title: ATAC-seq-Bulk-Day4

city: Brussels

first: Cedric

last: Blanpain

state: anderlecht

address: Route de Lennik 808, Bat C, C6-126

country: Belgium

institute: Université Libre de Bruxelles (ULB)

data_processing:
Quality filtering using trimmomatic
Alignment using bowtie2
Quality filtering using samtools and picard tools
Peak calling using Macs2
Genome_build: mm10
Supplementary_files_format_and_content: BED file of peaks and bigwig files for each sample

source_name: Differentiating mouse embryonic pluripotent stem cells at day 4

growth_protocol: Pluripotent stem cells were differentiated using published hanging drop protocols (1000 initial cells in serum-condtining medium)

extract_protocol: Nextera DNA sample Preparation Kit

treatment_protocol: Doxycyclin was added to induce the expression of Mesp1

value: WT

tag: time

tag: condition

value: Bulk


title: PDAC_T_16, replicate 1, snRNAseq

status: Public on May 18 2022

type: SRA

city: Cambridge

first: Karthik

last: Jagadeesh

state: MA

address: 415 Main St

department: Human Cell Atlas

country: USA

institute: Broad Institute

description:
10x Genomics
totaldata-final-toshare.h5ad

library_source: transcriptomic single cell

data_processing:
BCL files were converted to FASTQ using bcl2fastq2-v2.20.
CellRanger v3.0.2 was used to demultiplex the FASTQ reads, align them to the hg38 human transcriptome (pre-mRNA) reference and extract the UMI and nuclei barcodes.
We used CellBender remove-background to remove ambient RNA and other technical artifacts from the count matrices.
Nuclei with over 10,000 UMI counts were filtered.
UMI counts were normalized by the total number of UMIs per nucleus and converted to transcripts-per-10,000 (TP10K) as the final expression unit.
Assembly: Hg38
Supplementary files format and content: H5ad file of aggregated processed single-nuclei RNA sequencing data from all 45 human specimens; found in totaldata-final-toshare.h5ad
Supplementary files format and content: H5ad file of processed single-nuclei RNA sequencing data from the patient-derived organoid (untreated); found in adata_010nuc_10x.h5ad
Supplementary files format and content: H5ad file of processed single-nuclei RNA sequencing data from the patient-derived organoid (treated with 5-FU, SM38, and oxaliplatin); found in adata_010orgCRT_10x.h5ad

molecule: total RNA

organism: Homo sapiens

source_name: Pancreas

extract_protocol:
Resected primary tumor samples were snap frozen and stored at -80°C. Selected tissue was transferred into an NSTcPA buffer and manually minced.
Nuclei from each sample were loaded into each channel of a Chromium single-cell 3’ chip according to the manufacturer’s instructions. Single nuclei were partitioned into droplets with gel beads in the Chromium Controller to form emulsions, after which nuclear lysis, barcoded reverse transcription of mRNA, cDNA amplification, enzymatic fragmentation, and 5’ adaptor and sample index attachment were performed according to manufacturer’s instructions.
The snRNA-seq sample libraries were pooled (3-4 samples per flow cell line) and sequenced on the HiSeq X Version 2.5 (Illumina) with the following paired end read configuration: read 1, 26-28 nt; read 2, 96-98 nt; index read, 8 nt.

tag: tissue

value: Pancreas

tag: cell line

tag: cell type

value: Tumor

tag: treatment

value: CRTL


title: PDAC_T_22, replicate 1, snRNAseq

value: FOLFIRINOX, Gy/cisplatin


title: PDAC_T_14, replicate 2, snRNAseq

value: CRT


title: PDAC_T_18, replicate 1, snRNAseq


title: PDAC_T_15, replicate 1, snRNAseq


title: KO_LPS_194 [mRNA-seq]

city: Groningen

first: Bart

last: Eggen

state: Groningen

address: Antonius Deusinglaan 1

department: Department of Biomedical Sciences

country: Netherlands

institute: UMCG Groningen

description:
Ercc1Δ/ko
KO_LPS_194
training.featurecounts

library_source: transcriptomic

data_processing:
Adapter sequences and were removed with bbduk (v38.69).
Alignment to the Ensembl genome Mus musculus (GRCm38.82) was performed with STAR (v2.7.3a).
Sorting of the aligned reads was done with bamsort tool from biobambam2 tools (v2.0.95).
featureCounts (v2.0.0) was used to quantify the reads.
Picard (v1.130) and samtools were used to perform the quality control check and the generation of the fastq files.
Genome_build: GRCm38.82
Supplementary_files_format_and_content: 2 tab-delimited files containing gene counts of PBS- and LPS-treated mice; n=3 per condition, 4 conditions per model (tolerance and training).
ATAC samples were aligned to the Mus musculus genome (mm10/GRCm38) with the use of Bowtie 2 (v2.3.5.1) using the -very-sensitive flag.
Bamsort and bammarkduplicates from biobambam2 tools (v2.0.95) were used to sort the aligned files and to remove duplicated reads.
Samtools (v.1.1.0) was used to remove low quality (q<30) and blacklisted alignments.
ATAC-seq peaks were called using Genrich (v.0.5) with the ATAC-seq mode (-j switch), and -p parameter set to 0.01.
BigWig files were generated using deepTools bamCoverage (v.3.5.0) with RPGC normalization.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: A tab-delimited text file containing called peaks per sample.
ChIP samples were aligned to the Mus musculus genome (mm10/GRCm38) with the use of Bowtie 2 (v2.3.5.1) using the -very-sensitive flag.
Bamsort and bammarkduplicates from biobambam2 tools (v2.0.95) were used to sort the aligned files and to remove duplicated reads.
Samtools (v.1.1.0) was used to remove low quality (q<30) and blacklisted alignments.
Peak calling was performed using the JetBrains SPAN peak analyzer (v.0.11.0) using default parameters, which were later manually refined upon visual inspection using the JetBrains JBR browser (v.1.0 beta) on each sample.
BigWig files were generated using deepTools bamCoverage (v.3.5.0) with RPGC normalization.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: A tab-delimited text file containing called peaks per sample.

organism: Mus musculus

source_name: microglia

extract_protocol:
Microglia were isolated by mechanical tissue dissociation and Percoll gradient centrifugation at 4°C followed by flow cytometry of single, DAPI(-),CD11b(+),CD45(+),Ly6c(-) cells. RNA was isolated using a Qiagen RNeasy Micro Kit (Qiagen, 74004) according to the manufacturer’s instructions.
After RNA isolation, sequencing libraries were generated using NEXTflex® Rapid Illumina Directional RNA-Seq Library Prep Kit (BiooScientific, NOVA-5138-10) with polyA selection. Pooled libraries of the training model were sequenced using the NextSeq 500/550 High Output v2 kit (75 cycles, Illumina, FC-404-2005) with single reads on a NextSeq500 (Illumina). Pooled libraries of the tolerance model were sequenced with a HiSeq Rapid SBS kit (50 cycles, Illumina, FC-402-4022) using single reads on a HiSeq 2500 (Illumina).

tag: strain

value: FVB/ C57BL/6J

tag: genotype

value: LPS


title: PDAC_T_14, replicate 1, snRNAseq


title: PDAC_T_13, replicate 3, snRNAseq


title: KO_LPS_600 [mRNA-seq]

description:
Ercc1Δ/ko
KO_LPS_600
training.featurecounts


title: KO_LPS_193 [mRNA-seq]

description:
Ercc1Δ/ko
KO_LPS_193
training.featurecounts


title: Control_LPS_185 [mRNA-seq]

description:
Ercc1wt/Δ, Ercc1wt/ko or Ercc1wt/wt
Control_LPS_185
training.featurecounts

value: Ercc1wt/delta, Ercc1wt/ko or Ercc1wt/wt


title: PDAC_T_17, replicate 1, snRNAseq


title: Control_LPS_149 [mRNA-seq]

description:
Ercc1wt/Δ, Ercc1wt/ko or Ercc1wt/wt
Control_LPS_149
training.featurecounts


title: Control_LPS_184 [mRNA-seq]

description:
Ercc1wt/Δ, Ercc1wt/ko or Ercc1wt/wt
Control_LPS_184
training.featurecounts


title: KO_PBS_642 [mRNA-seq]

description:
Ercc1Δ/ko
KO_PBS_642
training.featurecounts

value: PBS


title: PDAC_T_13, replicate 2, snRNAseq


title: KO_PBS_641 [mRNA-seq]

description:
Ercc1Δ/ko
KO_PBS_641
training.featurecounts


title: PDAC_T_13, replicate 1, snRNAseq


title: KO_PBS_638 [mRNA-seq]

description:
Ercc1Δ/ko
KO_PBS_638
training.featurecounts


title: PDAC_T_12, replicate 2, snRNAseq


title: Control_PBS_175 [mRNA-seq]

description:
Ercc1wt/Δ, Ercc1wt/ko or Ercc1wt/wt
Control_PBS_175
training.featurecounts


title: PDAC_T_12, replicate 1, snRNAseq


title: Control_PBS_171 [mRNA-seq]

description:
Ercc1wt/Δ, Ercc1wt/ko or Ercc1wt/wt
Control_PBS_171
training.featurecounts


title: PDAC_T_11, replicate 1, snRNAseq


title: PDAC_T_11, replicate 2, snRNAseq


title: Control_PBS_170 [mRNA-seq]

description:
Ercc1wt/Δ, Ercc1wt/ko or Ercc1wt/wt
Control_PBS_170
training.featurecounts


title: PDAC_T_10, replicate 2, snRNAseq


title: PDAC_T_10, replicate 1, snRNAseq


title: PDAC_T_9, replicate 2, snRNAseq


title: PDAC_T_8, replicate 3, snRNAseq


title: PDAC_T_9, replicate 1, snRNAseq


title: Input-12h-dox

library_source: genomic

data_processing:
Quality filtering using trimmomatic
Alignment using bowtie2
Quality filtering using samtools and picard tools
Peak calling using Macs2
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

source_name: Differentiating mouse embryonic pluripotent stem cells where forced expression of Mesp1 is dox-inducible

extract_protocol: Truseq ChIP Library Preparation kit (Illumina)

treatment_protocol: Doxycycline was added to induce the expression of Mesp1 or Zic3

tag: target-protein

value: Input

tag: chip antibody

value: dox

value: embryonic pluripotent stem cells


title: Input-24h-dox


title: Input-12h-no-dox


title: Input-24h-no-dox


title: MCF7 cells, DMSO, 16h, rep3

city: Wuhan

first: Zilun

last: RUAN

state: Hubei

address: Donghu Road, No. 115, Wuchang District

department: Department of Infectious Diseases, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University

country: China

institute: Wuhan University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Raw RNA-seq reads are aligned to Homo sapiens. GRCh38 by using Tophat2 (version 2.0.13) with the default parameters.
Gene counts are quantified by using HT-seq (version 2.0.0) with REFSEQ annotation.
Differentially expressed genes are identified by using DEseq2 (version 1.36.0)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts of sequencing reads values for each Sample

growth_protocol: MCF7 cells were cultured in phenol-red free medium supplemented with 10% carbon absorbed FBS for four days.

extract_protocol:
Total RNA was extracted from cells using TRIzol Reagent (Invitrogen, cat. NO 15596026) following standard methods.
2 ug of total RNA was used for the construction of sequencing libraries using KCTM Stranded mRNA Library Prep Kit for Illumina

treatment_protocol: MCF7 cells were treated or untreated with PPT (5 nM) for 16 hours.

value: breast cancer cells

value: treated with DMSO


title: MCF7 cells, PPT, 16h, rep2

value: treated with PPT (5nM)


title: MCF7 cells, PPT, 16h, rep3

value: WT


title: MCF7 cells, PPT, 16h, rep1


title: MCF7 cells, DMSO, 16h, rep1


title: H3K27Ac-ChIP-seq-24h-no-dox

value: Rabbit anti-H3K27ac (Cat:ab4279,Abcam, ChIP-grade)


title: AOSD_II-D18

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

data_processing:
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome hg19 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
Trimmed RNA-seq data were aligned to the human V, D and J genes and obtained immune clonotypes using MiXCR (Bolotin et al., Nat Methods, 2015; Bolotin et al., Nat Biotechnol, 2017).
Assembly: hg19
Supplementary files format and content: HTSeq counts from RNA-seq samples

molecule: polyA RNA

source_name: PBMCs

growth_protocol: Blood samples were collected from the AOSD patient before and after vaccinations.

extract_protocol:
The buffy coat was extracted by centrifuge after blood sample collection and RBC was removed using RBC lysis buffer in the buffy coat. Total RNA was isolated using a Maxwell RSC simply RNA Blood purification kit.
Libraries for sequencing were prepared with TruSeq Stranded mRNA Kit following standard Illumina protocols.

tag: disease status

value: adult-onset Still’s disease

tag: age

tag: vaccination

value: 2nd dose

tag: timepoint

value: PBMCs


title: AOSD_II-D7


title: H3K27Ac-ChIP-seq-24h-dox


title: MCF7 cells, DMSO, 16h, rep2


title: H3K27Ac-ChIP-seq-12h-dox


title: Chronic_D21_CD4_PD1_RNA_rep2

city: Stanford

first: Ansuman

middle: T

last: Satpathy

state: CA

address: 240 Pasteur Drive

institute: Stanford University

data_processing:
Reads were processed with Cell Ranger v3.1.0.
R1 contains barcode at 1-16bp and UMI at bp 17-26.
R2 contains the biological sequence.
I1 contains the i7 sample index.
Assembly: mm10 (GRCm38)
Supplementary files format and content: "barcodes.tsv" contains filtered cellular barcodes, "features.tsv" contains genes, "matrix.mtx" contains the barcoded gene expression matrix.

source_name: spleen

extract_protocol: 10x Chromium Next Gem Single Cell V(D)J Reagent Kit (v1.1).

tag: infection

value: LCMV clone 13

value: 21 dpi

tag: sorted population

value: CD4+PD1+ T cells


title: AOSD_II-D1


title: Chronic_D21_CD4_PD1_RNA_rep1


title: H3K27Ac-ChIP-seq-12h-no-dox


title: PDAC_T_8, replicate 1, snRNAseq

value: Pancreas

value: Tumor

value: CRT


title: AOSD_II-D0


title: PDAC_T_6, replicate 1, snRNAseq


title: PDAC_T_8, replicate 2, snRNAseq


title: RH16_KO-Veh

city: Madison

first: Xinyu

last: Zhao

state: Wisconsin

address: 1500 HIghland Ave, Wiasman Center North Tower T513

institute: University of Wisconsin Madison

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: tab-delimited files include count values for each Sample

source_name: KO-Veh

extract_protocol:
Dissection immediately after eutanasia, the tissue was frozen in -80 degree freezer until use
essenger 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. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.
single read on Illumina sequencer HWI-ST1276, flow cell C1162ACXX; Illumina index sequence: CGATGT

treatment_protocol: mice were injected with either Nutlin-3 or Vehicle through ip at 2-month of age and euthanized for tissue collection at 6- month of age.

value: Vehicle injected

value: brain hippocampus


title: PDAC_T_6, replicate 2, snRNA-seq


title: PDAC_T_5, replicate 1, snRNAseq


title: AOSD_I-D1

value: 1st dose


title: RH14_WT-Nut3

value: Wild type

value: Nutlin-3 injected


title: AOSD_I-D0


title: Mesp1-ChIP-seq-12h-dox

value: Rabbit anti-HA (cat:ab9110, Abcam, ChIP-grade)

value: dox

value: embryonic pluripotent stem cells


title: PDAC_T_7, replicate 1, snRNAseq


title: Mesp1-ChIP-seq-24h-dox


title: PDAC_T_4, replicate 1, snRNAseq


title: MNKPL10 tumor WGS

city: Tokyo

first: Akira

last: Nishimura

address: 1-5-45 Yushima, Bunkyo-ku

department: Department of Pediatrics and Developmental Biology

country: Japan

institute: Tokyo Medical and Dental University

description: MNKPL10 tumor WGS

data_processing:
Library strategy: Whole genome sequence
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR 2.7.8a.
Trimmed mean of M values (TMM) normalized counts were calculated using edgeR protocol.
Genome_build: hg19
Supplementary_files_format_and_content: Raw_counts.txt: Tab-delimited text files include values of raw counts for each Sample.
Supplementary_files_format_and_content: Normalized_counts.txt: Tab-delimited text files include values of TMM normalized counts for each Sample.

source_name: Bone marrow

extract_protocol:
Genomic DNA was extracted from cells using QIAGEN AllPrep kit. The construction of sequencing libraries was carried out using NEBNext DNA Library Prep Kit.
DNA libraries were prepared for sequencing using standard NEB protocols.

tag: Sex

value: Male

value: Bone marrow

tag: subgroup


title: RH13_KO-Nut3


title: RH15_WT-Veh

source_name: WT-Veh


title: ATAC-seq-WT-24h-no-dox-rep1

data_processing:
Quality filtering using trimmomatic
Alignment using bowtie2
Quality filtering using samtools and picard tools
Peak calling using Macs2
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

treatment_protocol: Doxycycline was added to induce the expression of Mesp1

value: WT

tag: time

tag: condition


title: RH10_KO-Veh

tag: tissue


title: MNKPL7 germline WES

description: MNKPL7 germline WES

data_processing:
Library strategy: Whole exome sequence
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR 2.7.8a.
Trimmed mean of M values (TMM) normalized counts were calculated using edgeR protocol.
Genome_build: hg19
Supplementary_files_format_and_content: Raw_counts.txt: Tab-delimited text files include values of raw counts for each Sample.
Supplementary_files_format_and_content: Normalized_counts.txt: Tab-delimited text files include values of TMM normalized counts for each Sample.

source_name: Peripheral blood

extract_protocol:
Genomic DNA was extracted from cells or tissues using QIAGEN AllPrep kit or QIAGEN DNA FFPE kit. Exome capture was carried out using SureSelect QXT Reagents or SureSelect low input XT for the construction of sequencing libraries.
DNA libraries were prepared for sequencing using standard Agilent protocols.

value: Female

value: Peripheral blood


title: ATAC-seq-WT-12h-dox-rep1

tag: cell type


title: MNKPL7 tumor WES

description: MNKPL7 tumor WES


title: ATAC-seq-WT-12h-no-dox-rep1


title: RH8_KO-Nut3

tag: treatment


title: PDAC_T_2, replicate 1, snRNAseq

tag: cell line


title: ATAC-seq-WT-0h-no-dox-rep1

tag: genotype


title: MNKPL6 tumor RNA-seq

description: MNKPL6 tumor RNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR 2.7.8a.
Trimmed mean of M values (TMM) normalized counts were calculated using edgeR protocol.
Genome_build: hg19
Supplementary_files_format_and_content: Raw_counts.txt: Tab-delimited text files include values of raw counts for each Sample.
Supplementary_files_format_and_content: Normalized_counts.txt: Tab-delimited text files include values of TMM normalized counts for each Sample.

extract_protocol:
Single cell RNA-seq
RNA libraries were prepared for sequencing using standard NEB or Takara protocols.


title: MNKPL6 tumor WGS

description: MNKPL6 tumor WGS

extract_protocol:
RNA libraries were prepared for sequencing using standard BD protocols.
DNA libraries were prepared for sequencing using standard NEB protocols.


title: PDAC_T_1, replicate 2, snRNAseq


title: PDAC_T_3, replicate 2, snRNAseq


title: PDAC_T_3, replicate 1, snRNAseq


title: RH7_KO-Veh


title: gDNA_tumor_MNKPL6

type: genomic

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing: GenomeStudio software V2011.1.

label: Cy5 and Cy3

source_name: bone marrow

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified from samples using Qiagen AllPrep DNA/RNA Mini Kit according to standard protocol.

tag: diagnosis

value: Myeloid/natural killer cell precursor acute leukemia (MNKPL)

value: Tumor sample

tag: tumor site

value: BM


title: PDAC_T_1, replicate 1, snRNAseq

value: Pancreas

value: Tumor

value: CRT


title: RH9_WT-Nut3

value: brain hippocampus


title: gDNA_tumor_MNKPL1

source_name: lymph node

value: Lymph node


title: RH6_KO-Nut3

value: Nutlin-3 injected


title: MNKPL5 tumor WGS

description: MNKPL5 tumor WGS


title: HCC_37_T

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina Casava v1.8.2 software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg19) using TopHat2 default settings. The aligned BAM files sorted (SAMTools). Gene expression quantification were obtained using HTSeq-count with Gencode v7. RSEM quantification at gene level was produced with NCBI Refseq (2011).
gene count measurements were obtained using HTSeq-count
Assembly: hg19
Supplementary files format and content: The processed data files are in tabular format.  For HTSeq, the first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count. For RSEM, the results are combined to three output files: expected read counts, RPKM and TPM value for each gene for all 20 samples in each column.

source_name: normal liver tissue adjacent to tumor

extract_protocol:
Total RNA was isolated from the tissues using RNA Mini Spin Column of Enzy Max LLC (Lexington, KY) according to the manufacturer’s instructions. DNase (Thermo Scientific, Rockford, IL, Cat.# EN0521) was added to the first wash solution at 10µg/70µl and incubated for 15 min at room temperature to remove genomic DNA contamination
RNA-seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide

value: normal liver

tag: gender

value: male


title: HCC_37_N

source_name: liver tumor

value: Hepatocellular carcinoma


title: HCC_36_N

value: female


title: RH5_WT-Veh

value: Wild type

value: Vehicle injected


title: RH2_WT-Veh


title: PDAC_U_17, replicate 2, snRNAseq

value: Untreated


title: gDNA_tumor_MNKPL4

value: Female


title: HCC_36_T


title: gDNA_tumor_MNKPL7

value: Myeloid/natural killer cell precursor acute leukemia (MNKPL)


title: gDNA_tumor_MNKPL9

value: Tumor sample


title: scRD21AP

data_processing:
Reads were processed with Cell Ranger v3.1.0
R1 contains barcode at 1-16bp and UMI at bp 17-26
R2 contains the biological sequence
I1 contains the i7 sample index
Genome_build: mm10
Supplementary_files_format_and_content: "barcodes.tsv.gz" contains filtered cellular barcodes, "features.tsv.gz" contains genes, "matrix.mtx.gz" contains the barcoded gene expression matrix

extract_protocol: 10x Chromium Next Gem Single Cell V(D)J Reagent Kit (v1.1)

value: LCMV Armstrong

value: 21 dpi

value: I-Ab-LCMV-gp66 tetramer+

tag: strain


title: gDNA_tumor_MNKPL10

value: Male

value: BM


title: MNKPL1 tumor WGS

description: MNKPL1 tumor WGS

source_name: Lymph node

value: Lymph node


title: PDAC_U_18, replicate 2, snRNAseq

value: Pancreas

value: Tumor


title: RH1_WT-Nut3

value: Nutlin-3 injected

value: brain hippocampus


title: PDAC_U_18, replicate 1, snRNAseq


title: PDAC_U_17, replicate 1, snRNAseq


title: Independent_uEVs_Patient_20

city: Paris

first: Antonin

last: Morillon

state: Paris

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: total ribo-depleted RNA

data_processing:
Reads were mapped on hg38 genome with STAR version 2.6.1a, with the following parameters : --outSAMprimaryFlag OneBestScore --outSAMattrRGline --outSAMmultNmax 1 --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1.
bam files were converted into bedgraph files using bedtools version 2.29.0. RPM normalization (reads per million of mapped reads) was applied on these files, then they were converted into bigwig files using bedGraphToBigWig from UCSC.
Genome_build: hg38
Supplementary_files_format_and_content: coverage files for minus and plus strand in bigwig format  (RPM normalization)

source_name: urinary extracellular vesicles

growth_protocol: FFPE and urinary extracellular vesicules were obtained from prostate cancer patients who provided informed consent and were approved for collection and distribution by Mondor institutional board. PC3, DU145 and LNCaP human prostate cancer cell lines, were obtained from American Type Culture Collection (Manassas, VA, USA).

extract_protocol:
miRNeasy micro kit (Qiagen)
Total RNA-seq libraries were prepared with SMARTer Stranded Total RNA-Seq Kit v2-Pico Input Mammalian

tag: individual

value: Patient 20

tag: disease state

value: prostate cancer (PCa)

tag: samsple type

value: urinary extracellular vesicules from tumor patient


title: gDNA_tumor_MNKPL5


title: HCC_34_N

value: Hepatocellular carcinoma

value: female


title: HCC_19_T

value: normal liver

value: male


title: ATAC-seq-WT-24h-dox-rep1

value: WT

value: dox

value: embryonic pluripotent stem cells


title: scRD21AN

tag: infection

value: LCMV Armstrong

tag: timepoint

value: 21 dpi

tag: sorted population

value: I-Ab-LCMV-gp66 tetramer-


title: MNKPL4 tumor WGS

description: MNKPL4 tumor WGS

tag: Sex

value: Female

value: Bone marrow

tag: subgroup


title: Independent_uEVs_Patient_18

description: total ribo-depleted RNA

value: Patient 18


title: PDAC_U_15, replicate 1, snRNAseq

tag: tissue

value: Pancreas

value: Tumor

value: Untreated


title: HCC_34_T


title: Independent_uEVs_Patient_19

description: total ribo-depleted RNA

value: Patient 19

value: prostate cancer (PCa)

value: urinary extracellular vesicules from tumor patient


title: SCRD21_8

value: LCMV clone 13


title: HCC_19_N

value: Hepatocellular carcinoma

value: male


title: PDAC_U_16, replicate 1, snRNAseq

tag: cell type


title: PDAC_U_14, replicate 1, snRNAseq

tag: treatment


title: Independent_uEVs_Patient_16

description: total ribo-depleted RNA

value: Patient 16


title: SCRD21_7

value: I-Ab-LCMV-gp66 tetramer+


title: Independent_uEVs_Patient_17

description: total ribo-depleted RNA

value: Patient 17


title: SCRD21_5

value: LCMV Armstrong

value: 21 dpi


title: PDAC_U_13, replicate 1, snRNAseq

tag: cell line


title: PDAC_U_12, replicate 1, snRNAseq


title: Independent_uEVs_Patient_15

description: total ribo-depleted RNA

value: Patient 15


title: HCC_15_N


title: HCC_15_T

value: normal liver


title: HCC_13_N


title: Independent_uEVs_Patient_14

description: total ribo-depleted RNA

value: Patient 14


title: PDAC_U_10, replicate 2, snRNAseq

value: Pancreas


title: PDAC_U_11, replicate 1, snRNAseq

value: Tumor


title: HCC_13_T


title: SCRD21_3


title: Independent_uEVs_Patient_13

description: total ribo-depleted RNA

value: Patient 13


title: SCRD21_2

value: I-Ab-LCMV-gp66 tetramer-


title: Independent_uEVs_Patient_11

description: total ribo-depleted RNA

value: Patient 11

value: prostate cancer (PCa)


title: HCC_12_T


title: PDAC_U_10, replicate 1, snRNAseq

value: Untreated


title: Independent_uEVs_Patient_12

description: total ribo-depleted RNA

value: Patient 12

value: urinary extracellular vesicules from tumor patient


title: PDAC_U_9, replicate 1, snRNAseq


title: PDAC_U_8, replicate 2, snRNAseq


title: scR_D8CP

value: LCMV clone 13

value: 8 dpi


title: SCRD21_1

value: I-Ab-LCMV-gp66 tetramer+


title: SCRD21_4


title: HCC_1_T

value: female


title: HCC_12_N

value: Hepatocellular carcinoma

value: male


title: Independent_uEVs_Patient_9

description: total ribo-depleted RNA

value: Patient 9


title: Independent_uEVs_Patient_10

description: total ribo-depleted RNA

value: Patient 10


title: PDAC_U_8, replicate 1, snRNAseq

value: Pancreas


title: HCC_1_N


title: Hepatic stellate cells - NCMC treated - replicate 3

city: Boston

first: Alan

middle: C.

last: Mullen

address: 55 Fruit St.

department: Department of Medicine

institute: Massachusetts General Hospital

data_processing:
Reads were quality asssed using the FASTQC (v 0.11.8).
RNA-seq reads were aligned to the human reference genome (GRCh38_release_37) from Gencode with Star aligner (v2.7.3) using RSEM (v1.3.1) with default parameters. First, the human reference genome was indexed using the Gencode annotations (v37) with rsem-prepare-reference from RSEM software. Next, rsem-calculate-expression was used to aligh the reads and quantify the gene abundance. The output of rsem-calculate-expression gives separately the read count and transcripts per million value for each gene.
Genes with at least five reads were selected for the differential expression analysis.
Differential expression analysis was performed using gene read counts with DESeq2 package (v 1.32.0) to produce LFC values and corresponding p-values (FDR) applying a Benjamini-Hochberg correction for multiple testing.
Genome_build: GRCh38_release_37
Supplementary_files_format_and_content: a txt file contains differential expression analysis results

source_name: Hepatic stellate cells - NCMC treated

growth_protocol: Isolated primary human hepatic stellate cells were cultured routinely on coated plastic tissue culture dishes in DMEM medium supplemented with 10% FBS and 1% Pennicillin/Streptomycin.

extract_protocol:
RNA was extracted using Rneasy Mini kit (Qiagen). RNA quality was assessed using Agilen 2200 Tape Station. All samples have an RNA integrity number greater than 9.
RNA library was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: Two replicates were treated with DMSO for 48 hours. Three replicates were treated with 1 µM NCMC for 48 hours.

value: Primary hepatic stellate cells isolated from human liver tissues and cultured on plastic cell culture dish

tag: race

value: Caucasian

tag: race and gender

value: NCMC for 48 hours


title: scR_D8AP

value: LCMV Armstrong


title: PDAC_U_7, replicate 1, snRNAseq

value: Tumor


title: scR_D8AN

value: I-Ab-LCMV-gp66 tetramer-


title: Hepatic stellate cells - NCMC treated - replicate 2


title: Independent_uEVs_Patient_8

description: total ribo-depleted RNA

value: Patient 8

value: prostate cancer (PCa)


title: PDAC_U_6, replicate 1, snRNAseq

value: Untreated


title: PDAC_U_5, replicate 1, snRNAseq


title: PDAC_U_4, replicate 1, snRNAseq


title: TCRD21AN

data_processing:
Library strategy: TCR-seq
Reads were processed with Cell Ranger v3.1.0
R1 contains barcode at 1-16bp and UMI at bp 17-26
R2 contains the biological sequence
I1 contains the i7 sample index
Genome_build: mm10
Supplementary_files_format_and_content: "clonotypes.csv" contains TCR clonotype information, "filtered_contig_annotations.csv" contains productive TCR contigs per cell, "consensus_annotations.csv" contains clonotype consensus annotations

extract_protocol:
10x Chromium Next Gem Single Cell V(D)J Reagent Kit (v1.1)
10x Chromium Next Gem Single Cell V(D)J Reagent Kit (v1.1)

value: 21 dpi


title: Hepatic stellate cells - DMSO treated - replicate 2

source_name: Hepatic stellate cells - DMSO treated

value: DMSO for 48 hours


title: Independent_uEVs_Patient_5

description: total ribo-depleted RNA

value: Patient 5

value: urinary extracellular vesicules from tumor patient


title: Hepatic stellate cells - NCMC treated - replicate 1

value: male


title: TCRD21AP

value: I-Ab-LCMV-gp66 tetramer+


title: Hepatic stellate cells - DMSO treated - replicate 1


title: Independent_uEVs_Patient_7

description: total ribo-depleted RNA

value: Patient 7


title: Independent_uEVs_Patient_6

description: total ribo-depleted RNA

value: Patient 6


title: MNKPL9 tumor WGS

description: MNKPL9 tumor WGS

value: Female

value: Bone marrow


title: TCRD21_8

value: LCMV clone 13


title: PDAC_U_3, replicate 1, snRNAseq

data_processing:
BCL files were converted to FASTQ using bcl2fastq2-v2.20.
CellRanger v3.0.2 was used to demultiplex the FASTQ reads, align them to the hg38 human transcriptome (pre-mRNA) reference and extract the UMI and nuclei barcodes.
We used CellBender remove-background to remove ambient RNA and other technical artifacts from the count matrices.
Nuclei with over 10,000 UMI counts were filtered.
UMI counts were normalized by the total number of UMIs per nucleus and converted to transcripts-per-10,000 (TP10K) as the final expression unit.
Assembly: Hg38
Supplementary files format and content: H5ad file of aggregated processed single-nuclei RNA sequencing data from all 45 human specimens; found in totaldata-final-toshare.h5ad
Supplementary files format and content: H5ad file of processed single-nuclei RNA sequencing data from the patient-derived organoid (untreated); found in adata_010nuc_10x.h5ad
Supplementary files format and content: H5ad file of processed single-nuclei RNA sequencing data from the patient-derived organoid (treated with 5-FU, SM38, and oxaliplatin); found in adata_010orgCRT_10x.h5ad

source_name: Pancreas

extract_protocol:
Resected primary tumor samples were snap frozen and stored at -80°C. Selected tissue was transferred into an NSTcPA buffer and manually minced.
Nuclei from each sample were loaded into each channel of a Chromium single-cell 3’ chip according to the manufacturer’s instructions. Single nuclei were partitioned into droplets with gel beads in the Chromium Controller to form emulsions, after which nuclear lysis, barcoded reverse transcription of mRNA, cDNA amplification, enzymatic fragmentation, and 5’ adaptor and sample index attachment were performed according to manufacturer’s instructions.
The snRNA-seq sample libraries were pooled (3-4 samples per flow cell line) and sequenced on the HiSeq X Version 2.5 (Illumina) with the following paired end read configuration: read 1, 26-28 nt; read 2, 96-98 nt; index read, 8 nt.

value: Pancreas


title: Independent_uEVs_Patient_4

description: total ribo-depleted RNA

value: Patient 4


title: scR_D8CN

value: 8 dpi

value: I-Ab-LCMV-gp66 tetramer-


title: B55

city: Shanghai

first: rui

last: Dong

address: 399 Wan Yuan Road

institute: Department of Pediatric Surgery, Children’s Hospital of Fudan University, and Shanghai Key Laboratory of Birth Defect

description: Wilms tumor_FPKM

data_processing:
RNA-seq reads were trimmed to remove low-quality bases and adaptor contamination using TrimGalore  and mapped to the hs37d5 genome assembly with the GENCODE v.13 annotation as a transcript guide using Tophat.
Expression values were reported as fragments per kilobase of exon per million fragments mapped (FPKM) as calculated by CuffDiff.
Genome_build: hs37d5
Supplementary_files_format_and_content: A tab-delimited text file include all the expression values in each sample.

source_name: Adjacent normal tissue

extract_protocol:
Tumor tissues and adjacent normal tissue were collected freshly during surgery, immediately stored in liquid nitrogen for subsequent extraction of RNA.
RNA-seq libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit v.2

value: female

tag: age


title: B32

description: Wilms tumor_FPKM


title: PDAC_U_2, replicate 1, snRNAseq

value: Tumor

value: Untreated


title: TCRD21_5

value: LCMV Armstrong

value: 21 dpi


title: Independent_uEVs_Patient_2

description: total ribo-depleted RNA

value: Patient 2

value: prostate cancer (PCa)

value: urinary extracellular vesicules from tumor patient


title: TCRD21_7

value: I-Ab-LCMV-gp66 tetramer+


title: PDAC_U_1, replicate 1, snRNAseq


title: B28

description: Wilms tumor_FPKM


title: B24

description: Wilms tumor_FPKM


title: TCRD21_4


title: Independent_uEVs_Patient_1

description: total ribo-depleted RNA

value: Patient 1


title: BT379 shRNA18-2

city: Roma

first: Silvia Anna

last: Ciafrè

address: Via Montpellier, 1

department: Biomedicine and Prevention

country: Italy

institute: University of Rome Tor Vergata

description: BT273 patient-derived glioblastoma stem-like cells (described in De Bacco F. et al, 2012 doi: 10.1158/0008-5472.CAN-11-3490)

data_processing:
Raw sequence data (.bcl files) generated from Illumina NovaSeq 6000 was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Genome_build: GRCh38 reference genome available on ENSEMBL
Supplementary_files_format_and_content: text files including unique hit counts for each sample
Supplementary_files_format_and_content: one csv file including raw gene hit counts of all samples used in the experiment

source_name: human glioblastoma stem cells

growth_protocol: GSCs were cultured as floating spheres in DMEM/F-12 (1:1) (1X) + GlutaMAX (Gibco) containing 1% penicillin/streptomycin (Corning), 1% L-glutamine (Aurogene), 2% B27 (Gibco), 0.1% heparin (Sigma-Aldrich), 0.002% bFGF (PeproTech) and 0.002% EGF (PeproTech) at 37 °C in a humidified 5% CO2 incubator.

extract_protocol:
Total RNA was prepared from the GSCs using the Direct-zol™ RNA MiniPrep kit (Zymo Research).
The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA), at GENEWIZ Germany GmbH (Leipzig, Germany).

treatment_protocol: To deplete MEOX2 endogenous expression, BT273 and BT379 cells were transduced with lentiviral particles containing the pLKO.1 vector (Merck) expressing shRNAs directed against MEOX2, or the puro Non-Mammalian shRNA Control Plasmid DNA. The MEOX2-targeting shRNA sequences were TRCN0000018253 (Merck), which we renamed shRNA53 for simplicity, and TRCN0000427218 (Merck), renamed shRNA18 for simplicity.

tag: shRNA

value: shRNA18 targeting human MEOX2 mRNA


title: TCRD21_2

tag: strain


title: B23

description: Wilms tumor_FPKM

value: male


title: A55

description: Wilms tumor_FPKM

source_name: Wilms tumor tissue


title: TCRD21_1

source_name: spleen

value: LCMV clone 13


title: A28

description: Wilms tumor_FPKM


title: BT379 non targeting C2

description: BT379 patient-derived glioblastoma stem-like cells (described in De Bacco F. et al, 2012 doi: 10.1158/0008-5472.CAN-11-3490)

value: non targeting negative control


title: BT379 shRNA18-1


title: A32

description: Wilms tumor_FPKM


title: TCR_D8CP


title: A24

description: Wilms tumor_FPKM


title: Independent_uEVs_Patient_3

description: total ribo-depleted RNA

tag: individual

value: Patient 3


title: BT379 non targeting C1


title: TCR_D8CN

value: 8 dpi


title: TCR_D8AP


title: BT273 shRNA18-2

description:
BT273 patient-derived glioblastoma stem-like cells (described in De Bacco F. et al, 2012 doi: 10.1158/0008-5472.CAN-11-3490)
The read1 paired-end file was not provided due to corruption


title: TCR_D8AN

value: I-Ab-LCMV-gp66 tetramer-


title: BT273 shRNA53-1

value: shRNA53 targeting human MEOX2 mRNA


title: BT273 shRNA53-2


title: KO4

city: ADELAIDE

first: Kirsten

last: Smith

address: Lvl 5, AHMS, North Terrace

country: Australia

institute: University of Adelaide

data_processing:
initial data processing was conducted by Austrlaina Genome Research Facility AGRF, Melbourne, Australia
Salmon was used to align and quantify reads on mouse trancriptome. Quantification mode: Reads, Kmer Length 31, Paired end, Type of index: Quasi, Discard orphan quasi: No.
Genome_build: GRCm39 M26 release
Supplementary_files_format_and_content: fastq Raw data files
Supplementary_files_format_and_content: Tabular file of Salmon Exports read counts

source_name: Ovarian Stroma

extract_protocol:
female PRKO mice at 21-27 days old were hormonally stimulated with 5IU PMSG (44hrs) followed by 5IU hCG and ovaries collected at 8hrs post-hCG. Ovaries were repeatedly and thoroughly punctured to remove GCs and the residual ovary was snap frozen in liquid nitrogen. A total of 4 biological replicates per genotype were obtained, each consisting of tissue pooled from 3 mice. RNA was extracted from the unprocessed residual ovarian tissue using the RNeasy Mini Kit (Qiagen), including DNase treatment, as per manufacturer’s instructions
mRNA libraries were prepared using the Illumina Truseq Stranded mRNA kit. Paired end, 100bp sequencing was performed on NovaSeq 600 SP, 200 cycle (Illumina) sequencing system with a depth of 54-72M reads per sample

value: PRKO; Pgrtm1Bwo

value: GC depleted ovary

tag: genotype

value: PGR -/-


title: A23

description: Wilms tumor_FPKM


title: TCRD21_3

value: 21 dpi


title: Mutant2227input

city: Dallas

first: Ronak

last: Lakhia

address: 5323 Harry Hines Blvd

department: Internal Medicine

institute: UTSW

data_processing:
raw reads were aligned to the mouse reference genome (GRCh38/mm10)
The aligned reads were subsequently filtered for quality and uniquely mappable reads were reatine dfor furher analysis using Samtools version 1.6 and Sambamba version 0.6
Libarary complexity was measured using BEDTools version 2.26.0 and meets ENCODE data quality standards
relaxed peask were called using MACS version 2.1.0 with a p-value of 1x10^-2 for each replicate, pooled replicates' reads, and pseudoreplicates
Peak calls from the pooled replicates that were either observed in all replicates or both pseudoreplicates were used for subsequent analysis
Potential enhancers were defined as peaks that were > 2kb away from known TSS, protein coding genes.
To detect differentially bound enhancers, we used the R package DiffBind version 2.2.12 with a p- value of < 0.05 and default parameters
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file with fold change signal

source_name: kidney

growth_protocol: Pkd1F/F mice were bred with KspCre;Pkd1RC/RC mice.  Pkd1 mutant (KspCre:Pkd1F/RC) and Control (Pkd1F/RC) mice underwent terminal disection at 16 days of age.

extract_protocol:
kidneys were removed, flash frozen in liquid nitrogen and chromatin with H3K27ac deposition was enriched using Cell Signaling ChIP kit.  Kapa HTP libaray preparation kit was used for construction of sequencing libararies
ChIP-seq libraries were prepared using Kapa HTP Libarary Preparation Kit

value: kidney

value: post natal day 16

tag: antibody


title: KO3


title: BT273 non targeting C2


title: Mutant2276input


title: BT273 non targeting C1


title: KO2


title: Control2382input


title: WT2

value: PGR +/+


title: WT4


title: Mutant2286input


title: WT1


title: RNA-seq-WT-day4-Sorted-Flk1+/Pdgfra+_rep2

data_processing:
Quality filtering using Trimmomatic
alignment using STAR
Read counting in genes using HT-seq count
Differential expression analysis using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Table of normalized (read per million) reads for the three different batches

source_name: Differentiating mouse embryonic pluripotent stem cells where forced expression of Mesp1 is dox-inducible

extract_protocol: Qiagen RNA extraction kit

value: WT

tag: differentiation time

tag: condition

value: Differentiating embryonic pluripotent stem cells


title: WT3


title: Control2347input


title: MOLM-13 treated with I1_3

city: Weifang

first: Liuya

last: Wei

address: 7166 number, Baotong West Street

institute: Weifang Medical University

description: MOLM-13 treated with I1 3#

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Genome_build: hg38
Supplementary_files_format_and_content: FPKM value

source_name: MOLM-13 cell line treated with I1 3

extract_protocol:
Total RNA was extracted using using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

tag: protocol

value: incubating with I1 for 48 h

tag: agent

value: 1 uM I1


title: Zic3-ChIP-seq-Mesp1WT-24hdox

data_processing:
Quality filtering using trimmomatic
Alignment using bowtie2
Quality filtering using samtools and picard tools
Peak calling using Macs2
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file for each sample

extract_protocol: NEB Next Ultra II DNA library Prep Kit for Illumina

tag: target-protein

tag: chip antibody

value: Rabbit anti-Zic3 (Cat:ab222124,Abcam, ChIP-grade)

tag: time

value: dox


title: THP-1 treated with I1_3

description: THP-1 treated with I1 3#

source_name: THP-1 cell line treated with I1 3


title: THP-1 treated with I1_1

description: THP-1 treated with I1 1#

source_name: THP-1 cell line treated with I1 1


title: MOLM-13 treated with I1_1

description: MOLM-13 treated with I1 1#

source_name: MOLM-13 cell line treated with I1 1


title: THP-1  treated with control_3

description: THP-1 control 3#

source_name: THP-1 cell line treated with control 3

value: incubating with control for 48 h

value: Control


title: THP-1  treated with control_2

description: THP-1 control 2#

source_name: THP-1 cell line treated with control 2


title: THP-1 treated with I1_2

description: THP-1 treated with I1 2#

source_name: THP-1 cell line treated with I1 2


title: Mutant 3

tag: tissue

tag: treatment


title: Control 3


title: Mutant 2


title: BT273 shRNA18-1

value: shRNA18 targeting human MEOX2 mRNA

tag: cell line


title: Input_KO [ChIP-seq-Input]

data_processing:
Adapter sequences and were removed with bbduk (v38.69).
Alignment to the Ensembl genome Mus musculus (GRCm38.82) was performed with STAR (v2.7.3a).
Sorting of the aligned reads was done with bamsort tool from biobambam2 tools (v2.0.95).
featureCounts (v2.0.0) was used to quantify the reads.
Picard (v1.130) and samtools were used to perform the quality control check and the generation of the fastq files.
Genome_build: GRCm38.82
Supplementary_files_format_and_content: 2 tab-delimited files containing gene counts of PBS- and LPS-treated mice; n=3 per condition, 4 conditions per model (tolerance and training).
ATAC samples were aligned to the Mus musculus genome (mm10/GRCm38) with the use of Bowtie 2 (v2.3.5.1) using the -very-sensitive flag.
Bamsort and bammarkduplicates from biobambam2 tools (v2.0.95) were used to sort the aligned files and to remove duplicated reads.
Samtools (v.1.1.0) was used to remove low quality (q<30) and blacklisted alignments.
ATAC-seq peaks were called using Genrich (v.0.5) with the ATAC-seq mode (-j switch), and -p parameter set to 0.01.
BigWig files were generated using deepTools bamCoverage (v.3.5.0) with RPGC normalization.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: A tab-delimited text file containing called peaks per sample.
ChIP samples were aligned to the Mus musculus genome (mm10/GRCm38) with the use of Bowtie 2 (v2.3.5.1) using the -very-sensitive flag.
Bamsort and bammarkduplicates from biobambam2 tools (v2.0.95) were used to sort the aligned files and to remove duplicated reads.
Samtools (v.1.1.0) was used to remove low quality (q<30) and blacklisted alignments.
Peak calling was performed using the JetBrains SPAN peak analyzer (v.0.11.0) using default parameters, which were later manually refined upon visual inspection using the JetBrains JBR browser (v.1.0 beta) on each sample.
BigWig files were generated using deepTools bamCoverage (v.3.5.0) with RPGC normalization.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: A tab-delimited text file containing called peaks per sample.

source_name: microglia

extract_protocol:
Microglia were isolated by mechanical tissue dissociation and Percoll gradient centrifugation at 4°C followed by flow cytometry of single, DAPI(-),CD11b(+),CD45(+),Ly6c(-) cells.
After formaldehyde fixation and cell and nuclear lysis, chromatin was sonicated. Fragmented chromatin was precleared with protein A agarose beads and incubated over night with antibodies binding to the investigated histone modifications. Immune complexes were precipitated with protein A  beads. Chromatin was eluted, decrosslinked and DNA was purified with the GeneJET PCR purification kit. Sequencing libraries were generated from the purified DNA by MicroPlex Library Preparation Kit according to the manufacturer's protocol and sequenced on a Illumina HiSeq 2500..

value: FVB/ C57BL/6J

value: PBS


title: Control 1


title: Mutant 1


title: MOLM-13 treated with I1_2

description: MOLM-13 treated with I1 2#

source_name: MOLM-13 cell line treated with I1 2


title: Control2377input


title: RNA-seq-Bulk-day4-ND_Rep1

tag: cell type


title: Input_WT [ChIP-seq-Input]

description: Ercc1wt/Δ, Ercc1wt/ko or Ercc1wt/wt

value: Ercc1wt/delta, Ercc1wt/ko or Ercc1wt/wt


title: RNA-seq-Bulk-day4-ND_Rep2


title: RNA-seq-WT-day4-Sorted-Flk1+/Pdgfra+_rep1


title: THP-1 treated with control_1

description: THP-1 control 1#

source_name: THP-1 cell line treated with control 1


title: Control 2

tag: age


title: input-Mesp1WT-24hdox

value: Input


title: Zic2-ChIP-seq-Mesp1WT-24hdox

value: Rabbit anti-Zic2 (Cat:epr7790,Abcam, ChIP-grade)


title: MOLM-13 treated with control_2

description: MOLM-13 control 2#

source_name: MOLM-13 cell line treated with control 2


title: H3K27me3_WT-PBS [ChIP-seq-H3K27me3]

description: Ercc1wt/Δ, Ercc1wt/ko or Ercc1wt/wt


title: H3K4me1-Mesp1WT-24hdox

value: mouse anti-H3K4me1 (Cat:39635, Actif Motif,ChIP-grade)


title: 8-week Teratoma Cells

city: Minneapolis

first: Sunny

last: Chan

institute: University of Minnesota

description: single-cell barcoded total RNA

data_processing:
Data was processed using 10x cellranger (v3.0.2) using default parameters
Genome_build: hg38
Supplementary_files_format_and_content: 10x cellranger (v3.0.2) output

source_name: Teratoma Cells

extract_protocol:
Eight-week EGFP-labeled H1 ESC-derived teratoma cells were sorted for GFP by FACS and were then loaded into a 10x Genomics Chromium system for single-cell capture
The library was constructed according to the 10x Genomics Chromium Single Cell 3’ Reagent Kits v2 protocol
single-cell RNA-seq

value: embryonic stem cell-derived teratoma cells

value: Bulk teratoma


title: H3K27me3_KO-PBS [ChIP-seq-H3K27me3]


title: MOLM-13 treated with control_1

description: MOLM-13 control 1#

source_name: MOLM-13 cell line treated with control 1


title: input-Mesp1WT-0h

city: Brussels

first: Cedric

last: Blanpain

institute: Université Libre de Bruxelles (ULB)


title: H3K27ac_WT-PBS [ChIP-seq-H3K27ac]

description: Ercc1wt/Δ, Ercc1wt/ko or Ercc1wt/wt


title: input-Mesp1WT-24hnodox


title: Zic3-ChIP-seq-Mesp1WT-24hnodox


title: H3K27ac_KO-PBS [ChIP-seq-H3K27ac]


title: H3K4me3_KO-PBS [ChIP-seq-H3K4me3]


title: Zic2-ChIP-seq-Mesp1WT-24hnodox


title: H3K4me3_WT-PBS [ChIP-seq-H3K4me3]

description: Ercc1wt/Δ, Ercc1wt/ko or Ercc1wt/wt


title: MOLM-13 treated with control_3

description: MOLM-13 control 3#

source_name: MOLM-13 cell line treated with control 3


title: miRNA-seq_NETs-biological replicate 2

city: Harbin

first: Yanan

last: Jiang

address: 157 Baojian Road

department: Pharmacology

institute: Harbin Medical University

description: miRNA

data_processing:
The original image data file obtained by Illumina Hiseq recognition was transformed into the  original sequencing sequence (Sequenced Reads) base on the CASAVA(latest version) base recognition  (Base Calling) analysis
For ncRNA-seq, Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules:  1) Removing reads containing adapters;  2) Removing reads consisting of all A bases;  3) Removing reads containing more than 10% of unknown nucleotides (N);  4) Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.  Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were   further used in assembly and analysis of transcriptome.   The rRNA removed reads of each sample were then mapped to reference genome by TopHat2   [2] (version 2.1.1), respectively. The alignment parameters were as follows:   1) Maximum read mismatch is 2   2) Disables the coverage based search for junctions   3) The distance between mate-pair reads is 50bp   4) The standard deviation for the distribution on inner distance between mate-pair reads is 80bp   After aligned with reference genome, unmapped reads (or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well. A set of splice sites was built with initial unmapped reads by TopHat2 without relying on the known genes annotation. Not only be used for identifying expressed genes and their quantitative expression, the sequence alignment will also be helpful to find alternative splicing and new transcripts.  The reconstruction of transcripts was carried out with software Cufflinks, which together with TopHat2, allow biologists to identify new genes and new splice variants of known ones. The program reference annotation based transcripts (RABT) was preferred. Cufflinks constructed faux reads according to reference to make up for the influence of low coverage sequencing. During the last step of assembly, all of the reassembles fragments were aligned with reference genes and then similar fragments were removed.  Then we used Cuffmerge to merge transcripts from different replicas of a group into a comprehensive set of transcripts, and then merge the transcripts from multiple groups into a finally comprehensive set of transcripts for further downstream differential expression analysis.  To identify the new transcripts, all of the reconstructed transcripts were aligned to reference genome and were divided into twelve categories by using Cuffcompare. Transcripts with one of the classcodes “u,i,j,x,c,e,o” were defined as novel transcripts. We used the following parameters to identify reliable novel genes:   the length of transcript waslonger than 200bp and the exon number was more than 2 .   Novel transcripts were then aligned to the Nr, KEGG, and GO database to obtain protein functional annotation.     Two softwares CNCI (version 2)and CPC( http://cpc.cbi.pku.edu.cn/) were used to assess the protein-coding potential of novel transcripts by default parameters. In the mean time, novel transcripts were mapped to SwissProt database to assess protein annotation. The intersection of both non protein-coding potential results and non protein annotation results were chosen as long non-coding RNAs.   lncRNAs were classified into five classes according to their location relative to protein-coding genes: intergenic lncRNAs, bidirectional lncRNAs, intronic lncRNAs, antisense lncRNAs, and sense overlapping lncRNAs. Different types of lncRNAs may have different biological functions.   Transcripts abundances were quantified by software RSEM. There were two steps for RSEM to quantify transcripts abundances. Firstly, a set of reference transcript sequences were generated and preprocessed according to known transcripts and new transcripts (in FASTA format) and gene annotation files (in GTF format). Secondly, reads were realigned to the reference transcripts by Bowtie alignment program and the resulting alignments were used to estimate transcript abundances.  The transcript expression level was normalized by using FPKM (Fragments Per Kilobase of transcript per Million mapped reads) method. Given FPKM(A) to be the expression of transcripts A, C to be number of fragments mapped   to transcripts A, N to be total number of fragments that mapped to reference genes, and L to be number of bases on transcripts A. The FPKM method is able to eliminate the influence of different transcripts lengths and sequencing data amount on the calculation of transcripts expression. Therefore, the calculated transcripts expression can be directly used for comparing the difference of transcripts expression among samples.
For miRNA-seq,Reads obtained from the sequencing machines included dirty reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get clean tags, raw reads were further filtered according to the following rules:  1) Removing low quality reads containing more than one low quality (Q-value≤20) base or   containing unknown nucleotides(N);  2) Removing reads without 3’adapters;  3) Removing reads containing 5’adapters;  4) Removing reads containing 3’ and 5’ adapters but no small RNA fragment between them;  5) Removing reads containing ployA in small RNA fragment;  6) Removing reads shorter than 18nt (not include adapters).    All of the clean tags were aligned with small RNAs in GeneBank database(Release 209.0) to identify and remove rRNA,scRNA,snoRNA,snRNA and tRNA.   All of the clean tags were also aligned with reference genome. Those mapped to exons or introns might be fragments from mRNA degradation, so these tags were removed. The tags mapped to repeat sequences were also removed.  All of the clean tags were then searched against miRBase database(Release 22) to identify known (Species studied) miRNAs (exist miRNAs).  So far the miRNA sequences of some species were still not included in miRBase database.   For those species the miRNAs alignment with other species was a dependable way to identify the known miRNAs.  All of the unannotated tags were aligned with reference genome. According to their genome positions and hairpin structures predicted by software mirdeep2, the novel miRNA candidates were identified.   After tags were annotated as mentioned previously, the annotation results were determined in this priority order: rRNA etc > exist miRNA > exist miRNA edit > known miRNA > repeat > exon > novel miRNA > intron.The tags that cannot be annotated as any of the above molecules were recorded as unann.   Total miRNA consists of exist miRNA, known miRNA and novel miRNA, based on their expression in each sample, the miRNA expression level was calculated and normalized to transcripts per million (TPM).
The differentially expressed transcripts were analyzed respectively. To identify differentially expressed transcripts across samples or groups, the edgeR package (http://www.r-project.org/ ) was used. We identified transcripts with a fold   change ≥2 and a false discovery rate (FDR) <0.05 in a comparison as significant DEGs.   We identified miRNAs with a fold change ≥2 and P value <0.05 in a comparison as significant DE miRNAs.  Differentially expressed coding RNAs were then subjected to enrichment analysis of GO functions and KEGG pathways.   the candidate target genes were predicted by two softwares Miranda(Version 3.3a) and TargetScan(Version 7.0).
Genome_build: GRCH38
Supplementary_files_format_and_content: ncRNAseq_A-vs-N.all.annot.txt:raw counts and FPKM of ncRNA tran

source_name: adenocarcinoma gastric cell line (AGS)

growth_protocol: Human primary gastric cancer cell line AGS,was purchased from PROCELL (Wuhan, China). All cell lines were authenticated by short tandem repeat (STR) profiling and mycoplasma contamination negative test. All cell lines were cultured at 37 °C in a 5% CO2 humidified chamber, and grown in RPMI1640 (Gibco, USA) , medium with 10% fetal bovine serum(FBS,Gibco,USA). The CM was prepared when cells were grown at 90% confluence in the medium with 10%FBS, the medium was changed without FBS, and cells were cultured for a further 48 h. Then the supernatant was removed and centrifuged at 1,500× g for 10 min at 4 ℃ to remove cell debris. CM was aliquoted and stored at -80℃ for further experiments.

extract_protocol:
total RNA was extracted by using Trizol
For ncRNA-seq,rRNAs were removed from total RNA retain mRNAs and ncRNAs. The enriched mRNAs and ncRNAs were fragmented into short fragments by using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP (dUTP instead of dTTP) and buffer. Next, the cDNA fragments were purified with QiaQuick PCR extraction kit, end repaired, poly(A) added, and ligated to Illumina sequencing adapters. Then UNG (Uracil-N-Glycosylase) was used to digest the second-strand cDNA. The digested products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced. For miRNA-seq,the RNA   molecules in a size range of 18–30nt were enriched by polyacrylamide gel   electrophoresis(PAGE). Then the 3’ adapters were added and the 36-48nt RNAs were enriched.   The 5’ adapters were then ligated to the RNAs as well. The ligation products were reverse   transcribed by PCR amplification and the 140-160bp size PCR products were enriched to   generate a cDNA library and sequenced.

treatment_protocol: AGS cells(2×105) were co-cultured at 37℃ and 5%CO2 for 4h with nets

value: adenocarcinoma gastric cell line

value: AGS

value: with neutrophil extracellular traps


title: miRNA-seq_NETs-biological replicate 3

description: miRNA


title: miRNA-seq_AGS-biological replicate 2

description: miRNA

value: without treatment


title: miRNA-seq_NETs-biological replicate 1

description: miRNA


title: H3K27ac-Mesp1WT-0h

address: Route de Lennik 808, Bat C, C6-126

value: Rabbit anti-H3K27ac  (Cat:39133, Actif Motif, ChIP-grade)

value: Differentiating embryonic pluripotent stem cells


title: Zic2-ChIP-seq-Mesp1WT-0h


title: Zic2-ChIP-seq-Zic2/3KO-24hdox

value: dox


title: miRNA-seq_AGS-biological replicate 1

description: miRNA


title: Input_LL [ChIP-seq-Input]

city: Groningen

first: Bart

last: Eggen

institute: UMCG Groningen

description: wt

value: wt

value: LPS-LPS


title: NETs-biological replicate 3

description: mRNA and ncRNA


title: Input-Zic2/3KO-24hdox


title: Input_LP [ChIP-seq-Input]

description: wt

value: LPS-PBS


title: Input_PL [ChIP-seq-Input]

description: wt

value: PBS-LPS


title: NETs-biological replicate 2

description: mRNA and ncRNA


title: Mesp1-ChIP-seq-ESC-2i-24hdox

source_name: mouse embryonic pluripotent stem cells culture in 2i medium where forced expression of Mesp1 is dox-inducible

value: Rabbit anti-HA (cat:ab9110, Abcam, ChIP-grade)

value: embryonic pluripotent stem cells


title: Zic3-ChIP-seq-Mesp1WT-0h

source_name: Differentiating mouse embryonic pluripotent stem cells where forced expression of Mesp1 is dox-inducible

value: Rabbit anti-Zic3 (Cat:ab222124,Abcam, ChIP-grade)


title: miRNA-seq_AGS-biological replicate 3

description: miRNA


title: AGS-biological replicate 3

description: mRNA and ncRNA


title: Input-ESC-2i-24hdox

value: Input


title: Input_PP [ChIP-seq-Input]

description: wt

value: PBS-PBS


title: NETs-biological replicate 1

description: mRNA and ncRNA


title: H3K27ac_LL [ChIP-seq-H3K27ac]

description: wt


title: H3K4me1_WT-PBS [ChIP-seq-H3K4me1]

description: Ercc1wt/Δ, Ercc1wt/ko or Ercc1wt/wt

value: FVB/ C57BL/6J

value: Ercc1wt/delta, Ercc1wt/ko or Ercc1wt/wt

value: PBS


title: H3K4me1_KO-PBS [ChIP-seq-H3K4me1]


title: H3K27ac_PL [ChIP-seq-H3K27ac]

description: wt


title: ATAC-seq-ESC-2i-24h-dox_Rep2

data_processing:
Quality filtering using trimmomatic
Alignment using bowtie2
Quality filtering using samtools and picard tools
Peak calling using Macs2
Genome_build: mm10
Supplementary_files_format_and_content: BED file of peaks and bigwig files for each sample

source_name: mouse embryonic pluripotent stem cells cultured in 2i medium where forced expression of Mesp1 is dox-inducible

extract_protocol: Nextera DNA sample Preparation Kit

value: WT


title: AGS-biological replicate 1

description: mRNA and ncRNA

value: adenocarcinoma gastric cell line

value: AGS

value: without treatment


title: AGS-biological replicate 2

description: mRNA and ncRNA


title: H3K27ac_LP [ChIP-seq-H3K27ac]

description: wt


title: TC71-ID2KO-Clone2-Rescue-3

city: Iowa City

first: David

middle: Jon

last: Gordon

state: Iowa

address: 25 S Grand Ave

department: Pediatric Hematology/Oncology

institute: University of Iowa

data_processing:
FastQC was used to assess the quality of the sequencing reads. Reads were then mapped against the human reference genome (version hg38) using the STAR aligner.
The raw counts were normalized and transformed using the rlog function and principal components analysis (PCA) was performed to visualize sample clusters. No outlier samples were identified or removed from the analysis.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for each gene and sample

source_name: TC71 Ewing sarcoma cell line

growth_protocol: The cell lines were cultured in DMEM with 10% FBS.

extract_protocol:
RNA was isolated from cell lines using RNeasy Plus Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina TruSeq Stranded mRNA protocols.

value: TC71 Ewing sarcoma cell line

tag: id2 status

value: knockout

tag: id2 rescue

value: yes


title: ATAC-seq-ESC-2i-24h-nodox_Rep2


title: CDK12

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

country: United Kingdom

institute: University of Leicester

data_processing:
Adapters were trimmed with Cutadapt v1.18
Mapping to the hg38 genome was performed with STAR v2.7.3a
Extraction of properly paired and properly mapped reads and PCR deduplication was done with SAMtools v1.9
Reads mapping to the DAC Exclusion List Regions (accession: ENCSR636HFF) were removed with BEDtools version 2.29.2
Bigwig files were generated with the deeptools v3.5.0 bamCoverage tool
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

source_name: ChIP-seq

growth_protocol: HEK293 cells were maintained in DMEM with 10% fetal bovine serum

extract_protocol:
DNA were purified from chromatin IP products.
Libraries were prepared using Illumina's TruSeq ChIP library Preparation Kit

value: LS-C288466:Anti-CDK12 / CRKRS Antibody (aa1-50). LSBio


title: H3K27ac_PP [ChIP-seq-H3K27ac]

address: Antonius Deusinglaan 1

description: wt

tag: strain

value: wt


title: Mesp1-ChIP-seq-Zic2/3KO-24hdox

value: Rabbit anti-HA (cat:ab9110, Abcam, ChIP-grade)

value: dox

value: Differentiating embryonic pluripotent stem cells


title: ATAC-seq-ESC-2i-24h-dox_Rep1

tag: genotype

value: embryonic pluripotent stem cells


title: TC71-ID2KO-Clone2-3

value: no


title: Input CDK12

tag: antibody


title: Chronic_D21_CD4_TetPos_RNA

city: Stanford

first: Ansuman

last: Satpathy

institute: Stanford University

data_processing:
Reads were processed with Cell Ranger v3.1.0
R1 contains barcode at 1-16bp and UMI at bp 17-26
R2 contains the biological sequence
I1 contains the i7 sample index
Genome_build: mm10
Supplementary_files_format_and_content: "barcodes.tsv.gz" contains filtered cellular barcodes, "features.tsv.gz" contains genes, "matrix.mtx.gz" contains the barcoded gene expression matrix

source_name: spleen

extract_protocol: 10x Chromium Next Gem Single Cell V(D)J Reagent Kit (v1.1)

tag: infection

value: LCMV clone 13

tag: timepoint

value: 21 dpi

tag: sorted population

value: I-Ab-LCMV-gp66 tetramer+


title: H3K4me3_PL [ChIP-seq-H3K4me3]

description: wt

value: PBS-LPS


title: K2

city: beijing

first: Tongtong

last: Liu

address: Peking University Health Science Center, 38 Xueyuan Road, Haidian District, Beijing

institute: Peking University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome
Sam format files were output by HISAT2. Samtools was used to convert these sam format files to bam format files and resort these bam format files. Then the gene reads were counted by HTSeq and analysis by DEseq2.
Genome_build: hg38
Supplementary_files_format_and_content: txt file of normalized gene counts for each sample

source_name: cell line

extract_protocol:
RNA of WT CACO2 and ELF4-/- CACO2 cells was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: TC71-ID2KO-Clone2-Rescue-2


title: TC71-ID2KO-Clone2-2


title: H3K4me3_LP [ChIP-seq-H3K4me3]

description: wt

value: LPS-PBS


title: ATAC-seq-Sorted_Flk1+/Pdgfra+

source_name: Differentiating mouse embryonic pluripotent stem cells at day 4

value: WT

tag: condition


title: H3K4me3_PP [ChIP-seq-H3K4me3]

description: wt

value: PBS-PBS


title: ATAC-seq-ESC-2i-24h-nodox_Rep1


title: TC71-ID2KO-Clone2-1

value: TC71 Ewing sarcoma cell line


title: TC71-ID2KO-Clone2-Rescue-1

value: knockout


title: H3K4me3_LL [ChIP-seq-H3K4me3]

description: wt

value: LPS-LPS


title: Chronic_D21_CD4_TetNeg_RNA

address: 240 Pasteur Drive

value: I-Ab-LCMV-gp66 tetramer-


title: K1


title: ATAC_KO-LPS [ATAC-seq]

extract_protocol:
Microglia were isolated by mechanical tissue dissociation and Percoll gradient centrifugation at 4°C followed by flow cytometry of single, DAPI(-),CD11b(+),CD45(+),Ly6c(-) cells.
After cell lysis, ATAC-sequencing libraries were generated according to the manufacturer’s protocol of the Nextera DNA Sample Preparation Kit (Illumina, FC-121-1030). Per 80,000 cells, 50 µl tagmentation mix was added. Samples were sequenced on an Illumina HiSeq 2500 using 75 bp paired-end reads.

value: FVB/ C57BL/6J

value: LPS


title: Chronic_D8_CD4_TetPos_RNA

value: 8 dpi


title: TC71-ID2KO-Clone1-3


title: C2

value: wild type


title: ATAC_KO-PBS [ATAC-seq]

value: PBS


title: C1


title: ATAC_WT-LPS [ATAC-seq]

description: Ercc1wt/Δ, Ercc1wt/ko or Ercc1wt/wt

value: Ercc1wt/delta, Ercc1wt/ko or Ercc1wt/wt


title: TC71-ID2KO-Clone1-2

value: no


title: Acute_D8_CD4_TetPos_RNA

value: LCMV Armstrong


title: OVCAR-5 transduced with shFOXK2 rep2

city: Chicago

first: Daniela

last: Matei

state: Illinois

address: 303 E Superior St

department: Ob-Gyn

institute: Northwestern University

data_processing:
Trimmed reads were aligned to the ENSEMBL human genome version GRCh38 using STAR (2.5.2)
HTSeq and EdgeR is used for generating raw count and differntial gene lists for RNAseq data
Genome_build: GRCh38
Supplementary_files_format_and_content: counts

source_name: ascites

growth_protocol: OVCAR5 ovarian cancer cells were cultured in RPMI medium with 10% FBS, 1% Penicillin-Streptomycin at 37 degree with 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent. DNA was removed by QIAGEN RNase-Free DNase Set. Total mRNA was isolated with Ambion Dynabeads mRNA purification kit.
RNA libraries were prepared for sequencing using NEBNext Ultra II RNA Library Prep kit for Illumina.

treatment_protocol: OVCAR5 cells transduced with control shRNA (shCtrl) or shRNA targeting FOXK2 (shFOXK2) were prepared for RNA extraction.

value: ovarian cancer cell

tag: tumor stage

value: high grade serous

tag: passage


title: TC71-ID2KO-Clone1-1


title: ATAC_WT-PBS [ATAC-seq]

description: Ercc1wt/Δ, Ercc1wt/ko or Ercc1wt/wt

source_name: microglia


title: Acute_D8_CD4_TetNeg_RNA


title: Chronic_D8_CD4_TetNeg_RNA

value: LCMV clone 13


title: OVCAR-5 transduced with shFOXK2 rep1


title: TC71-2

value: wildtype


title: TC71-3


title: TC71-1


title: ATAC_LL [ATAC-seq]

description: wt

value: wt


title: ATAC_PL [ATAC-seq]

description: wt

value: PBS-LPS


title: OVCAR-5 transduced with shCtrl rep1

value: shCtrl


title: OVCAR-5 transduced with shCtrl rep2


title: OVCAR-5 Input ChIP-seq rep2

data_processing:
Quality of fastq files were checked by fastQC
Raw single-end 50bp sequencing reads were mapped to human genome build hg38 using Bowtie2 (v.2.2.6)
HTSeq and EdgeR is used for generating raw count and differntial gene lists for RNAseq data
FOXK2 ChIP-seq peaks were identified by HOMER (v.4.10)
Normalized read counts and differential enrichment statistics for each peak were analyzed by DESeq2 Software (Bioconductor).
Motif analysis was performed by HOMER (v.4.10)
Genome_build: GRCh38
Supplementary_files_format_and_content: Peak files

extract_protocol:
Chromatin in cells was crosslinked with 1% paraformaldehyde and fragmented to an average size of approximately 300-500 bp by sonication. 10 μg chromatin and 5 µg antibodies were proceeded to immunoprecipitation.
ChIP-seq libraries were prepared by using KAPA Hyper Prep kit (Roche Sequencing) with KAPA UDI Adaptor (Roche Sequencing).

value: input


title: Chronic_D21_CD4_TetNeg_TCR

data_processing:
Library strategy: TCR-seq
Reads were processed with Cell Ranger v3.1.0
R1 contains barcode at 1-16bp and UMI at bp 17-26
R2 contains the biological sequence
I1 contains the i7 sample index
Genome_build: mm10
Supplementary_files_format_and_content: "clonotypes.csv" contains TCR clonotype information, "filtered_contig_annotations.csv" contains productive TCR contigs per cell, "consensus_annotations.csv" contains clonotype consensus annotations

extract_protocol:
10x Chromium Next Gem Single Cell V(D)J Reagent Kit (v1.1)
10x Chromium Next Gem Single Cell V(D)J Reagent Kit (v1.1)

value: 21 dpi

value: I-Ab-LCMV-gp66 tetramer-


title: Chronic_D8_CD4_TetPos_TCR

value: I-Ab-LCMV-gp66 tetramer+


title: ATAC_PP [ATAC-seq]

description: wt

value: PBS-PBS


title: Chronic_D8_CD4_TetNeg_TCR

value: 8 dpi


title: PC3_EVs_rep3

data_processing:
Reads were mapped on hg38 genome with STAR version 2.6.1a, with the following parameters : --outSAMprimaryFlag OneBestScore --outSAMattrRGline --outSAMmultNmax 1 --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1.
bam files were converted into bedgraph files using bedtools version 2.29.0. RPM normalization (reads per million of mapped reads) was applied on these files, then they were converted into bigwig files using bedGraphToBigWig from UCSC.
Genome_build: hg38
Supplementary_files_format_and_content: coverage files for minus and plus strand in bigwig format

source_name: extracellular vesicles from human cell line PC3

growth_protocol: FFPE and urinary extracellular vesicles were obtained from prostate cancer patients who provided informed consent and were approved for collection and distribution by Mondor institutional board. PC3, DU145 and LNCaP human prostate cancer cell lines, were obtained from American Type Culture Collection (Manassas, VA, USA).

extract_protocol:
miRNeasy micro kit (Qiagen)
total ribo-depleted RNA
Total RNA-seq libraries were prepared with SMARTer Stranded Total RNA-Seq Kit v2-Pico Input Mammalian

value: PC3 tumor cell line

tag: sample type

value: EVs from PC3 tumor cell line


title: OVCAR-5 FOXK2 ChIP-seq rep2


title: PC3_EVs_rep2


title: LL3_7 [mRNA-seq]

description:
wt
LL3_7
tolerance.featurecounts

extract_protocol:
Microglia were isolated by mechanical tissue dissociation and Percoll gradient centrifugation at 4°C followed by flow cytometry of single, DAPI(-),CD11b(+),CD45(+),Ly6c(-) cells. RNA was isolated using a Qiagen RNeasy Micro Kit (Qiagen, 74004) according to the manufacturer’s instructions.
After RNA isolation, sequencing libraries were generated using NEXTflex® Rapid Illumina Directional RNA-Seq Library Prep Kit (BiooScientific, NOVA-5138-10) with polyA selection. Pooled libraries of the training model were sequenced using the NextSeq 500/550 High Output v2 kit (75 cycles, Illumina, FC-404-2005) with single reads on a NextSeq500 (Illumina). Pooled libraries of the tolerance model were sequenced with a HiSeq Rapid SBS kit (50 cycles, Illumina, FC-402-4022) using single reads on a HiSeq 2500 (Illumina).

value: LPS-LPS


title: Acute_D8_CD4_TetPos_TCR

value: LCMV Armstrong


title: Acute_D8_CD4_TetNeg_TCR


title: OVCAR-5 Input ChIP-seq rep1

value: ovarian cancer cell


title: LL2_7 [mRNA-seq]

description:
wt
LL2_7
tolerance.featurecounts


title: OVCAR-5 FOXK2 ChIP-seq rep1

value: high grade serous


title: PC3_cellLines_rep2

source_name: human cell line PC3

extract_protocol:
miRNeasy mini kit (Qiagen)
total ribo-depleted RNA
Total RNA-seq libraries were prepared with SMARTer Stranded Total RNA-Seq Kit v2-Pico Input Mammalian


title: PC3_cellLines_rep3


title: WC5Skin

city: Rochester

first: jinlong

last: lu

state: NY

address: 213 Hutchinson Hall

institute: University of Rochester

data_processing:
raw fastq reads files were cleaned by Trimmomatic-0.36
gene expression (reads counts) were calculated by salmon 1.4.0
Supplementary_files_format_and_content: gene expression

organism: Marmota monax

source_name: Skin

growth_protocol: Wild caught

extract_protocol:
Tissues were extracted from recently (<12hr) deceased or euthanized animals and flash frozen in liquid nitrogen. Animals not euthanized in lab were kept at 4°C and processed within 12hr of death. Frozen tissues were pulverized using a Cell Crusher piston chilled with liquid nitrogen to produce uniform powdered tissue. Approximately 30mg of frozen tissue powder was used for Trizol RNA extraction. Contaminating DNA was removed from RNA samples using Purelink DNase kit along with Purelink RNA columns. Purified RNA quality was checked using agarose gel examination for rRNA integrity and Qubit analysis
For RNAseq, the RNA samples were processed with the Illumina TruSeq stranded total RNA RiboZero Gold kit and then subjected to Illumina HiSeq 4000 paired-end 150bp sequencing; For MeDIP, genomic DNA samples were processed using the NEBNext UltraII DNA Library Prep kit.
Ribo-depletion for RNAseq

treatment_protocol: No treatment

tag: tissue

value: Skin


title: LL1_7 [mRNA-seq]

description:
wt
LL1_7
tolerance.featurecounts

tag: treatment


title: Chronic_D21_CD4_PD1_ATAC_rep1

data_processing:
Reads were processed with Cell Ranger ATAC v1.2.0
R1 contains the transposed DNA sequence
R2 contains the 10x barcode
R3 contains the transposed DNA sequence
I1 contains the i7 sample index
Genome_build: mm10
Supplementary_files_format_and_content: "fragments.tsv.gz" contains fragments and corresponding cell barcodes

extract_protocol: 10x Chromium Next Gem Single Cell ATAC kit (v1.1)

tag: replicate


title: PC3_EVs_rep1

city: Paris

first: Antonin

last: Morillon

institute: Institut Curie

tag: cell line


title: PL3_7 [mRNA-seq]

description:
wt
PL3_7
tolerance.featurecounts


title: Chronic_D21_CD4_TetPos_TCR

value: LCMV clone 13


title: WC5Lung

source_name: Lung

value: Lung


title: Granulosa cells - PGR-B KO - WT rep 4 [B_WT4]

city: Adelaide

first: Thao

last: Dinh

state: South Australia

address: North Terrace

data_processing:
Overrepresented adapters were checked using FastQC and adapters were trimmed using AdapterRemoval when required.
Quasi-aligment of dataset to the GENCODE mouse transcriptome and transcript quantification via Salmon.
Expression profiles and differential gene expression were assessed with limma 62 and edgeR.
Genome_build: GRCm38.p6, M25 release
Supplementary_files_format_and_content: tabular, transcript read count output of Salmon

source_name: Granulosa cells - PGR-B KO - WT

growth_protocol: 21-27 days old mice

extract_protocol:
cells from 3 mice were pooled together per replicate. Total RNA was extracted using the RNeasy Mini Kit (Qiagen) and DNase-treated.
Library preparation was through the Universal RNA-Seq with NuQuant, Mouse AnyDeplete kit (Nugen). 101-bp paired-end sequencing was on the NovaSeq 6000 S1 Sequencing System (Illumina).

treatment_protocol: mice were injected with 5 IU eCG, following by 5 IU hCG after 46 hours. After 8 hours of hCG mice were culled for granulosa cell collection.

tag: genotype/variation

value: PGR-B KO

value: 21-27 days old

value: 5IU eCG per mouse for 46 hours, then 5IU hCG per mouse for 8 hours

tag: cell type

value: peri-ovulatory granulosa cells


title: LNCaP_EVs_rep3

address: 26 rue d'Ulm

source_name: extracellular vesicles from human cell line LNCaP

value: LNCaP tumor cell line

value: EVs from LNCaP tumor cell line


title: PL2_7 [mRNA-seq]

description:
wt
PL2_7
tolerance.featurecounts

value: wt

value: PBS-LPS


title: WC5Kidney

source_name: Kidney

value: Kidney


title: LNCaP_EVs_rep2


title: PL1_7 [mRNA-seq]

description:
wt
PL1_7
tolerance.featurecounts


title: Granulosa cells - PGR-B KO - WT rep 2 [B_WT2]


title: Granulosa cells - PGR-B KO - WT rep 1 [B_WT1]


title: LNCaP_EVs_rep1


title: LP3_7 [mRNA-seq]

description:
wt
LP3_7
tolerance.featurecounts

value: LPS-PBS


title: Chronic_D21_CD4_PD1_ATAC_rep2

value: 21 dpi


title: WC4Skin


title: LP2_7 [mRNA-seq]

description:
wt
LP2_7
tolerance.featurecounts


title: Granulosa cells - PGR-B KO - KO rep 3 [B_KO3]

source_name: Granulosa cells - PGR-B KO - KO


title: LNCaP_cellLines_rep3

source_name: human cell line LNCaP


title: WC4Kidney


title: Granulosa cells - PGR-B KO - KO rep 1 [B_KO1]


title: LNCaP_cellLines_rep2


title: LP1_7 [mRNA-seq]

description:
wt
LP1_7
tolerance.featurecounts


title: PC3_cellLines_rep1

value: PC3 tumor cell line


title: WC4Brain

source_name: Brain

value: Brain


title: PP3_7  [mRNA-seq]

description:
wt
PP3_7
tolerance.featurecounts

value: PBS-PBS


title: Granulosa cells - PGR-A KO - WT rep 3 [A_WT3]

source_name: Granulosa cells - PGR-A KO - WT

value: PGR-A KO


title: PP2_7 [mRNA-seq]

description:
wt
PP2_7
tolerance.featurecounts


title: LNCaP_cellLines_rep1


title: WC5Brain


title: DU_EVs_rep3

source_name: extracellular vesicles from human cell line DU145

value: DU145 tumor cell line

value: EVs from DU145 tumor cell line


title: PP1_7 [mRNA-seq]

description:
wt
PP1_7
tolerance.featurecounts


title: Granulosa cells - PGR-A KO - WT rep 1 [A_WT1]


title: WC3Lung

value: Lung


title: DU_EVs_rep2


title: WC3Kidney


title: WC4Lung


title: HEL cells, KDM4C KO sg3, R4

city: Jena

first: Philipp

last: Ernst

address: Am Klinikum 1

country: Germany

institute: Jena University Hospital

data_processing:
Sequence reads were trimmed with trimmomatic (v0.39) (parameters: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10, SLIDINGWINDOW:4:20)
Trimmed reads were aligned to the human genome (hg38) using STAR (v2.7.4a) (default parameters)
Counts were generated from bam.-files using Subread featureCounts (v2.0.1) (parameters: -pB)
Assembly: hg38
Supplementary files format and content: Excel file include RPKM values for each Sample

source_name: HEL

growth_protocol: HEL-Cas9 cells were cultured in Roswell Park Memorial Institute (RPMI) medium with 10% fetal bovine serum (FBS) and blasticidin 15 µg/mL in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated from 2 x 106 cells using innuPREP RNA Mini Kit (Analytik Jena AG, Jena, Germany) according to the manufacturer’s instructions.
Library preparation and next generation sequencing were performed by GENEWIZ GmbH (Leipzig, Germany).

treatment_protocol: KDM4C knockout was induced using CRISPR/Cas9 by lentiviral transduction of KDM4C single guide RNAs (sg2 and sg3) on HEL-Cas9 cells following puromycin puromycin 1.5 µg/mL selection over 11 days.

value: HEL

value: erythroleukemia cells

value: KDM4C Knockout


title: HEL cells, KDM4C KO sg3, R3


title: Granulosa cells - PGR-A KO - KO rep 4 [A_KO4]

source_name: Granulosa cells - PGR-A KO - KO

value: 21-27 days old

value: 5IU eCG per mouse for 46 hours, then 5IU hCG per mouse for 8 hours

value: peri-ovulatory granulosa cells


title: Granulosa cells - PGR-B KO - KO rep 2 [B_KO2]

value: PGR-B KO


title: DU_cellLines_rep3

source_name: human cell line DU145


title: WC2Skin

value: Skin


title: DU_cellLines_rep2


title: Granulosa cells - PGR-A KO - KO rep 2 [A_KO2]


title: Granulosa cells - PGR-A KO - KO rep 3 [A_KO3]


title: WC2Lung


title: WC2Kidney

value: Kidney


title: DU_cellLines_rep1


title: WC3Skin


title: Granulosa cells - PGR-A KO - WT rep 2 [A_WT2]


title: uEVs_patient_6

source_name: urinary extracellular vesicles

tag: individual

tag: disease state

value: prostate cancer (PCa)

tag: gleason score (biopsy)

value: urinary EVs from prostate tumor patient


title: HEL cells, KDM4C KO sg3, R1

tag: genotype


title: HEL cells, KDM4C KO sg2, R4


title: Granulosa cells - PGR KO - WT rep 3 [KO_WT3]

source_name: Granulosa cells - PGR KO - WT

value: PGR KO


title: Granulosa cells - PGR KO - WT rep 2 [KO_WT2]


title: Granulosa cells - PGR KO - WT rep 1 [KO_WT1]


title: DU_EVs_rep1


title: WC1Skin


title: HEL cells, KDM4C KO sg2, R3


title: WC1Lung


title: HEL cells, KDM4C KO sg3, R2


title: HEL cells, KDM4C KO sg2, R2


title: Granulosa cells - PGR KO - KO rep 3 [KO_KO3]

source_name: Granulosa cells - PGR KO - KO


title: uEVs_patient_4


title: WC1Kidney


title: HEL cells, KDM4C KO sg2, R1


title: WC1Brain

value: Brain


title: HEL cells, Control, R3

value: WT


title: uEVs_patient_2


title: uEVs_patient_5


title: uEVs_patient_1


title: uEVs_patient_3


title: W5Heart

source_name: Heart

value: Heart


title: RNA-seq_batch3_Zic2_3_dKO_24h_dox_rep2

data_processing:
Quality filtering using Trimmomatic
alignment using STAR
Read counting in genes using HT-seq count
Differential expression analysis using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: count_file

source_name: Differentiating mouse embryonic pluripotent stem cells where forced expression of Mesp1 is dox-inducible

extract_protocol: Qiagen RNA extraction kit

tag: time

value: dox

value: embryonic pluripotent stem cells


title: FFPE_tumor_patient_6

source_name: prostate

extract_protocol:
RecoverAll Total Nucleic Acid Isolation Kit for FFPE (Life technologies)
total ribo-depleted RNA
Total RNA-seq libraries were prepared with SMARTer Stranded Total RNA-Seq Kit v2-Pico Input Mammalian

value: FFPE prostate tumor


title: FFPE_tumor_patient_5


title: Granulosa cells - PGR KO - KO rep 2 [KO_KO2]

tag: timepoint


title: W4Liver

source_name: Liver

value: Liver


title: HEL cells, Control, R4

value: HEL

value: erythroleukemia cells


title: WC2Brain


title: FFPE_tumor_patient_4


title: W4Heart


title: ATAC_LP [ATAC-seq]

description: wt

data_processing:
Adapter sequences and were removed with bbduk (v38.69).
Alignment to the Ensembl genome Mus musculus (GRCm38.82) was performed with STAR (v2.7.3a).
Sorting of the aligned reads was done with bamsort tool from biobambam2 tools (v2.0.95).
featureCounts (v2.0.0) was used to quantify the reads.
Picard (v1.130) and samtools were used to perform the quality control check and the generation of the fastq files.
Genome_build: GRCm38.82
Supplementary_files_format_and_content: 2 tab-delimited files containing gene counts of PBS- and LPS-treated mice; n=3 per condition, 4 conditions per model (tolerance and training).
ATAC samples were aligned to the Mus musculus genome (mm10/GRCm38) with the use of Bowtie 2 (v2.3.5.1) using the -very-sensitive flag.
Bamsort and bammarkduplicates from biobambam2 tools (v2.0.95) were used to sort the aligned files and to remove duplicated reads.
Samtools (v.1.1.0) was used to remove low quality (q<30) and blacklisted alignments.
ATAC-seq peaks were called using Genrich (v.0.5) with the ATAC-seq mode (-j switch), and -p parameter set to 0.01.
BigWig files were generated using deepTools bamCoverage (v.3.5.0) with RPGC normalization.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: A tab-delimited text file containing called peaks per sample.
ChIP samples were aligned to the Mus musculus genome (mm10/GRCm38) with the use of Bowtie 2 (v2.3.5.1) using the -very-sensitive flag.
Bamsort and bammarkduplicates from biobambam2 tools (v2.0.95) were used to sort the aligned files and to remove duplicated reads.
Samtools (v.1.1.0) was used to remove low quality (q<30) and blacklisted alignments.
Peak calling was performed using the JetBrains SPAN peak analyzer (v.0.11.0) using default parameters, which were later manually refined upon visual inspection using the JetBrains JBR browser (v.1.0 beta) on each sample.
BigWig files were generated using deepTools bamCoverage (v.3.5.0) with RPGC normalization.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: A tab-delimited text file containing called peaks per sample.

source_name: microglia

tag: strain

value: wt

value: LPS-PBS


title: HEL cells, Control, R2


title: W5Liver


title: FFPE_tumor_patient_3


title: HEL cells, Control, R1


title: RNA-seq_batch3_Zic2_3_dKO_24h_dox_rep1

tag: condition


title: RNA-seq_batch3_WT_24h_dox_rep2


title: W3Heart


title: FFPE_tumor_patient_2


title: RNA-seq_batch3_WT_24h_dox_rep1


title: HEL cells, sglibrary, RUX, D12, R4

data_processing:
library strategy: CRISPR screen amplicon seq
Alignment and statistical analysis of the data was performed using MAGeCK (https://sourceforge.net/p/ mageck/wiki/Home/)
sgRNA counts were retrieved from raw data (fastq files) via "mageck count"
Counts were generated from bam.-files using Subread featureCounts (v2.0.1)
Beta scores and p values were generated from the counts via "mageck mle" using normalization against controls (control sgRNAs) and CNV-normalization (copy number variations in HEL cells).
Assembly: hg38
Supplementary files format and content: text files include normalized RPKM values for each Sample

growth_protocol: HEL-Cas9 cells were cultured in Roswell Park Memorial Institute (RPMI) medium with 10% fetal bovine serum (FBS) puromycin 15 µg/mL and blasticidin 15 µg/mL in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Genomic DNA was isolated using phenol chloroform extraction method.
CRISPR screen amplicon library preparation: 1. amplification of lentiviral construct from U6 to EF-1α, 2. sample indexing and Illumina adapters addition, 3. enrichment for full-length library species

treatment_protocol: HEL cells were infected with the human CRISPR Brunello lentiviral pooled library including 76,441 guide RNAs targeting against 19,114 genes and 1,000 control guide RNAs and treated with 200nM RUX (or DMSO, as control) for 12 days.

value: Genom-wide Knockout

value: Ruxolitinib


title: FFPE_tumor_patient_1


title: RNA-seq_batch3_Zic2_KO_24h_dox_rep2


title: Granulosa cells - PGR KO - KO rep 1 [KO_KO1]

value: 21-27 days old

value: 5IU eCG per mouse for 46 hours, then 5IU hCG per mouse for 8 hours

value: peri-ovulatory granulosa cells


title: RNA-seq_batch3_Zic2_KO_24h_dox_rep1


title: RNA-seq_batch2_Zic3_KO_24h_dox_rep4


title: siNC_3

city: Ji'nan

first: Ning

last: Zhang

state: Shandong

address: 107, West wenhua Xi road

institute: Qilu hospital of Shandong Universit

data_processing:
Mapping to reference genome (HISAT2)
Quantification (HTSeq)
Differential Expression Analysis (DESeq2)
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: renal cancer cells

growth_protocol: Cells grow in DMEM medium suplemented with 10% FBS

extract_protocol:
Trizol
NEBNext® UltraTM RNA Library Prep Kit for Illumina

treatment_protocol: Transient transfection with siRNA

value: 786-O cells

value: renal cancer

value: siNC


title: HEL cells, sglibrary, RUX, D12, R2


title: W2Liver


title: HEL cells, sglibrary, RUX, D12, R1


title: HEL cells, sglibrary, RUX, D12, R3


title: RNA-seq_batch2_Zic3_KO_24h_dox_rep3

growth_protocol: Pluripotent stem cells were differentiated using published hanging drop protocols (1000 initial cells in serum-condtining medium)


title: HEL cells, sglibrary, DMSO, D12, R3

value: control (DMSO)


title: W1Liver


title: HEL cells, sglibrary, DMSO, D12, R2


title: HEL cells, sglibrary, DMSO, D12, R4


title: W3Liver


title: W2Heart

value: Heart


title: W1Heart


title: RNA-seq_batch2_Zic3_KO_24h_no_dox_rep2

value: embryonic pluripotent stem cells


title: siNC_2


title: RNA-seq_batch2_Zic3_KO_24h_no_dox_rep1


title: HEL cells, sglibrary, DMSO, D12, R1


title: siBRD9_3

value: BRD9 siRNA


title: siBRD9_2


title: Shrew221Skin

organism: Blarina brevicauda

source_name: Skin

value: Skin


title: HEL cells, sglibrary, Baseline, D0

value: HEL


title: siBRD9_1


title: RNA-seq_batch2_WT_24h_dox_rep4

value: WT

value: dox


title: MNKPL1 tumor HC BMMNC scRNA-seq

city: Tokyo

first: Akira

last: Nishimura

address: 1-5-45 Yushima, Bunkyo-ku

institute: Tokyo Medical and Dental University

description: MNKPL1 tumor HC BMMNC scRNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR 2.7.8a.
Trimmed mean of M values (TMM) normalized counts were calculated using edgeR protocol.
Genome_build: hg19
Supplementary_files_format_and_content: Raw_counts.txt: Tab-delimited text files include values of raw counts for each Sample.
Supplementary_files_format_and_content: Normalized_counts.txt: Tab-delimited text files include values of TMM normalized counts for each Sample.

source_name: Lymph node, bone marrow

extract_protocol:
The preparation of single cell suspension was performed using lymph node and bone marrow. The extraction of RNA and RNA libraries were generated by BD Rhapsody system and BD Rhapsody Whole Transcriptome Analysis kit.
RNA libraries were prepared for sequencing using standard BD protocols.

tag: Sex

value: Male

value: Lymph node, bone marrow

tag: subgroup


title: RNA-seq_batch2_WT_24h_no_dox_rep2


title: siGPD1L_3

value: GPD1L siRNA


title: Shrew221Liver

value: Liver


title: RNA-seq_batch2_Zic3_KO_24h_dox_rep2


title: 293T FLAG-HA-RBM33 replicate B input

city: Dallas

first: Joshua

last: Mendell

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: UT Southwestern Medical Center

data_processing:
Raw data from machine are de-multiplexed and converted to fastq files using bcl2fastq
Adapters were trimmed using Cutadapt v3.1
UMI information for each read was extracted using UMI-tools v1.1.2
Pseudogenes of NORAD were masked from the reference genome GRCh38, and reads were mapped to the masked genome using STAR v2.7.1a
PCR duplicates were marked based on UMI information using UMI-tools and removed. Only uniquely mapped reads were used for the following analyses
Annotation of the transcripts were based on GENCODE v30
Read depth was calculated for each genomic position using Samtools v1.10
Normalized reads per million (PRM) was calculated using an in-house script
Genome_build: hg38
Supplementary_files_format_and_content: NA

source_name: 293T cell line

growth_protocol: Cell lines were obtained from ATCC. HCT116 cells (male) were cultured in McCoy’s 5A media (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (Gibco, Sigma-Aldrich) and 1X Antibiotic-Antimycotic (Gibco). 293T cells were cultured in DMEM media (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (Gibco, Sigma-Aldrich) and 1X Antibiotic-Antimycotic (Gibco)

extract_protocol:
anti-FLAG-M2 immunoprecipitation of crosslinked RNAs
Custom library
eCLIP

treatment_protocol: 250 nm UV irradiation 400 mJ/cm2

tag: transfection

value: FLAG-HA-RBM33 transfected

value: B

tag: input/ip

value: Input


title: 293T FLAG-HA-RBM33 replicate A FLAG immunoprecipitation

value: A

value: IP


title: RNA-seq_batch2_WT_24h_dox_rep3


title: Shrew221Kidney

source_name: Kidney

tag: tissue

value: Kidney


title: Shrew221Heart

value: Heart


title: siGPD1L_1

value: 786-O cells

value: renal cancer

tag: treatment

tag: replicate


title: RNA-seq_batch2_WT_24h_no_dox_rep1

value: embryonic pluripotent stem cells


title: 293T FLAG-HA-RBM33 replicate B FLAG immunoprecipitation


title: Shrew220Skin

value: Skin


title: siGPD1L_2

tag: cell line


title: 293T FLAG-HA-RBM33 replicate A input


title: siGABPA_3

tag: cell type

value: GABPA siRNA


title: siNC_1

value: siNC


title: Shrew221Brain

source_name: Brain

value: Brain


title: Shrew220Liver


title: RNA-seq_batch2_WT_24h_dox_rep2

value: WT

value: dox


title: 293T empty vector control replicate B FLAG immunoprecipitation

value: Empty vector transfected


title: RNA-seq_batch2_Zic3_KO_24h_dox_rep1


title: Shrew220Heart


title: siGABPA_2


title: 293T empty vector control replicate B input


title: M3_IP

city: Shanghai

first: Congshan

address: 207 Rui Jin Er Road

institute: National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention

data_processing:
Fastq files for male and female mosquitoes were trimmed using Fastp software
RNA-seq data from control mRNA and m6A mRNA were mapped to Anopheles sinensis reference genome sequence (Version: v49) using HISAT2 package
Mapped reads of IP and input cDNA libraries from male and female mosquitoes were used to identify peaks by R package exomePeak
The m6A peaks were annotated using R package ChIPseeker and visualized using IGV software
The read counts per gene were then normalized to obtain FPKM values (total exon fragments /mapped reads (millions) × exon length (kB)) using StringTie
Genome_build: Anopheles sinensis reference genome sequence (Version: v49)
Supplementary_files_format_and_content: peak text files

organism: Anopheles sinensis

source_name: Anopheles sinensis

extract_protocol:
Total RNA of male and female adult Anopheles sinensis was extracted separately using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's instructions. The Poly (A) RNA was purified from 200 μg total RNA using one round Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) purification.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Stage

value: adult

value: male

tag: m6a antibody

value: No.202003, Synaptic Systems, Germany


title: siGABPA_1


title: RNA-seq_batch2_WT_24h_dox_rep1


title: Shrew220Kidney


title: RNA-seq_batch2_WT_0h_rep2


title: Shrew220Brain


title: M2_IP


title: 293T empty vector control replicate A input

value: A

value: Input


title: M3_input


title: HCT116 FLAG-HA-RBM33 replicate B FLAG immunoprecipitation

source_name: HCT116 colon cancer cell line

value: FLAG-HA-RBM33 transfected

value: B

value: IP


title: Shrew218Skin