested, incubated for 20 min at 37C in HBSS buffer with 5 mM EDTA and 5% fetal calf serum, and then digested for 45 min in RPMI media with collagenase D (Roche)/DNase I (Sigma) and 10% fetal bovine serum .
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: Peyer's patch in terminal ileum

value: BALB/c

value: DC

value: female


title: cultured PP_CD11c+MHCII+SIRPa+ cells_scRNAseq

description: 10x Genomics


title: GFP_Sigma_MEL

value: GFP ( Sigma, #SAB4301138)


title: GFP_Sigma_MEL_Myb_GFP


title: Ctrl_fast_2_b1

value: Liver

value: fasted


title: Histone ChIP-seq from prostate gland (ENCLB146XJE)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR499FXI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR499FXI
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR113QDZ
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB146XJE
fragmentation methods: sonication (generic)
size range: 200-600

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens male adult (54 years) prostate gland tissue

tag: antibody

value: prostate gland

value: tissue

tag: description

tag: biosample encode accession

value: male

tag: dev stage

value: adult

value: 54 year

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: Kristin Ardlie

tag: link

value: ENCBS619YXY at ENCODE; https://www.encodeproject.org/ENCBS619YXY/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: normal endothelial cells derived exosomes rep1

source_name: HUVEC, untreated ,

tag: cell type

value: HUVEC, untreated ,

value: untreated


title: normal endothelial cells derived exosomes rep3

source_name: HUVEC, untreated

value: HUVEC, untreated


title: normal endothelial cells derived exosomes rep2


title: 28126B iPSC, WT control, replicate 3

city: Cambridge

first: Richard

last: She

state: Massachusetts

address: 455 Main St Rm 639, Whitehead Institute

institute: Whitehead Institute

data_processing:
Adapters were removed using cutadapt with option -b AGATCGGAAGAGCACACGTCTGAACTCCAGTCA)
Reads were then pseudo-aligned to species-specific transcriptomes using kallisto with options --single -l 200 -s 20
Transcriptomes were extracted from species-specific gtf annotations using the gffread utility using the -w output option
Human transcripts were obtained from the Gencode comprehensive gene annotation v36 (GTF), using genome assembly hg38.
Chimpanzee annotations were obtained from a recent study that produced a hierarchical alignment of primate genome assemblies and annotated the assemblies using the Comparative Annotation Toolkit
Assembly: hg38
Supplementary files format and content: tab-delimited text files are VST-transformed counts for each sample
Supplementary files format and content: using the function vst with option blind=TRUE and ran the DESeq linear model fitting using the function DESeq with betaPrior=TRUE

source_name: Pluripotent stem cells

growth_protocol: Pluripotent stem cells were maintained in StemFlex media and Accutase passaged with ROCK inhibitor

extract_protocol:
High quality RNA was extracted by adding RNAse-free Trizol to each pellet and processing with the Zymo Research Direct-zol RNA miniprep kit
RNA-seq library prep was performed using the Illumina TruSeq Stranded Total RNA kit .

tag: tissue

value: Pluripotent stem cells

tag: cell line

value: induced pluripotent stem cells

tag: genotype

value: WT

value: Growth in StemFlex media


title: RT104_3-cfMCC-SEQ

value: Serum

value: Recovery


title: +MyoD+F/R/C+SP_3

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

institute: ETH Zurich

data_processing:
bcl2Fastq v2.20 software used for demultiplexing + basecalling.
Reads trimmed with fastp 0.20.0, options: --out1 trimmed_R1.fastq.gz --thread 8 --trim_front1 0 --trim_tail1 0 --average_qual 0 --adapter_fasta adapters.fa --max_len1 0 --max_len2 0 --disable_trim_poly_g --trim_poly_x --poly_x_min_len 10 --length_required 18 --compression 4
Pseudocounts generated with kallisto v0.46.1, options: -t 8 --bias --bootstrap-samples 10 --seed 42 --single --fragment-length 180 --sd 50
Differential expression analysis: DESeq2
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited raw counts

source_name: Embryonic fibroblasts

extract_protocol:
Total RNA was isolated using the RNAeasy  Mini Kit (Qiagen, #74104) as per the manufacturer’s protocol.
Samples with RIN above 8 were only used for further library preparation steps and library preparation was conducted according to the TruSeq Stranded mRNA protocol (Illumina, Inc., California, USA). Briefly, poly-A enrichment was carried out for total RNA (100-1000 ng), followed by reverse-transcription of poly-A enriched RNA into cDNA. The cDNA was then ligated with TrueSeq adapters including unique dual indices (UDI) after fragmentation, end-repair and adenylation steps. Using PCR, cDNA containing TruSeq adapters on both ends was selectively amplified which was further applied to a Fragment Analyzer to determine the quality and quantity of libraries. The average fragment size was approximately 360 bp.

value: Embryonic fibroblasts

value: Primary MEFs

value: 4x transfected with synthetic MyoD-mRNA (iMPC medium+B18R); in presence of F/R/C+SP

tag: time

value: day 10


title: +MyoD+F/R/C+CP_3

value: 4x transfected with synthetic MyoD-mRNA (iMPC medium+B18R); in presence of F/R/C+CP


title: TIAN-SNI-NAc-6

city: New York

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

description:
TIAN-SNI-NAc-6_S2
counts_matrix.txt
fpkm_matrix.txt

data_processing:
Reads were processed with the NGS-Data-Charmer pipeline. In brief, adaptors and low-quality bases were removed with Trim Galore.
Trimmed reads were aligned to the human genome with HISAT2 and alignments were de-duplicated with samtools rmdup.
Gene expression was calculated using featureCounts with parameters "-p -O --fraction -t gene" to the GENCODE annotation (vM25).
Assembly: mm10
Supplementary files format and content: counts_matrix.txt is a tab-delimited text file containing the non-normalized gene expression matrix. fpkm_matrix.txt is a tab-delimited text file containing the normalized FPKM (Fragments Per Kilobase per Million) gene expression matrix.

source_name: brain

extract_protocol:
TRIzol Phase Separation
Stranded mRNA Prep Kit (Illumina)

treatment_protocol: Tibial SNI or Sham Surgery (4 weeks) followed by 3 weeks of Saline, 30 mg/kg Tianeptine, or 15 mg/kg Desipramine (intraperitoneal, twice daily)

value: brain

tag: tissue region

value: nucleus accumbens

tag: surgery

value: sni

tag: strain

value: TIAN


title: 28126B iPSC, WT control, replicate 2

tag: treatment


title: RT104_1-cfMCC-SEQ

value: Baseline


title: day 3, sample5, rep2

description: 10x Genomics

value: reprogrammed MEFs

value: Mouse E13.5

tag: age

tag: time point

value: day 3


title: TIAN-SNI-NAc-5

description:
TIAN-SNI-NAc-5_S1
counts_matrix.txt
fpkm_matrix.txt


title: RT103_3-cfMCC-SEQ


title: +MyoD+F/R/C_3

value: 4x transfected with synthetic MyoD-mRNA (iMPC medium+B18R); in presence of F/R/C


title: 28126B iPSC, WT control, replicate 1

value: Pluripotent stem cells

value: induced pluripotent stem cells

value: WT

value: Growth in StemFlex media


title: RT103_2-cfMCC-SEQ

value: Serum

value: Radiation


title: TIAN-SNI-NAc-4

description:
TIAN-SNI-NAc-4_S4
counts_matrix.txt
fpkm_matrix.txt