title: CUT&RUN_H3K4me3_OCILY1_FOXO1_FKBP_6hA

data_processing:
Adaptor trimming: Adaptors were trimmed using Trimmomatic with flollowing settings ILLUMINACLIP:adaptorfile:2:30:7, LEADING:15, TRAILING:15, MINLEN:15
File conversion and read filtering: SAM fies were converted to BAM files using samtools view with the options -S -b. Low quality reads were removed using samtools view with the following options -F 4 and -q 10. Filtered BAM files were sorted and indexed using samtools sort and samtools index respectively.
Spike-in quantication and removal: Spike-in reads were quantified using samtools idxstats to quantify reads aligned to each chromosome. Reads aligned to dm3 chromosomes were summed in R to calculate the total number of spike-in reads. A bam file containing only hg19 reads was created using samtools view with the following options -bh and the names of the hg19 chromosomes. These files were resorted and indexed as described in the previous step.
Differential analysis: Peaks were called using MACS2, reads were quantified with DiffBind, and differential analysis was performed with DEseq2.
Assembly: hg19/dm3 (ChiP) hg19/Ecoli (C&R)
Supplementary files format and content: Counts tables. Tab delimted file containing peak location, raw counts for each replicate, normalized counts for each replicate, and DEseq2 output for indicated comparison.
Library strategy: CUT&RUN


title: CUT&RUN_H3K4me3_OCILY1_FOXO1_FKBP_0hB

status: Public on Mar 25 2024

type: SRA

city: Nashville

first: Scott

last: Hiebert

state: Tennessee

address: 2220 Pierce Ave, Hiebert Lab PRB 512

country: USA

institute: Vanderbilt University

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: DLBCL Cell Line

growth_protocol: NU-DUL-1 and SU-DHL-4 cells were cultured in RPMI 1640 + 10% Fetalplex +1% L-Glutamine + 1% PenStrep. OCI-LY1 cells were cultured in IDMDM + 10% FetalPlex +1% L-Glutamine + 1% PenStrep. Cells were subcultured the day before the experiment, incubated at 37C with 5% CO2, and harvested while in log phase growth.

extract_protocol:
ChIP-seq experiments were performed as previously described (Zhang et al., Molecular Cell, 2022). CUT&RUN experients were performed using the EpiCypher CUTANA CUT&RUN Kit according to the manufacturer's reccommendations.
Libraries were constucted using the NEBNext Ultra II DNA Library Prep kit according to the manufacturer's protocol.

treatment_protocol: dTAG-47 was added to culture medium to a final concentration of 500 nm at the indicated timepoints.

tag: cell line

tag: cell type

value: GC-DLBCL

tag: genotype

tag: treatment

value: 0h (untreated)

tag: chip antibody


title: CUT&RUN_H3K4me3_OCILY1_FOXO1_FKBP_0hA


title: CUT&RUN_H3K4me3_OCILY1_FOXO1_FKBP_6B

value: 6h dTAG-47


title: ChIPseq_H3K27ac_OCILY1_FOXO1_FKBP_6hA

data_processing:
Adaptor trimming: Adaptors were trimmed using Trimmomatic with flollowing settings ILLUMINACLIP:adaptorfile:2:30:7, LEADING:15, TRAILING:15, MINLEN:15
File conversion and read filtering: SAM fies were converted to BAM files using samtools view with the options -S -b. Low quality reads were removed using samtools view with the following options -F 4 and -q 10. Filtered BAM files were sorted and indexed using samtools sort and samtools index respectively.
Spike-in quantication and removal: Spike-in reads were quantified using samtools idxstats to quantify reads aligned to each chromosome. Reads aligned to dm3 chromosomes were summed in R to calculate the total number of spike-in reads. A bam file containing only hg19 reads was created using samtools view with the following options -bh and the names of the hg19 chromosomes. These files were resorted and indexed as described in the previous step.
Differential analysis: Peaks were called using MACS2, reads were quantified with DiffBind, and differential analysis was performed with DEseq2.
Assembly: hg19/dm3 (ChiP) hg19/Ecoli (C&R)
Supplementary files format and content: Counts tables. Tab delimted file containing peak location, raw counts for each replicate, normalized counts for each replicate, and DEseq2 output for indicated comparison.


title: ChIPseq_H3K27ac_OCILY1_FOXO1_FKBP_0hB


title: ChIPseq_H3K27ac_OCILY1_FOXO1_FKBP_0hA


title: AS3CHIPZEB1

city: LYON

first: Julie

last: CARAMEL

address: 28 Rue Laennec

country: France

institute: Cancer Research Center of Lyon

description: IP ZEB1

data_processing:
Raw sequencing reads were processed through nf-core-chipseq-2.0.0 pipeline.
https://github.com/nf-core/chipseq/releases
Assembly: GRCh38
Supplementary files format and content: BigWig files containing normalized coverage for IP samples and pooled control samples.
Supplementary files format and content: BedGraph files containing narrowPeak calling (IP sample vs. pooled control samples).

growth_protocol: Cells were seeded in 15cm dishes and cultivated in RPMI (GLO) or DMEM (AS3) media supplemented with 10% FBS.

extract_protocol:
Cells from one 15-cm dish were cross-linked with 1% formaldehyde at RT for 10 min and quenched in 125 mM glycine for 5 min. Cross-linked chromatin was isolated and sonicated to generate DNA fragments averaging 200-500 bp in length by Bioruptor plus sonication device (Diagenode). Chromatin fragments were immunoprecipitated with antibodies directed against ZEB1 (1 μg, Genetex, GTX105278), or IgG (1 µg, Bio-Rad, PRABP01) as negative control.
5 ng of input and 30 pg of IP were used. Sequencing was performed with Illumina NovaSeq machine with a paired-end protocol (2x75bp, 64Mp reads).

treatment_protocol: Cells were treated with TNF-α (100 ng/mL) for 14 days, the treatment was replaced every 3 days.

value: 10% FBS

value: Melanoma cell line

tag: antibody


title: GLO_n_1_TNF_J14_chip_ZEB1

description: IP ZEB1

source_name: GLO

value: GLO

value: 10% FBS + TNF-alpha (14 days)

value: Melanoma short-term cultures


title: GLO_n_1_TNF_J14_input

description: input


title: AS3INPUT

description: input


title: GLO_n_1_NT_chip_IgG

description: IP IgG

value: IgG


title: 3_CTR-C-09.10

description:
C-09.10_CTR_3
GIC_CTR_3
mRNA

library_source: transcriptomic

data_processing:
Raw sequencing reads were aligned on the human genome (GRCh38) with STAR (v2.7.8a), with the annotation of known genes from gencode v37.
Gene expression was quantified using Salmon (1.4.0) and the annotation of protein coding genes from gencode v37.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file with normalized expression (log2 TPM) from salmon for each sample.

molecule: total RNA

growth_protocol: Cells were seeded in 6 well plates and cultivated in media containing TNF-α (100 ng/mL) or TNF-α (100 ng/mL) + TGF-β (10 ng/mL).

extract_protocol:
Total RNA was isolated using the RNeasy Kit (QIAGEN) following to manufacturer's recommendations. RNA was quantified and integrity was measured by optic density using a 2100 BioAnalyzer.
Libraries were prepared with the TruSeq poly-A+ kit from Illumina.

treatment_protocol: Cells were treated with TNF-α (100 ng/mL) or TNF-α (100 ng/mL) + TGF-β (10 ng/mL) for 7 and 14 days, the treatment was replaced every 3 days.

tag: vector

value: Empty control vector

value: 7% FBS


title: GLO_n_1_NT_input

description: input


title: GLO_n_1_NT_chip_ZEB1

description: IP ZEB1


title: 2_CTR-C-09.10

description:
C-09.10_CTR_2
GIC_CTR_2
mRNA


title: 2_ZEB1_OE-C-09.10

description:
C-09.10_Z1_2
GIC_Z1_2
mRNA

value: ZEB1 OE


title: 3_untreated-C-09.10

description:
C-09.10_NT_3
GIC_NT_3
mRNA


title: 3_TNF-TGF_D14

description:
GLO_J14_3
mRNA

value: 7% FBS + TNF-alpha and TGF-beta (14 days)


title: 3_untreated

description:
GLO_NT_3
mRNA


title: 1_ZEB1_OE-C-09.10

description:
C-09.10_Z1_1
GIC_Z1_1
mRNA


title: 1_CTR-C-09.10

description:
C-09.10_CTR_1
GIC_CTR_1
mRNA


title: 3_TNF-TGF_D14-C-09.10

description:
C-09.10_J14_3
GIC_J14_3
mRNA


title: 2_TNF-TGF_D14-C-09.10

description:
C-09.10_J14_2
GIC_J14_2
mRNA


title: 1_TNF-TGF_D14-C-09.10

description:
C-09.10_J14_1
GIC_J14_1
mRNA


title: 1_untreated-C-09.10

description:
C-09.10_NT_1
GIC_NT_1
mRNA


title: 1_untreated

description:
GLO_NT_1
mRNA


title: 1_TNF_D14

description:
GLO_J14_1
mRNA


title: 1_TNF-TGF_D7-C-09.10

description:
C-09.10_J7_1
GIC_J7_1
mRNA

value: 7% FBS + TNF-alpha and TGF-beta (7 days)


title: 2_TNF_D14

description:
GLO_J14_2
mRNA


title: GLO_n_1_TNF_J14_chip_IgG

description: IP IgG


title: 1_TNF_D7

description:
GLO_J7_1
mRNA

value: 10% FBS + TNF-alpha (7 days)


title: PATC69_1KPa_R1

city: Milan

first: Pierluigi

last: Di Chiaro

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology (IEO)

data_processing:
Reads were pre-processed (quality trimming and adapter clipping) using Trim Galore v0.6.5, then reads with a minimum of 30 bp were aligned to human genome build GRCh38/hg38 using TopHat2 v2.1.1 with parameter “–b2‐very‐sensitive”. Only uniquely mapped reads were retained.
Gene expression counts were estimated using summarizeOverlaps function (GenomicRanges R package v1.38) with "IntersectionStrict" mode.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file providing raw read count values for each sample

growth_protocol: DMEM supplemented with 10% FBS, 2mM L-glutamine and 1% Pen/Strep.

extract_protocol: Cells are lysed and processed according to SMART-Seq2 protocol. Briefly, 10 ng of poly-A containing mRNA molecules are copied into first strand cDNA by reverse transcription and template-switching using oligo(dt) primers and LNA-containing template-switching oligo (TSO). cDNA is pre-amplified using limited number of cycles, purified and tagmented with Tn5 transposase. cDNA fragments generated after tagmentation are gap-repaired, enriched by PCR and purified to create the final cDNA library for Illumina sequencing.

treatment_protocol: 5x10^5 cells were cultured on collagen-coated plates with different stiffness (12kPa and 1kPa) for 48 h.

tag: source

value: human PDAC primary cell line


title: 2_TNF_D7

description:
GLO_J7_2
mRNA


title: 3_ZEB1_OE-C-09.10

description:
C-09.10_Z1_3
GIC_Z1_3
mRNA


title: PROseq_OCILY1_FOXO1_FKBP_1hA

library_source: other

data_processing:
Adaptor trimming: Adaptors were trimmed using Trimmomatic with flollowing settings CROP:75, ILLUMINACLIP:adaptorfile:2:30:7, TRAILING:15, MINLEN:15
Reverse complement: Reverse complements of the R1 files were created using fastx_reverse_complement from the FASTX toolkit.
Alignment: The reverse complement reads were aligned to a concatenated genome containing the hg19 and dm3 assembiles by Bowtie2.
File conversion and read filtering: SAM fies were converted to BAM files using samtools view with the options -S -b. Low quality reads were removed using samtools view with the following options -F 4 and -q 10. Filtered BAM files were sorted and indexed using samtools sort and samtools index respectively.
Spike-in quantication and removal: OCI-LY1 and NU-DUL-1 -Spike-in reads were quantified using samtools idxstats to quantify reads aligned to each chromosome. Reads aligned to dm3 chromosomes were summed in R to calculate the total number of spike-in reads. A bam file containing only hg19 reads was created using samtools view with the following options -bh and the names of the hg19 chromosomes. These files were resorted and indexed as described in the previous step. SU-DHL-4 - Spike-in reads were quantified using the grep command to quantify and remove reads aligned to the GFP, NeoR, Luciferase, and Gal4 sequences.
Differential analysis: Peak calling, read quantification, and differential expression were performed with NRSA.
Assembly: hg19/dm3
Supplementary files format and content: Normalized counts for promoter proximal and gene body polymerase. Tab delimted file containing Transcript ID, Gene Name, promoter proximal counts (ppc) for each replicate, promoter proximal density (ppd) for each replicate, gene body counts (gbc) for each replicate, and gene body density (gdb) for each replicate. Counts were noramlized in DEseq2.
Supplementary files format and content: Normalized counts for intergenic polymerase (enhancers). Tab delimted file containing Enhancer ID, chr, start, end, and counts for each replicate. Counts were noramlized in DEseq2.
Library strategy: PRO-seq

molecule: other

extract_protocol:
Biotinylated RNAs were extracted with Trizol LS after nuclear run on.
Libraries were constructed as previously described (Mahat et al., Nature Protocols, 2016).

tag: tissue

value: DLBCL Cell Line

value: 1h dTAG-47


title: PATC69_1KPa_R2


title: PROseq_OCILY1_FOXO1_FKBP_1hB

value: GC-DLBCL


title: PROseq_OCILY1_FOXO1_FKBP_2hA

value: 2h dTAG-47


title: PATC69_12KPa_R2


title: PROseq_NUDUL1_FOXO1_FKBP_2hB

value: ABC-DLBCL


title: PATC69_12KPa_R1


title: PROseq_OCILY1_FOXO1_FKBP_0hA

value: 0h (untreated)


title: PROseq_OCILY1_FOXO1_FKBP_0hB


title: PROseq_NUDUL1_FOXO1_FKBP_1hB


title: PROseq_OCILY1_FOXO1_FKBP_0.5hB


title: PROseq_NUDUL1_FOXO1_FKBP_1hA


title: 2_TNF-TGF_D7-C-09.10

description:
C-09.10_J7_2
GIC_J7_2
mRNA


title: PROseq_NUDUL1_FOXO1_FKBP_2hA


title: PROseq_NUDUL1_FOXO1_FKBP_0hB


title: 2_untreated-C-09.10

description:
C-09.10_NT_2
GIC_NT_2
mRNA


title: 2_untreated

description:
GLO_NT_2
mRNA

value: GLO

value: 10% FBS


title: PROseq_NUDUL1_FOXO1_FKBP_0hA


title: RNAseq_SUDHL4_FOXO1_FKBP_24hB

description: DHL4_T0vT24_genes.read_group_tracking.txt

data_processing:
Adaptor trimming: Adaptors were trimmed using Trimmomatic with flollowing settings ILLUMINACLIP:adaptorfile:2:30:7
Alignment: Data was aligned to the hg19 assembly using TopHat.
Differential Analysis: Read quantification and differential expression were performed using CuffDiff.
Assembly: hg19
Supplementary files format and content: CuffDiff counts tables. Tab delimted file containing Gene Name, condition, replicate, raw counts, internally normalized counts, externally noramlized counts, FPKM, effective length, and status.

molecule: polyA RNA

extract_protocol:
RNA was extracted with Trizol according to the manufacturer's protocol.
Libraries were constructed using the NEB Next PolyA isolation module and Ultra II directional RNA library prep kit.

value: 24h dTAG-47


title: RNAseq_SUDHL4_FOXO1_FKBP_24hA


title: RNAseq_SUDHL4_FOXO1_FKBP_0hB


title: RNAseq_SUDHL4_FOXO1_FKBP_6hA

description: DHL4_T0vT6_genes.read_group_tracking.txt

value: 6h dTAG-47


title: PROseq_OCILY1_FOXO1_FKBP_2hB


title: RNAseq_SUDHL4_FOXO1_FKBP_0hA


title: RNAseq_OCILY7_0B


title: RNAseq_SUDHL4_parB

description: DHL4_parvT0_genes.read_group_tracking.txt

value: parental


title: RNAseq_OCILY7_0A


title: RNAseq_OCILY7_parA

description: LY7_parvT0_genes.read_group_tracking.txt


title: RNAseq_OCILY1_FOXO1_FKBP_24hB

description: LY1_T0vT24_genes.read_group_tracking.txt


title: RNAseq_OCILY1_FOXO1_FKBP_6hB


title: PROseq_OCILY1_FOXO1_FKBP_0.5hA


title: RNAseq_OCILY1_FOXO1_FKBP_6hA


title: RNAseq_OCILY1_FOXO1_FKBP_0hA


title: RNAseq_OCILY1_FOXO1_FKBP_0hB


title: RNAseq_OCILY1_parA

description: LY1_parvT0_genes.read_group_tracking.txt


title: RNAseq_NUDUL1_FOXO1_FKBP_24hB

description: NUDUL1_T0vT24_genes.read_group_tracking.txt


title: RNAseq_OCILY1_parB


title: RNAseq_NUDUL1_FOXO1_FKBP_6hB

description: NUDUL1_T0vT6_genes.read_group_tracking.txt


title: RNAseq_NUDUL1_FOXO1_FKBP_0hB


title: RNAseq_NUDUL1_FOXO1_FKBP_6hA


title: RNAseq_NUDUL1_parB

description: NUDUL1_parvT0_genes.read_group_tracking.txt


title: RNAseq_SUDHL4_FOXO1_FKBP_6hB


title: RNAseq_NUDUL1_parA


title: ATACseq_SUDHL4_FOXO1_FKBP_2hC

description:
DHL4_T0VT2_DEseq2.txt
DHL4_T0VT2_bindetect_results.txt

data_processing:
Adaptor trimming: Adaptors were trimmed using Trimmomatic with flollowing settings ILLUMINACLIP:adaptorfile:2:30:7, LEADING:15, TRAILING:15, MINLEN:15
File conversion and read filtering: SAM fies were converted to BAM files using samtools view with the options -S -b. Low quality reads were removed using samtools view with the following options -F 4 and -q 10. Filtered BAM files were sorted and indexed using samtools sort and samtools index respectively.
Spike-in quantication and removal: Spike-in reads were quantified using samtools idxstats to quantify reads aligned to each chromosome. Reads aligned to dm3 chromosomes were summed in R to calculate the total number of spike-in reads. A bam file containing only hg19 reads was created using samtools view with the following options -bh and the names of the hg19 chromosomes. These files were resorted and indexed as described in the previous step.
Differential analysis: Peaks were called using Genrich, reads were quantified with DiffBind, and differential analysis was performed with DEseq2.
Transcription factor footprinting: Transcription factor footprinting was performed with TOBIAS.
Assembly: hg19/dm3
Supplementary files format and content: Counts tables. Tab delimted file containing peak location, raw counts for each replicate, normalized counts for each replicate, and DEseq2 output for indicated comparison.
Supplementary files format and content: Differential binding data for transcription factor motifs. Tab delimtied file containing motif, total transcription factor binding sites, 0hr score, 0hr bound sites, indicated time point score, indicated time point binding sites, differential binding score, pvalue.

extract_protocol:
Genomic DNA was extracted using the Active Motif ATAC-seq kit according to the manfacturer's protocol.
Libraries were constucted using the Active Motif ATAC-seq kit according to the manufacturer's protocol.


title: RNAseq_NUDUL1_FOXO1_FKBP_0hA


title: RNAseq_SUDHL4_parA


title: ATACseq_SUDHL4_FOXO1_FKBP_0.5hB

description:
DHL4_T0VT0.5_DEseq2.txt
DHL4_T0VT0.5_bindetect_results.txt


title: RNAseq_OCILY7_parB


title: ATACseq_SUDHL4_FOXO1_FKBP_1hB

description:
DHL4_T0VT1_DEseq2.txt
DHL4_T0VT1_bindetect_results.txt


title: ATACseq_SUDHL4_FOXO1_FKBP_2hA


title: ATACseq_SUDHL4_FOXO1_FKBP_0.5hA


title: ATACseq_SUDHL4_FOXO1_FKBP_0hB


title: ATACseq_SUDHL4_FOXO1_FKBP_0hA


title: ATACseq_SUDHL4_FOXO1_FKBP_1hA


title: RNAseq_OCILY1_FOXO1_FKBP_24hA


title: ATACseq_OCILY1_FOXO1_FKBP_2hB

description:
LY1_T0VT2_DEseq2.txt
LY1_T0VT2_bindetect_results.txt


title: ATACseq_OCILY1_FOXO1_FKBP_2hA


title: RNAseq_NUDUL1_FOXO1_FKBP_24hA


title: ATACseq_OCILY1_FOXO1_FKBP_1hB

description:
LY1_T0VT1_DEseq2.txt
LY1_T0VT1_bindetect_results.txt


title: ATACseq_OCILY1_FOXO1_FKBP_0.25hB

description:
LY1_T0VT0.25_DEseq2.txt
LY1_T0VT0.25_bindetect_results.txt


title: ATACseq_OCILY1_FOXO1_FKBP_1hA


title: ATACseq_OCILY1_FOXO1_FKBP_0.25hA


title: ATACseq_OCILY1_FOXO1_FKBP_0.5hA

description:
LY1_T0VT0.5_DEseq2.txt
LY1_T0VT0.5_bindetect_results.txt


title: ATACseq_OCILY1_FOXO1_FKBP_0hB


title: ATACseq_OCILY1_FOXO1_FKBP_0hA


title: ATACseq_NUDUL1_FOXO1_FKBP_2hA

description:
NUDUL1_T0VT2_DEseq2.txt
NUDUL1_T0VT2_bindetect_results.txt


title: ATACseq_OCILY1_FOXO1_FKBP_0.5hB


title: ATACseq_NUDUL1_FOXO1_FKBP_2hB


title: ATACseq_NUDUL1_FOXO1_FKBP_0.5hA

description:
NUDUL1_T0VT0.5_DEseq2.txt
NUDUL1_T0VT0.5_bindetect_results.txt


title: ATACseq_NUDUL1_FOXO1_FKBP_0.5hB


title: ATACseq_SUDHL4_FOXO1_FKBP_2hB


title: ATACseq_NUDUL1_FOXO1_FKBP_0.25hB

description:
NUDUL1_T0VT0.25_DEseq2.txt
NUDUL1_T0VT0.25_bindetect_results.txt


title: ATACseq_NUDUL1_FOXO1_FKBP_1hA

description:
NUDUL1_T0VT1_DEseq2.txt
NUDUL1_T0VT1_bindetect_results.txt


title: ATACseq_NUDUL1_FOXO1_FKBP_0hA


title: ATACseq_NUDUL1_FOXO1_FKBP_0hB


title: MDA-MB-231, Noc CM, rep 2

city: Singapore

first: Matius

last: Robert

state: Singapore

address: 28 Medical Drive

department: Physiology

country: Singapore

institute: National University of Singapore

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. Clean reads were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
To count the reads numbers mapped to each gene, featureCounts v1.5.0-p3 was utilized. Subsequently, FPKM of each gene was calculated based on the length of the gene and reads count mapped to the gene.
Differential expression analysis of two conditions/groups was performed using the DESeq2 R package (1.20.0).
Assembly: hg38
Supplementary files format and content: xls file that includes FPKM values for each sample

growth_protocol: MDA-MB-231 was maintained in DMEM medium (Gibco) supplemented with 10% FBS (Cytiva) and 1% P/S in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was harvested using Rneasy Mini Plus Kit (Qiagen)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis. Subsequently, a series of enzymatic steps were done for end repair, A-Tailing and ligation with NEB adapters, followed by PCR amplification and purification.

treatment_protocol: Cells were incubated for 72h either with No CM (media only), or with CM harvested from non-senescent MDA-MB-231 cells (designated as Cont CM), or with CM harvested from TIS MDA-MB-231 cells induced by 72h nocodozole treatment (designated as TIS CM)

value: breast cancer cell line

value: WT

value: TIS CM

tag: time


title: ATACseq_NUDUL1_FOXO1_FKBP_0.25hA


title: M397 cells,vemurafenib removal,48 hours

city: SEATTLE

first: Wei

last: Wei

state: Washington

address: 401 Terry Ave N

institute: Institute For Systems Biology

data_processing:
Reads were aligned against the human genome (hg19) using STAR (v2.7.3a). Read counts were quantified using htseq-count with known gene annotations from UCSC.The gene expression level was calculated from Fragments Per Kilobase per Million reads (FPKM) normalized expression values
Assembly: hg19
Supplementary files format and content: tab-delimited txt file includes FPKM values for each samples
Supplementary files format and content: tab-delimited txt file includes FPKM values for each samples

growth_protocol: Cells were cultured in a water-saturated incubator at 37 °C with 5% CO2 in RPMI 1640 with L-glutamine (Life Technologies), supplemented with 10% fetal bovine serum (ATCC), and 0.2% antibiotics (MycoZapTM Plus-CL from Lonza).

extract_protocol:
Total RNA was extracted from the cell pellets using AllPrep DNA/RNA kit (Qiagen)
mRNA library was constructed with TruSeq RNA Sample Preparation Kit and sequenced on the Illumina Hiseq 2500 with pair-end 150bp reads following the manufacturer's recommendations by Novogene.

treatment_protocol: Cells were treated with 3 μM  BRAF inhibitor (vemurafenib, S1267),which is from SelleckChemicals LLC,at the selected time points.

value: melanoma cancer cell line

value: 3 μMvemurafenib removal,48h


title: M397 cells,vemurafenib removal,6 Days

value: 3 μMvemurafenib removal,6 days


title: M397 cells,vemurafenib removal,72 hours

value: 3 μMvemurafenib removal,72h


title: MDA-MB-231, Noc CM, rep 3


title: MDA-MB-231, Noc CM, rep 1


title: MDA-MB-231, Cont CM, rep 3

value: Cont CM


title: MDA-MB-231, No CM, rep 3

value: No CM


title: MDA-MB-231, Cont CM, rep 1


title: M397 cells,vemurafenib removal,24 hours

value: 3 μMvemurafenib removal,24h


title: MDA-MB-231, No CM, rep 1


title: MDA-MB-231, No CM, rep 2


title: M397 cells,vemurafenib removall,12 hours

value: 3 μMvemurafenib removal,12h


title: MDA-MB-231, Cont CM, rep 2


title: M397 cells,DMSO,Day0

description: control

value: DMSO


title: SUM1315MO2

city: Naples

first: Melania

last: Franchini

address: Via Campi Flegrei 34,

institute: Telethon Institute of Genetics and Medicine (TIGEM)

description: DROP-seq

library_source: transcriptomic single cell

data_processing:
STARsolo
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Breast

extract_protocol: Single-cell transcriptomic of the 5 cell lines was performed by implementing in-house the DROP-seq technology. The microfluidics device for the generation of the droplet was fabricated using a bio-compatible, silicon-based polymer, polydimethylsiloxane (PDMS) that was rendered hydrophobic with Aquapel treatment as per protocol. In each sequencing experiment, cell suspension, bead suspension and carrier oil (QX200 droplet generation oil, Bio-Rad) were first loaded in syringes and then placed in syringe pumps (Leafluid). Flow rates of syringe pumps were set at 4,000 μL/h for both cell and barcoded bead suspensions while carrier oil syringe pump was set at 15,000 μL/h. In each sequencing experiment, cells and barcoded beads were, respectively, diluted at the concentration of 200 cell/μL in PBS with BSA 0.01% (Merck) and 120 bead/μL in lysis buffer. A self-built magnetic stirrer system was used to keep in suspension barcoded beads. To count the occurrence of a single cell together with a barcoded bead several tests were performed without lyses buffer in the bead suspension. In these tests, we observed about 5% of generated droplets filled with just one bead and one cell.

value: Breast

value: TNBC cell line

value: No treatment


title: M397 cells,vemurafenib,72 hours

value: 3 μMvemurafenib,72h


title: ATACseq_NUDUL1_FOXO1_FKBP_1hB

value: DLBCL Cell Line

value: ABC-DLBCL

value: 1h dTAG-47


title: SUM185PE

description: DROP-seq


title: M397 cells,vemurafenib,12 hours

value: WT

value: 3 μMvemurafenib,12h


title: SDCHF2927R4Gy_a

city: Detroit

first: oluwademilade

last: Nuga

state: MI

address: 540 E canfield

department: Pharmacology

institute: Wayne State University

description:
tech rep 1
RNA-sequencing

data_processing:
100 bps paired-end libraries were sequenced on the Illumina HiSeq 2500 following cBot clustering.
Prior to alignment the sequencing adaptors were trimmed using FASTQ Toolkit v1.0 on Illumina's BaseSpace portal.
FastQC was used to generate quality metrics for assessment of FASTQ files
RNA seq reads were aligned using TopHat v2.1.0 using default alignment parameters and GRCh38 reference genome
After alignment, the mapped reads were further filtered by mappability score (MAPQ ≥ 10) and sorted by genomic position of the reads using samtools-0.1.19
PCR duplicate reads were processed and removed using rmdup function (options -S) in samtools.
The cleaned BAM files were further analyzed using Integrative Genome Viewer (http://software.broadinstitute.org/software/igv/), processed with R function “FeatureCount” to quantify reads on various RNA types from GencodeV28 annotation. Followed by RPKM normalization.
Supplementary files format and content: .xlsx files include counts data normalized to RPKM for each sample.

source_name: GBM primary tumor

growth_protocol: Cancer stem-like cells were maintained in DMEM F12 supplemented with N2 and antibiotics in humidified atmosphere with 5% CO2 at 37C Serum differentiated cells were maintained in DMEM F12 supplemented with N2 , 2% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells harvested and rinsed with PBS, followed by total RNA isolation using RNeasy Mini Kit (Qiagen) and used for RNA sequencing.
Library for RNA sequencing was prepared using  TruSeq Stranded Total RNA LT (Illumina).

treatment_protocol: Cancer stem-like cells were cultured in NMGF followed by treatment with IC30 concentration of temozolomide continuously for 4 days or once dose of Ionizing radiation (4Gy) with cells harvested after 4 days of treatment. Serum differentiation of CSCs was induced using 2% fetal bovine serum for 14 days followed by 4 day treatment with temozolomide (IC30) and ionizing radiation (4 Gy)

value: GBM primary tumor

value: Astrocyte

value: TP53 wild-type, CDKN2A homozygous deletion, EGFR VIII amplification, PTEN homozygous deletion, NF1 wild-type

value: ionizing radiation (4 Gy)


title: SUM149PT

description: DROP-seq


title: SUM229PE

description: DROP-seq


title: SDCHF2927R4Gy_c

description:
tech rep 3
RNA-sequencing


title: SUM159PT

description: DROP-seq


title: SDCHF2927R4Gy_b

description:
tech rep 2
RNA-sequencing


title: SDCHF2927Rcontrol_c

description:
tech rep 3
RNA-sequencing

value: Ionizing radiation conrol


title: M397 cells,vemurafenib,36 hours

value: melanoma cancer cell line

value: 3 μMvemurafenib,36h


title: M397 cells,vemurafenib,24 hours

value: 3 μMvemurafenib,24h


title: MDAMB468, IGFBP2 over-expression, replicate 2

description: Quantseq

data_processing:
Illumina novaSeq base call (BCL) files were transformed into fastq files through bcl2fastq (version v2.20.0.422, Illumina Inc.), and sequence reads were trimmed using bbduk software (bbmap suite 37.31, Joint Genome Institute, Walnut Creek, CA, USA).
Alignment was performed on hg38 reference assembly (Ensembl Assembly 93) with star 2.6.0a (GPL v3, open source) and gene expression levels were determined with htseq-count 0.9.1.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include log2(CPM+1) values for each Sample

extract_protocol:
Total RNA was purified from three biological replicates by Qiagen RNeasy Mini kit (Qiagen), according to the manufacturer's instructions. Total RNA was quantified using the Qubit 2.0 fluorimetric Assay (Thermo Fisher Scientific).
Libraries were prepared from 100 ng of total RNA using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria). Quality of libraries was assessed by using screen tape High-sensitivity DNA D1000 (Agilent Technologies).

value: IGFBP2 overexpression


title: MDAMB468, IGFBP2 over-expression, replicate 3

description: Quantseq

value: TNBC cell line


title: M397 cells,vemurafenib,48 hours

value: 3 μMvemurafenib,48h


title: MDAMB468, IGFBP2 over-expression, replicate 1

description: Quantseq

value: No treatment


title: SDCHF2927TMZ_c

description:
tech rep 3
RNA-sequencing

value: TMZ


title: SDCHF2927TMZ_b

description:
tech rep 2
RNA-sequencing


title: MDAMB468, Control, replicate 2

description: Quantseq


title: MDAMB468, Control, replicate 3

description: Quantseq


title: SDCHF2927TMZ_a

description:
tech rep 1
RNA-sequencing


title: SDCHF2927control_c

description:
tech rep 3
RNA-sequencing

value: TMZ control


title: MDAMB468, Control, replicate 1

description: Quantseq


title: SDCHF2927control_b

description:
tech rep 2
RNA-sequencing


title: 468, Day3, Afatinib, scRNAseq

description:
10x Genomics
TS_barcodes.tsv.gz
TS_features.tsv.gz
TS_matrix.mtx.gz
MDAMB468_Afa_T72

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Total RNA from cell lines were extracted using Qiagen RNeasy Mini kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. A total of 1 μg of total RNA from each sample was used to obtain double strand cDNA with the QuantiTect Reverse Transcription Kit (Qiagen).
MDAMB468 barcoded and DTP cells were trypsinized into single-cell suspensions and processed using a Chromium Single Cell Gene Expression 3′ Library and Gel Bead kit v3.1 following the manufacturer’s instructions (10x Genomics). Estimated 1 x 104 cells were counted and checked for viability using a LUNA-II™ Automated Cell Counter (Logos Biosystems) and then injected into microfluidic chips with the average recovery rate of 5 x 103 cells to form single-cell Gel Beads-in-Emulsion (GEMs) in the 10x Chromium instrument. Reverse transcription was carried out on the GEMs, and reverse-transcribed samples were purified and amplified. The quality of the amplified cDNA was quantified with the BioAnalyzer High Sensitivity DNA kit D5000 (Agilent Technologies) and its concentration was measured using the Qubit Fluorometer. Finally, amplified cDNAs were fragmented, and adapter and sample indexes or custom primer to selectively amplify barcodes, were incorporated into the libraries which were compatible with Illumine next-generation sequencing. The size profiles and the quality of the obtained libraries were profiled using BioAnalyzer High Sensitivity DNA kit D1000. NovaSeq 6000 SP 100 cycles flow cell was used to sequence the libraries.

value: Breast

value: Afatinib 250nM

value: Day 3


title: SDCHF2927control_a_V2

description:
tech rep 1
RNA-sequencing

value: GBM primary tumor


title: CSCHF2927R4Gy_c

description:
tech rep 3
RNA-sequencing

value: Astrocyte


title: 468, Day9, Afatinib, scRNAseq

description:
10x Genomics
TS_barcodes.tsv.gz
TS_features.tsv.gz
TS_matrix.mtx.gz
MDAMB468_Afa_T216

value: Day 9


title: CSCHF2927R4Gy_b

description:
tech rep 2
RNA-sequencing

value: TP53 wild-type, CDKN2A homozygous deletion, EGFR VIII amplification, PTEN homozygous deletion, NF1 wild-type

value: ionizing radiation (4 Gy)


title: 468, Day0, replicate2, scRNAseq

description:
10x Genomics
TS_barcodes.tsv.gz
TS_features.tsv.gz
TS_matrix.mtx.gz
MDAMB468_CTR_02

value: Day 0


title: 468, Day6, Afatinib, scRNAseq

description:
10x Genomics
TS_barcodes.tsv.gz
TS_features.tsv.gz
TS_matrix.mtx.gz
MDAMB468_Afa_T144

value: Day 6


title: CSCHF2927Rcontrol_c

description:
tech rep 3
RNA-sequencing

value: Ionizing radiation conrol


title: CSCHF2927R4Gy_a

description:
tech rep 1
RNA-sequencing


title: Tubular adenoma sample 1 from patient LS32

city: Houston

first: Eduardo

last: Vilar-Sanchez

state: TX

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

data_processing:
The mRNAseq data  was mapped and counted by STAR Ver. 2.7.9a and RSEM Ver. 1.3.1.
The raw counts were normolized by the TMM algorithme implemented in EdgeR Ver. 3.40.1.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include cpm values for each Sample

source_name: Tubular adenoma

extract_protocol:
DNA and RNA were extracted from all flash-frozen and FFPE tissue samples using the Quick-DNA/RNA Miniprep Kit (Zymo Research, CA) and AllPrep DNA/RNA FFPE Kit (Qiagen, MD), respectively.
Illumina Stranded mRNA Prep

value: Tubular adenoma

tag: patient id

tag: age

tag: gender

value: Female

tag: race

value: Caucasian

tag: ethnicity

value: Not hispanic or latino

tag: mutated gene

tag: history of_cancer

value: Yes

tag: type of_cancer

value: Ovarian, Breast

tag: pathology

tag: category

value: Advanced Precancerncer

tag: location

value: Rectum

tag: dysplasia

value: Low grade dysplasia

tag: size (mm)

tag: tissue preparation

value: FFPE

tag: msi status

value: MSI-H


title: Adenocarcinoma sample 1 from patient LS38

source_name: Adenocarcinoma

tag: tissue

value: Adenocarcinoma

value: Male

value: Other

value: Hispanic or latino

value: Colon

value: Adenocarcinoma Stage II

value: Cancer

value: Right Colon

value: Not applicable


title: CSCHF2927Rcontrol_b

description:
tech rep 2
RNA-sequencing

value: GBM primary tumor

tag: cell line

tag: cell type

value: Astrocyte

tag: genotype

value: TP53 wild-type, CDKN2A homozygous deletion, EGFR VIII amplification, PTEN homozygous deletion, NF1 wild-type

tag: treatment

value: Ionizing radiation conrol


title: 468, Day0, replicate1, scRNAseq

description:
10x Genomics
TS_barcodes.tsv.gz
TS_features.tsv.gz
TS_matrix.mtx.gz
MDAMB468_CTR_01

value: Breast

value: TNBC cell line

value: No treatment

tag: time

value: Day 0


title: SDCHF2927Rcontrol_a

description:
tech rep 1
RNA-sequencing


title: SDCHF2927Rcontrol_b

description:
tech rep 2
RNA-sequencing


title: Tubular adenoma sample 1 from patient LS22

value: Tubular adenoma

tag: patient id

tag: age

tag: gender

value: Female

tag: race

value: Caucasian

tag: ethnicity

value: Not hispanic or latino

value: Yes

value: Colon, Endometrial

value: Advanced Precancerncer

value: Ascending polyp/Hepatic Flexure

value: High grade dysplasia

value: FFPE

value: MSS


title: Tubular adenoma sample 1 from patient LS30

tag: mutated gene

tag: history of_cancer

tag: type of_cancer

value: Endometrial

tag: pathology

tag: category

value: Precancer

value: Ascending colon

value: Low grade dysplasia


title: CSCHF2927Rcontrol_a

description:
tech rep 1
RNA-sequencing

value: GBM primary tumor

value: Astrocyte

value: TP53 wild-type, CDKN2A homozygous deletion, EGFR VIII amplification, PTEN homozygous deletion, NF1 wild-type

value: Ionizing radiation conrol


title: CSCHF2927TMZ_b

description:
tech rep 2
RNA-sequencing

value: TMZ


title: Tubular adenoma sample 1 from patient LS19

value: Tubular adenoma

value: Female

value: Caucasian

value: Not hispanic or latino

value: Promyelocitic Leukemia

value: tubular adenoma

tag: location

value: Transverse Colon

tag: dysplasia

tag: size (mm)

tag: tissue preparation

tag: msi status


title: CSCHF2927TMZ_c

description:
tech rep 3
RNA-sequencing

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: CSCHF2927control_b_V2

description:
tech rep 2
RNA-sequencing

value: TMZ control


title: Tubular adenoma sample 1 from patient LS13

tag: patient id

tag: age

tag: gender

tag: race

value: Yes

value: Endometrial

value: Cecum

value: FFPE

value: MSS


title: Tubular adenoma sample 1 from patient LS11

tag: ethnicity

tag: mutated gene

tag: history of_cancer

tag: type of_cancer

value: Colon, Uterus, Ureter

value: Advanced Precancerncer

value: Sigmoid colon and rectum

value: High grade dysplasia

value: MSI-H


title: CSCHF2927TMZ_a

description:
tech rep 1
RNA-sequencing

value: GBM primary tumor

value: Astrocyte

value: TP53 wild-type, CDKN2A homozygous deletion, EGFR VIII amplification, PTEN homozygous deletion, NF1 wild-type

value: TMZ


title: CSCHF2927control_c

description:
tech rep 3
RNA-sequencing


title: Tubular adenoma sample 1 from patient LS14

value: Tubular adenoma

value: Female

value: Other

value: Hispanic or latino

value: Colon

tag: pathology

tag: category

value: Precancer

tag: location

value: Descending colon

tag: dysplasia

value: Low grade dysplasia


title: Adenocarcinoma sample 1 from patient LS12

tag: tissue

value: Adenocarcinoma

value: Yes

value: Adenocarcinoma Stage III

value: Cancer

value: Ascending colon

value: Not applicable

tag: size (mm)

tag: tissue preparation

value: FFPE

tag: msi status


title: CSCHF2927control_a

description:
tech rep 1
RNA-sequencing

value: GBM primary tumor

tag: cell line

tag: cell type

value: Astrocyte

tag: genotype

value: TP53 wild-type, CDKN2A homozygous deletion, EGFR VIII amplification, PTEN homozygous deletion, NF1 wild-type

tag: treatment

value: TMZ control


title: Tubular adenoma sample 3 from patient LS3

value: Tubular adenoma

tag: patient id

tag: age

tag: gender

value: Male

tag: race

value: Caucasian

value: Not hispanic or latino

value: Rectum

value: MSI-L


title: Adenocarcinoma sample 2 from patient LS3

value: Adenocarcinoma

tag: ethnicity

tag: mutated gene

tag: history of_cancer

tag: type of_cancer

value: Colon

value: sigmoid  colon

value: MSI-H


title: Tubular adenoma sample 2 from patient LS3

value: Yes

tag: pathology

tag: category

value: Advanced Precancerncer

tag: location

value: Sigmoid

tag: dysplasia

value: High grade dysplasia


title: SDCHF2303R4Gy_c

description:
tech rep 3
RNA-sequencing

tag: tissue

value: GBM primary tumor

value: Astrocyte

value: TP53 mutation, CDKN2A homozygous deletion, PTEN mutation, NF1 mutation

value: ionizing radiation (4 Gy)


title: SDCHF2303R4Gy_b

description:
tech rep 2
RNA-sequencing

tag: cell line


title: Tubular adenoma sample 1 from patient LS10

value: Tubular adenoma

value: Female

value: Endometrial

value: Precancer

value: Descending colon

value: Low grade dysplasia

tag: size (mm)

tag: tissue preparation

value: FFPE

tag: msi status

value: MSS


title: SDCHF2303R4Gy_a

description:
tech rep 1
RNA-sequencing

tag: cell type

tag: genotype

tag: treatment


title: Tubular adenoma sample 1 from patient LS2

tag: patient id

tag: age

tag: gender

tag: race

value: Caucasian

value: Not hispanic or latino

value: tubular adenoma

value: Transverse Colon and sigmoid


title: SDCHF2303Rcontrol_a

description:
tech rep 1
RNA-sequencing

value: Ionizing radiation conrol


title: SDCHF2303Rcontrol_b

description:
tech rep 2
RNA-sequencing

value: GBM primary tumor


title: SDCHF2303TMZ_c

description:
tech rep 3
RNA-sequencing

value: Astrocyte

value: TMZ


title: Tubular adenoma sample 1 from patient LS1

tag: ethnicity

tag: mutated gene

tag: history of_cancer

value: Yes

tag: type of_cancer

value: Vulva


title: Adenocarcinoma sample 1 from patient LS3

value: Adenocarcinoma

value: Male

value: Colon

tag: pathology

value: Adenocarcinoma Stage III

tag: category

value: Cancer

tag: location

value: Sigmoid

tag: dysplasia

value: Not applicable

value: MSI-H


title: SDCHF2303Rcontrol_c

description:
tech rep 3
RNA-sequencing

tag: tissue

tag: cell line

value: TP53 mutation, CDKN2A homozygous deletion, PTEN mutation, NF1 mutation


title: Tubular adenoma sample 1 from patient LS3

value: Tubular adenoma

value: Caucasian

value: Not hispanic or latino

value: Precancer

value: Transverse

value: Low grade dysplasia

tag: size (mm)

tag: tissue preparation

value: FFPE

tag: msi status


title: Tubular adenoma sample 1 from patient LS42

tag: patient id

value: Female

value: Yes

value: Urothelial tract

value: Hepatic Flexure

value: No dysplasia

value: MSS


title: Sessile serated adenoma sample 1 from patient LS46

source_name: Sessile serated adenoma

value: Sessile serated adenoma

tag: age

value: Patient refused

value: No

value: Descending colon


title: SDCHF2303control_b

description:
tech rep 2
RNA-sequencing

value: GBM primary tumor

tag: cell type

value: Astrocyte

tag: genotype

value: TP53 mutation, CDKN2A homozygous deletion, PTEN mutation, NF1 mutation

tag: treatment

value: TMZ control


title: SDCHF2303TMZ_b

description:
tech rep 2
RNA-sequencing

value: TMZ


title: SDCHF2303control_c

description:
tech rep 3
RNA-sequencing


title: CSCHF2303R4Gy_c

description:
tech rep 3
RNA-sequencing

value: ionizing radiation (4 Gy)


title: SDCHF2303control_a

description:
tech rep 1
RNA-sequencing


title: Hyperplastic polyp sample 1 from patient LS27

source_name: Hyperplastic polyp

value: Hyperplastic polyp

tag: gender

value: Male

tag: race

value: Caucasian

tag: ethnicity

value: Not hispanic or latino

tag: mutated gene

value: Not detected

value: Hyperplastic  polyp

value: Precancer

value: Sigmoid

value: FFPE


title: Tubulovillous adenoma sample 1 from patient LS18

source_name: Tubulovillous adenoma

value: Tubulovillous adenoma

value: Female

tag: history of_cancer

value: Yes

tag: type of_cancer

value: Colon

tag: pathology

tag: category

value: Advanced Precancerncer

value: Cecum

value: No dysplasia

value: MSS


title: Hyperplastic polyp sample 1 from patient LS12

tag: tissue

value: Hyperplastic polyp

value: Other

value: Hispanic or latino

tag: location

value: Ascending colon

tag: dysplasia


title: Sessile serated adenoma sample 1 from patient LS19

value: Sessile serated adenoma

value: Caucasian

value: Not hispanic or latino

value: Promyelocitic Leukemia

tag: size (mm)

tag: tissue preparation

tag: msi status


title: CSCHF2303R4Gy_a

description:
tech rep 1
RNA-sequencing

value: GBM primary tumor

tag: cell line

tag: cell type

value: Astrocyte

value: TP53 mutation, CDKN2A homozygous deletion, PTEN mutation, NF1 mutation

value: ionizing radiation (4 Gy)


title: CSCHF2303R4Gy_b

description:
tech rep 2
RNA-sequencing

tag: genotype

tag: treatment


title: Tubular adenoma sample 1 from patient LS18

value: Tubular adenoma

tag: patient id

tag: age

tag: gender

value: Female

tag: race

value: Yes

value: Colon

value: Precancer

value: Transverse

value: FFPE


title: Tubular adenoma sample 1 from patient LS44

tag: ethnicity

tag: mutated gene

tag: history of_cancer

value: No

tag: type of_cancer

value: tubular adenoma

value: Rectum

value: Low grade dysplasia

value: MSS


title: CSCHF2303Rcontrol_c

description:
tech rep 3
RNA-sequencing

tag: tissue

value: Ionizing radiation conrol


title: Tubular adenoma sample 1 from patient LS46

value: Caucasian

value: Patient refused

tag: pathology

tag: category

tag: location

value: Cecum

tag: dysplasia

value: No dysplasia


title: CSCHF2303Rcontrol_b

description:
tech rep 2
RNA-sequencing

value: GBM primary tumor

tag: cell line

value: Astrocyte

value: TP53 mutation, CDKN2A homozygous deletion, PTEN mutation, NF1 mutation


title: CSCHF2303TMZ_a

description:
tech rep 1
RNA-sequencing

tag: cell type

value: TMZ


title: Adenocarcinoma sample 1 from patient LS29

value: Adenocarcinoma

value: Female

value: Unknown

value: Not hispanic or latino

value: Yes

value: Colon

value: Adenocarcinoma Stage III

value: Cancer

value: Transverse Colon

value: Not applicable

tag: size (mm)

tag: tissue preparation

tag: msi status


title: CSCHF2303TMZ_c

description:
tech rep 3
RNA-sequencing

tag: genotype

tag: treatment


title: CSCHF2303TMZ_b

description:
tech rep 2
RNA-sequencing


title: Tubular adenoma sample 1 from patient LS5

value: Tubular adenoma

tag: patient id

tag: age

tag: gender

tag: race

value: Caucasian

value: Hispanic or latino

value: No

value: tubular adenoma

value: Precancer

value: FFPE

value: MSS


title: Adenocarcinoma sample 1 from patient LS25

value: Adenocarcinoma

value: Male

tag: ethnicity

tag: mutated gene

tag: history of_cancer

tag: type of_cancer

value: Adenocarcinoma Stage I

value: Ascending colon

value: MSI-H


title: CSCHF2303control_b

description:
tech rep 2
RNA-sequencing

tag: tissue

value: GBM primary tumor

value: Astrocyte

value: TP53 mutation, CDKN2A homozygous deletion, PTEN mutation, NF1 mutation

value: TMZ control


title: Tubular adenoma sample 2 from patient LS42

value: Tubular adenoma

value: Female

value: Not hispanic or latino

value: Yes

value: Urothelial tract

tag: pathology

tag: category

value: Advanced Precancerncer

tag: location

tag: dysplasia

value: No dysplasia


title: SDCHF2303TMZ_a

description:
tech rep 1
RNA-sequencing

tag: cell line

tag: cell type

value: TMZ


title: CSCHF2303control_a

description:
tech rep 1
RNA-sequencing

tag: genotype


title: Adenocarcinoma sample 1 from patient LS31

value: Adenocarcinoma

value: Other

value: Hispanic or latino

value: Colon

value: Adenocarcinoma Stage II

value: Cancer

value: Ileocolic anastomosis

value: Not applicable

tag: size (mm)

tag: tissue preparation

value: FFPE

tag: msi status


title: Adenocarcinoma sample 1 from patient LS7

tag: patient id

tag: age

tag: gender

value: Male

value: Caucasian

value: Rectum

value: Adenocarcinoma Stage III

value: Distal rectum

value: MSI-H


title: Adenocarcinoma sample 1 from patient LS8

tag: race

tag: ethnicity

value: Not hispanic or latino

tag: mutated gene

value: Yes

value: Colon, Lung, Melanoma

value: Tubular Adenoma with HGD/Tumor in situ

value: Hepatic Flexre

value: High grade dysplasia


title: HEMnDP1 UVR3

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

description: UVR

data_processing:
Adapter sequences were removed using TrimGalore!
Sequencing reads were mapped using Bowtie2 for each SmaI/XmaI site in the genome and signatures to methylated (5'CCGGG) and unmethylated (5'GGG) CpG were enumerated for each SmaI/XmaI site. Mouse genome (mm9) and human genome (hg19) was used.
For every CpG site within the SmaI/XmaI recognition site, the methylation was calculated. Let m be the number of tags corresponding to methylated CpG's (tags starting with CCGGG) and u be the number of tags corresponding to unmethylated CpG's (tags starting with GGG), the methylation percent was calculated as 100*(c*m)/(c*m+u), where c is the correction factor based on the observed vs expected methylation of spiked-in standards.
Genome_build: hg19 / mm9
Supplementary_files_format_and_content: The processed data are in tab-delimited text file. The columns of the file are: ID_SmaI_hg19 or ID_SmaI_mm9 (CCCGGG site ID), chromosome (chromosome of the CCCGGG site), position (position of the CCCGGG site), meth_reads (observed number of reads corresponding to methylated CpG, XmaI), unmeth_reads (observed number of reads corresponding to unmethylated CpG, SmaI), total_reads, raw_methylation (unadjusted methylation value), adjusted_methylation (methylation value adjusted based on spiked in standards). Summary table lists methylation percent values supported by more than 19 sequencing reads at individual CCCGGG sites.

growth_protocol: HEMn-DP1 cells were cultured in Medium 254 (Gibco) supplemented with human melanocyte growth supplement (Gibco) and phorbol 12-myristate acetate (200nM). Melan-a cells were cultured in RPMI 1640 media supplemented with 10% fetal bovine serum, 1% L-glutamine, and 0.1% gentamicin antibiotic [50mg/ml].

extract_protocol:
Cells were pelleted and lysed in 2% SDS, 25 mM EDTA; proteins were precipitated by the addition of 10M ammonium acetate and removed by centrifugation. DNA was precipitated by the addition of isopropanol and washed twice with 70% ethanol. The DNA pellet was dissolved in TE (Tris 10 mM, EDTA 1mM). High molecular DNA was recovered by immobilization on 0.4x AMPure XP beads (Beckman Coulter) prior to methylation analysis.
Two micrograms of genomic DNA were spiked with methylation standards and then sequentially digested with SmaI and XmaI restriction enzymes. DNA was digested with 20 units of SmaI for 8 h at 25°C. 20 units of XmaI was added and the digestion was continued for an additional 16 h at 37°C. 3' end filling and dA tailing was performed by 15 units of Klenow Fragment (3'>5' exonuclease deficient; NEB) with nucleotide mix (0.4 mM final concentration of each dCTP, dGTP, dATP).
Libraries were prepared by ligation of NEBNext adapters  at a 10:1 adapter to fragment ratio using T4 DNA ligase (NEB) at 16°C overnight. Hairpin loops of the adapters were cleaved with USER enzyme at 37°C for 15 min. Ligated DNA was dual-size selected using AMPure XP beads for fragments between 250 to 450 bp. Adapter-ligated DNA fragments were indexed with NEBNext Index  i7 primers (NEB). Libraries were amplified for 14 cycles and cleaned with AMPure XP beads prior to sequencing. Libraries were were pooled to 10 nM and spiked with 25% phiX library to ensure sequence diversity.
OTHER: DREAM

treatment_protocol: Cells were plated in 60mm tissue culture dishes in biological replicates 2 days before UVR exposure.  Cells were at 80% confluence at time of treatment. Cells were washed with DPBS and covered with a small amount of DPBS and Saran wrap for UVR exposure.  Two TL-20 lamps emitting a broad band UVR spectrum (35% UVA and 65% UVB) were used.  Cells received a total dose of 175 J/m2 over 90 s at a rate of 1.94 W/m2. The majority of the cells survive this exposure.  Cells were cultured for one month after UVR treatment before detecting changes in DNA methylation.

value: melanocyte cell line


title: CSCHF2303control_c

description:
tech rep 3
RNA-sequencing

tag: tissue

value: GBM primary tumor

value: Astrocyte

value: TP53 mutation, CDKN2A homozygous deletion, PTEN mutation, NF1 mutation

tag: treatment

value: TMZ control


title: Pa_44228_B

data_processing:
Reads were pre-processed (quality trimming and adapter clipping) using Trim Galore v0.6.5, then reads with a minimum of 20 bp were aligned to human genome build GRCh38/hg38 using bwa mem aligner v0.7.17 with default parameters. Sambamba v0.6.6 was used to remove unmapped reads and PCR duplicates were marked by Picard Tools v2.25.5.
The alignments were further processed using GATK best practices (part of GATK4 4.2.0.0 ) using the BaseRecalibrator, LearnReadOrientationModel, GetPileupSummaries and CalculateContamination.
Mutect2 (part of GATK4 v4.2.0.0 ) was used for the identification of somatic variants using 1000g_pon.hg38.vcf.gz (Broad Institute Bundle) as normal reference (--panel-of-normals option) and  af-only-gnomad.hg38.vcf.gz as  source of germline variants with estimated allele frequency (--germline-resource option).
The resulting somatic variations were filtered using FilterMutectCalls (part of GATK4 v4.2.0.0 ) and were annotated using ANNOVAR.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file of the identified somatic variants
Library strategy: AmpliSeq of targeted sequencing panel

source_name: tumor

extract_protocol:
FFPE sections (4 μm) were mounted on polyethylene naphthalate membrane (PEN) slides, were deparaffinized in xylene and then partially rehydrated in an ethanol gradient up to 75% EtOH. After that sections were  counterstained with freshly prepared Cresyl Violet for 30 seconds, they were washed twice in 75% EtOH and air dried completely before proceeding to the microdissection using a UV-based LMD7 laser microdissection system (Leica Microsystems) at 20x magnification. Microdissected areas were collected by gravity into strip-tube caps.
Microdissected areas were digested with 12 ml of Direct Reagent (Ion AmpliSeq™ Direct FFPE DNA Kit, MAN0014881, ThermoFisher Scientific) for 30 min at 65 C. The digested samples were subjected to DNA target enrichment by 15 cycles of PCR amplification using the Ion AmpliSeq Library Kit Plus (MAN0017003, ThermoFisher Scientific) and a custom pool of primers (GerSom, custom amplicon-based panel of 467 genes selected among cancer-predisposing and driver genes with a total sequencing space of 1.6 Mb). After partial amplicon digestion and phosphorylation, the fragments were purified and used for adapter ligation and library amplification using the NEBNext Ultra II Fs DNA Library kit for Illumina (NEB # E7805, New England BioLabs) according to the manufacturer’s instructions.

tag: disease

value: Pancreatic ductal adenocarcinomas (PDAC)

value: tumor

tag: tumor area

value: Gland forming


title: Pa_47691_D


title: HEMnDP1 UVR2

description: UVR


title: CSCHF2303Rcontrol_a

description:
tech rep 1
RNA-sequencing

value: Ionizing radiation conrol


title: Sessile serated adenoma sample 1 from patient LS41

value: Sessile serated adenoma

value: Male

value: Caucasian

tag: history of_cancer

tag: type of_cancer

value: Prostate

tag: pathology

tag: category

value: Precancer

tag: location

value: Ascending colon

tag: dysplasia

value: No dysplasia

value: FFPE

value: MSS


title: Pa_47691_H

value: Non-Gland forming


title: HEMnDP1 UVR1

description: UVR

tag: cell type

value: melanocyte cell line


title: Pa_44053_A


title: HEMnDP1 control2

description: Control


title: HEMnDP1 control3

description: Control


title: Pa_43840_F


title: HEMnDP1 control1

description: Control


title: Pa_43840_C


title: TIS sEV, Rep 3

data_processing:
For analysis of sequencing data, nfcore/rnaseq pipeline (https://github.com/nf-core/rnaseq) was used.
Briefly, data quality was monitored using fastqc 0.11.9 and low quality reads were removed by trimgalore 0.6.6.
Sequence were aligned using star 2.6.1d and gene expression was quantified by salmon 1.4.0
Differential expression was calculated by DESeq2 1.28.0
Assembly: GRCm38.p6
Supplementary files format and content: tsv file that includes TPM values for each sample

organism: Mus musculus

source_name: primary tumour

growth_protocol: 50 μl of sterile PBS containing 1 × 105 of stably transfected 4T1-12b(luc) cells were injected into the mammary fat pad of BALB/c mice. Tumours were left to grow, until they reached a tumor size of approximately 150mm3.

extract_protocol:
Total RNA was isolated using Rneasy mini plus kit (Qiagen).
Library preparation was done using standard Illumina protocol

treatment_protocol: Control EVs or TIS EVs generated from mouse breast cancer 4T1 cells after treatment with DMSO or 100 ng/ml of Nocodozole for 72h. After treatment cells were further released for 72h into complete media supplemented with 5% exo-free FBS. Conditioned media was collected and sEVs were isolated using diffrential centrifugation method. 50 μl of saline, control EVs or TIS EVs generated from mouse breast cancer 4T1 cells at a concentration of 4 × 109, were injected intratumorally every other day for 6 injections.

value: primary tumour

tag: genotype

value: WT

value: TIS sEV

tag: time

value: Day 12


title: Pa_43840_D

value: Pancreatic ductal adenocarcinomas (PDAC)

value: tumor

value: Gland forming


title: TIS sEV, Rep 2


title: TIS sEV, Rep 1


title: Pa_43840_A


title: Pa_37672_G


title: flt1mut, replicate 2, scRNAseq trunk

city: Karlsruhe

first: Laetitia

last: Preau

address: Fritz Haber Weg 4

country: Germany

institute: Karlsruhe Institute of Technology (KIT)

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software  (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCZ11 v107
Supplementary files format and content: matrix files

organism: Danio rerio

source_name: Trunk

extract_protocol:
Zebrafish embryos (3dpf) were anesthethised with Tricain prior the dissection of the trunk. Dissected trunks were dissociated using a mix of 0.25% Trypsin and collagenase (4mg/mL), centrifuged to collect the cells, resuspended into DMEM + 10% Fetal Bovine Serum and filtered to remove the debris.  Cells were washed and resuspend in PBS prior 10X genomic experiment
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics)

value: Trunk

tag: age


title: Saline, Rep 3

value: Saline


title: WT, replicate 2, scRNAseq trunk

description: 10x Genomics


title: Non-Tetracycline exposed time point 240 minue, 3rd replicate

city: Jefferson

first: Steven

last: Foley

state: AR

address: 3900 NCTR Road

department: Microbiology

institute: National Center for Toxicological Research, U.S. Food and Drug Administration

data_processing:
The reads were quality filtered and the demultiplexed raw sequencing files were imported into the BV-BRC3.33.16 program
The samples were analyzed with the RNA-Seq Analyses Service using Tuxedo and the HTSeq-DESeq2 pipelines with the mapping the reads to both S. enterica 452 and E. coli.
Assembly: Tuxedo
Supplementary files format and content: Excel file with raw counts for tetracycline non-treated sample at different time points
Supplementary files format and content: Excel file with raw counts for tetracycline  treated sample at different time points

organism:
Salmonella enterica
Escherichia coli J53

source_name: Mixture of Salmonella and E.coli strains

extract_protocol:
RNA was isolated using RNeasy RNA extraction kit (Qiagen)
Libraries were prepared using the Illumina TruSeq Stranded mRNA kit

value: Bacteria


title: Non-Tetracycline exposed time point 240 minue, 2nd replicate


title: Cont sEV, Rep 1

value: Cont sEV


title: flt1mut, replicate 1, scRNAseq trunk

description: 10x Genomics


title: Non-Tetracycline exposed time point 240 minue, 1st replicate


title: Pa_37672_E


title: Saline, Rep 2


title: Pa_37672_C


title: Pa_36203_H


title: Tetracycline exposed time point 240 minue, 2nd replicate


title: WT, replicate 1, scRNAseq trunk

description: 10x Genomics


title: Saline, Rep 1


title: flt1mut, replicate 2, scRNAseq

description: 10x Genomics

source_name: whole zebrafish embryo

extract_protocol:
Zebrafish embryos (3dpf) were anesthethised with Tricain. Embryos were dissociated using a mix of 0.25% Trypsin and collagenase (4mg/mL), centrifuged to collect the cells, resuspended into DMEM + 10% Fetal Bovine Serum and filtered to remove the debris.  Alive cells were then FACS sorted for GFP+ cells and using non transgenic animals as control. Cells were washed and resuspend in PBS prior 10X genomic experiment
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics)

value: Kdrl positive

value: whole zebrafish embryo

tag: strain

value: flt1ka604; Tg(kdrl:EGFP)zf531Tg


title: WT, replicate 2, scRNAseq

description: 10x Genomics


title: Tetracycline exposed time point 240 minue, 1st replicate


title: Pa_36203_E


title: flt1mut, replicate 1, scRNAseq

description: 10x Genomics


title: Pa_36203_D


title: Non-Tetracycline exposed time point 90 minue, 3rd replicate


title: Pa_36203_C


title: Non-Tetracycline exposed time point 90 minue, 2nd replicate


title: Primary nasal epithelial cells, mock infected, 48hpi, rep 2 (for IAV comparison)

city: Philadelphia

first: David

middle: Michael

last: Renner

state: Pennsylvania

address: 3610 Hamilton Walk

institute: University of Pennsylvania

description: Batch 3

data_processing:
Reads were trimmed for adaptor content and low quality sequences using BBDuk v38.73 (ktrim=r k=23 mink=11 hdist=1 minlength=35 tpe tbo qtrim=20 qin=33)
Trimmed sequence reads were aligned to hg38v98 using Salmon (-p 8 --validateMappings --numBootstraps 30 --rangeFactorizationBins 4 --seqBias --gcBias)
Read count extraction and normalization were performed using DESeq2 v1.22.1
Assembly: hg38 v98
Supplementary files format and content: comma-delimited text file includes normalized counts from DESeq2 for each sample

source_name: Primary nasal

growth_protocol: Primary nasal cells from 4-6 donors obtained from patient donors with informed consent, per protocol approved by the University of Pennsylvania Institutional Review Board (protocol #800614) and the Philadelphia VA Institutional Review Board (protocol #00781), were pooled together and grown to confluence in PneumaCult™-Ex Plus growth medium (STEMCELL Technologies 05040) present both apically and basally. Once cells reach confluency in 0.4 µM pore transwell inserts, apical medium was removed, and PneumaCult-ALI medium was used in the basal compartment to differentiate nasal ALI cultures. Basal media was replaced every 3-4 days for a minimum of 4 weeks.

extract_protocol:
Total RNA was harvested using Rneasy Mini Plus Kit (Qiagen). 2ug of RNA was sent to Azenta Life Sciences for sequencing library preparation
poly(A) selected libraries were prepared by Azenta Life Sciences

treatment_protocol:
Cultures were equilibrated at 33ºC or 37ºC for 48 hours prior to infection. Mucus was washed off of apical surface of cells using PBS.
Cells were infected apically with each indicated virus at MOI = 1 for 1 hour at 37oC (MERS-CoV, SARS-CoV-2, IAV) or 33oC (HCoV-229E, HCoV-NL63, HRV-16)
Unabsorbed virus was washed off with PBS 3 times before cells were returned to 37oC (MERS-CoV, SARS-CoV-2, IAV) or 33oC (HCoV-229E, HCoV-NL63, HRV-16) and incubated for 96 hours (MERS-CoV, SARS-CoV-2, HCoV-229E, HCoV-NL63) or 48 hours (HRV-16, IAV)

tag: cell line

value: Primary nasal

value: Nasal epithelium

value: Mock Infected


title: Primary nasal epithelial cells, mock infected, 48hpi, rep 1 (for IAV comparison)

description: Batch 3


title: D9 uninfected

city: Madison

first: Colin

last: Dewey

address: 425 Henry Mall, 5420 Genetics/Biotechnology Center

institute: University of Wisconsin-Madison

data_processing:
Reads were aligned to the genome using STAR v2.7.8a with default parameters except for except for outFilterMismatchNoverLmax (0.1), outFilterScoreMinOverLread (0.33), and outFilterMatchNminOverLread (0.33),
Gene abundances were estimated using RSEM v1.3.3 with additonal parameters --paired-end, --estimate-rspd, and --strandedness none
Assembly: GRCz11,Ensembl 95 annotation
Supplementary files format and content: The processed data file for each sample is the gene-level abundance output of RSEM and is a tab-delimited text file

source_name: caudal fin

growth_protocol: Upon fertilization, zebrafish embryos were transferred into E3 medium and maintained at 28.5°C.

extract_protocol:
Tail fins of 50 larvae were pooled and collected in ice cold PBS for each condition in each biological replicate. RNA was extracted from pooled tail fins using TRIzol reagent and RNAqueous Micro Kit (Invitrogen).
PolyA, NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® was used for library construction.

treatment_protocol: 3 dpf zebrafish were placed in 5 mL E3 medium containing Tricaine with ~5x108 CFU L. monocytogenes and caudal fins of larvae were transected using surgical blade (Feather no. 10) at the tip of the notochord without injury to the notochord. For uninfected wounds, sterile PBS was added in the medium instead of bacterial resuspension.

value: caudal fin

tag: tissue id

tag: line

value: AB

value: Larval:Day 4

tag: age id

value: control

tag: treatment id


title: Non-Tetracycline exposed time point 90 minue, 1st replicate

tag: treatment


title: Primary nasal epithelial cells, IAV infected, 48hpi, rep 2

description: Batch 3

value: WT

value: IAV (H1N1, Brisbane/2007) Infected


title: Pa_32572_H

tag: disease

value: Pancreatic ductal adenocarcinomas (PDAC)

tag: tissue

value: tumor

tag: tumor area

value: Gland forming


title: Primary nasal epithelial cells, IAV infected, 48hpi, rep 1

description: Batch 3


title: Tetracycline exposed time point 90 minue, 3rd replicate

value: Bacteria


title: Pa_32572_G

value: Non-Gland forming


title: Tetracycline exposed time point 240 minue, 3rd replicate


title: Primary nasal epithelial cells, mock infected, 48hpi, rep 3 (for HRV-16 and 229E comparison)

description: Batch 2


title: Pa_32572_F


title: D8 uninfected


title: Tetracycline exposed time point 90 minue, 2nd replicate


title: D7 uninfected


title: Tetracycline exposed time point 90 minue, 1st replicate


title: Primary nasal epithelial cells, mock infected, 48hpi, rep 2 (for HRV-16 and 229E comparison)

description: Batch 2


title: Pa_32572_D


title: D5 Pyro

value: infection

tag: pathogen

value: Listeria monocytogenes 10403S

tag: pathogen id

tag: pathogen genotype

value: Pyro


title: Primary nasal epithelial cells, mock infected, 48hpi, rep 3 (for IAV comparison)

description: Batch 3

value: Primary nasal

tag: cell type


title: D6 Pyro


title: Pa_32572_A


title: WT, replicate 1, scRNAseq

description: 10x Genomics

value: Kdrl positive

value: whole zebrafish embryo


title: D4 Pyro

value: caudal fin


title: Pa_30866_C


title: Primary nasal epithelial cells, HRV-16 infected, 48hpi, rep 3

description: Batch 2

value: Nasal epithelium

tag: genotype

value: HRV-16 (ATCC-VR283) Infected


title: Pa_29919_B


title: D3 wt listeria

value: AB

value: Larval:Day 4

value: wild type


title: Non-Tetracycline exposed time point 30 minue, 2nd replicate


title: Primary nasal epithelial cells, HRV-16 infected, 48hpi, rep 2

description: Batch 2

value: WT

tag: time


title: Pa_47691_A

value: Pancreatic ductal adenocarcinomas (PDAC)

value: tumor


title: Primary nasal epithelial cells, HRV-16 infected, 48hpi, rep 1

description: Batch 2


title: D2 wt listeria

tag: age


title: D1 wt listeria


title: Tetracycline exposed time point 30 minue, 2nd replicate

value: Bacteria


title: Primary nasal epithelial cells, HCoV-229E infected, 96hpi, rep 3

description: Batch 2

value: HCoV-229E (ATCC-VR-740) Infected


title: Pa_44228_H

value: Non-Gland forming


title: Primary nasal epithelial cells, mock infected, 48hpi, rep 1 (for HRV-16 and 229E comparison)

description: Batch 2

value: Mock Infected


title: Tetracycline exposed time point 30 minue, 3rd replicate


title: Pa_1860_G


title: BC CML T cells 6

city: Duarte

first: Hsun

middle: Teresa

last: Ku

state: CA

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

data_processing:
RNA-Seq reads were trimmed to remove sequencing adapters using Trimmomatic and polyA tails using FASTP.
The processed reads were mapped to the human genome hg19 using STAR (v. 2.6.0.a), and gene expression levels were summarized by HTSeq-count v.0.11.1.
Gene expression raw counts were normalized using TMM normalization method and differential expression analysis was conducted using log likelihood ratio test implemented in “edgeR”.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Spleen

extract_protocol:
Total RNA was extracted using the miRNeasy Micro Kit (Qiagen, Valencia, CA)
RNA sequencing libraries were prepared with Kapa mRNA HyperPrep kit (Kapa Biosystems) according to the manufacturer's protocol.
RNA-seq libraries were sequencing on Illumina NovaSeq6000 with the sequencing length of 2x101bp. RNA-Seq reads were trimmed to remove sequencing adapters using Trimmomatic and polyA tails using FASTP.

value: Spleen

value: T cells

value: MIr142 KO BCR-ABL


title: BC CML T cells 5


title: Pa_44228_F


title: Non-Tetracycline exposed time point 30 minue, 3rd replicate


title: Primary nasal epithelial cells, SARS-CoV-2 infected, 96hpi, rep 3

description: Batch 1

value: Primary nasal

value: SARS-CoV-2 (WA/01) Infected


title: BC CML T cells 4


title: Primary nasal epithelial cells, HCoV-229E infected, 96hpi, rep 1

description: Batch 2

value: Nasal epithelium


title: Non-Tetracycline exposed time point 0 minute, 3rd replicate


title: Pa_44053_G


title: Tetracycline exposed time point 30 minue, 1st replicate


title: Primary nasal epithelial cells, SARS-CoV-2 infected, 96hpi, rep 2

description: Batch 1


title: BC CML T cells 3


title: Pa_32572_E


title: Non-Tetracycline exposed time point 30 minue, 1st replicate


title: Non-Tetracycline exposed time point 0 minute, 2nd  replicate


title: Primary nasal epithelial cells, SARS-CoV-2 infected, 96hpi, rep 1

description: Batch 1


title: Pa_44053_C

value: Gland forming


title: Tetracycline exposed time point 0 minute, 3rd replicate


title: Primary nasal epithelial cells, HCoV-229E infected, 96hpi, rep 2

description: Batch 2


title: BC CML T cells 1


title: Pa_44053_H


title: CP CML T cells 8

value: BCR-ABL


title: Pa_47691_G


title: Tetracycline exposed time point 0 minute, 2nd  replicate


title: Tetracycline exposed time point 0 minute, 1st replicate


title: BC CML T cells 2


title: Non-Tetracycline exposed time point 0 minute, 1st replicate


title: CP CML T cells 7


title: Primary nasal epithelial cells, HCoV-NL63 infected, 96hpi, rep 2

description: Batch 1

value: HCoV-NL63 Infected


title: Primary nasal epithelial cells, HCoV-NL63 infected, 96hpi, rep 1

description: Batch 1


title: CP CML T cells 6


title: mutL*//polC* strain, with 100 µM IPTG, replicate 2

city: JOUY-EN-JOSAS

first: Ira

last: Tanneur

address: INRAE - Unité MaIAGE  Bât 210 et 233  Domaine de Vilvert

department: MaIAGE

institute: INRAE

data_processing:
Base calling was performed by Fasteris using NovaSeq Control Software 1.7.5, RTA v3.4.4, and bcl2fastq2.20 v2.20.0.422.
Reads were trimmed using sickle 1.33 with options-t sanger -x -q 20 -l 20.
Alignment to the reference sequence of the B. subtilis 168 genome (Genbank AL009126.3) used the BWA-MEM alignment tool version 0.7.17
Stranded read counts per gene annotated in AL009126.3 were obtained with htseq-count 2.0.1 (options “-s reverse -m union --nonunique all")
Fragment counts normalised per kilobase of feature length per million mapped fragments (FPKM) were computed with DESeq2 v1.38.3 based on robust estimation of library size.
Assembly: AL009126.3
Supplementary files format and content: tab-delimited text file
Supplementary files format and content: First six columns : location of the gene, locus tag, and gene name (as annotated in AL009126.3)
Supplementary files format and content: Next 12 columns : raw counts for each sample
Supplementary files format and content: Last 12 columns : normalized expression levels (FPKM) for each sample

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: planktonic exponential phase (0D600 ~0.4)

growth_protocol:
A single clone was cultured overnight in 10 mL in LB at 37°C. This preculture was diluted to OD600 = 0.01 in 2 mL of LB and grown at 37°C. When the culture reached OD600 = 0.4, it was diluted by 40 to OD600 = 0.01 in 5 mL.
This cycle of growth and dilution to OD600 = 0.01 was repeated twice in growing volumes (20 mL then 150 mL culture). In conditions with IPTG, 100µM IPTG was added in the 20 mL culture.
When the 150 mL culture reached OD600 = 0.4, 3 x 30 mL of culture were sampled.

extract_protocol:
Total RNA was isolated by acid-phenol extraction protocol consisting of two extractions with an equal volume of acid phenol/chloroform/isoamyl alcohol (25:24:1, [pH 4.5]) followed by one extraction with chloroform/isoamyl alcohol (24:1).
After adding 1/10 volume of 3 M sodium acetate (pH 5.2), RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 100 μl of RNase free water.
For transcriptome analysis, 35 μg RNA were DNase-treated using the RNase-Free DNase Set (Qiagen) and purified using the RNA Clean-Up and Concentration Micro Kit (Norgen).
Library construction -including ribosomal RNA depletion- and sequencing was performed by Fasteris (Plan-les-Ouates  Switzerland).
RNA depletion was performed with the Lexogen RiboCop META kit, library preparation used the Illumina TruSeq stranded mRNA kit, and the sequencing was paired-end (2 × 50 bp on Illumina NovaSeq 6000).

treatment_protocol: Samples were distributed in tubes containing 15mL of frozen killing buffer (20 mM Tris-HCl, ph 7.5, 5 mM MgCl2, 20 mM NaN3).

value: mutL*//polC*

value: 100 µM IPTG


title: CP CML T cells 5


title: Pa_44053_E

value: Pancreatic ductal adenocarcinomas (PDAC)


title: Pa_37672_H

value: tumor


title: Pa_36203_G


title: CP CML T cells 4


title: Primary nasal epithelial cells, mock infected, 96hpi, rep 1 (for MERS, SARS-2, NL63 comparison)

description: Batch 1

value: WT


title: mutL*//polC* strain, without IPTG, replicate 2

value: planktonic exponential phase (0D600 ~0.4)

value: no IPTG


title: Primary nasal epithelial cells, mock infected, 96hpi, rep 2 (for MERS, SARS-2, NL63 comparison)

description: Batch 1

value: Mock Infected


title: Primary nasal epithelial cells, HCoV-NL63 infected, 96hpi, rep 3

description: Batch 1


title: Pa_30866_A


title: Primary nasal epithelial cells, mock infected, 96hpi, rep 3 (for MERS, SARS-2, NL63 comparison)

description: Batch 1


title: mutL*//polC* strain, without IPTG, replicate 1


title: CP CML T cells 3

value: Spleen


title: Pa_29919_D


title: Primary nasal epithelial cells, MERS-CoV infected, 96hpi, rep 3

description: Batch 1

value: MERS-CoV (EMC/2012) Infected


title: polC* strain, with 100 µM IPTG, replicate 2

value: polC*


title: Primary nasal epithelial cells, MERS-CoV infected, 96hpi, rep 2

description: Batch 1

value: Primary nasal


title: polC* strain, with 100 µM IPTG, replicate 1


title: CP CML T cells 2

value: T cells


title: Pa_29919_A

value: Non-Gland forming


title: Primary nasal epithelial cells, MERS-CoV infected, 96hpi, rep 1

description: Batch 1

value: Nasal epithelium


title: Pa_1860_C


title: mutL*//polC* strain, with 100 µM IPTG, replicate 1


title: MDA-MB-231, TIS sEV, Rep 3

data_processing:
For analysis of sequencing data, nfcore/rnaseq pipeline (https://github.com/nf-core/rnaseq) was used.
Briefly, data quality was monitored using fastqc 0.11.9 and low quality reads were removed by trimgalore 0.6.6.
Sequence were aligned using star 2.6.1d and gene expression was quantified by salmon 1.4.0
Differential expression was calculated by DESeq2 1.28.0
Assembly: GRCh38.p13 (GCF_000001405.39)
Supplementary files format and content: txt files that includes gene-level tpm values for each sample

growth_protocol: MDA-MB-231 cells were maintained in DMEM supplemented with 10% FBS and 1% Pen-strep.

treatment_protocol: Donor MDA-MB-231 cells were treated with DMSO or 100 ng/ml of Nocodozole for 72 h and then released in exo-free media for further 72 h. Conditioned media was collected and sEVs were isolated using diffrential centrifugation method. Recipient MDA-MB-231 cells were incubated with No sEV, Cont sEV and TIS sEV (2 × 109 particles) for 72 h in 5% exo-free media.

value: Human Breast Cancer

value: TIS sEV


title: mutL* strain, with 100 µM IPTG, replicate 1

value: mutL*


title: cKO2

city: Beijing

first: Liu

last: Jiali

address: No.2 Yuanmingyuan West Road, Haidian District, Beijing, China

department: College of Biological Sciences

country: China

institute: China Agricultural University

description: knockout

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2 v2.0.5
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

source_name: testis

growth_protocol: All mice were bred and housed under specific pathogen-free conditions with controlled temperature (22 ± 1℃) and exposed to a constant 12-hour light-dark cycle in the animal facilities of China Agricultural University. All experiments were conducted following the guidelines and with the approval of the Institutional Animal Care and Use Committee of China Agricultural University

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v3-cBot-HS was used with 0.4 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Conditional knockout

value: testis

value: Germ cell

value: STRA8+ cell

value: knockout


title: Chassis strain, without IPTG, replicate 2

value: planktonic exponential phase (0D600 ~0.4)

value: Chassis


title: Pa_43840_G

value: Pancreatic ductal adenocarcinomas (PDAC)

value: tumor


title: MDA-MB-231, TIS sEV, Rep 1

value: WT


title: Pa_43840_E


title: Pa_44228_C

value: Gland forming


title: Chassis strain, with 100 µM IPTG, replicate 2

value: 100 µM IPTG


title: Chassis strain, without IPTG, replicate 1

value: no IPTG


title: Chassis strain, with 100 µM IPTG, replicate 1


title: Pa_44228_D

value: Non-Gland forming


title: Control3

description: Cre

value: Cre


title: MDA-MB-231, Cont sEV, Rep 3

value: Human Breast Cancer

value: Cont sEV


title: MDA-MB-231, Cont sEV, Rep 1


title: cKO1

description: knockout


title: Control2

description: Cre


title: Control1

description: Cre


title: 293T-WT-2,sgSUGP1,seqrun1,rep2

city: New York

first: Jahan

last: Rahman

state: New York

address: 417 E 68th St

department: Center for Hematologic Malignancies

institute: Memorial Sloan Kettering

data_processing:
A genome annotation (UCSC hg19/GRCh37) was created by combining the UCSC knownGene (PMID: 24270787), Ensembl 71 (PMID: 23203987), and MISO v2.0 (PMID: 21057496) annotations. Transcriptome mapping was accomplished using RSEM v1.2.4 (PMID: 21816040) with the argument ‘‘-v 2’’ which indicates Bowtie invocation (PMID: 19261174). Unaligned reads were mapped to the genome with TopHat v2.0.8b (PMID: 19289445), and to a custom annotation which includes all gene-level pairwise combinations of annotated 5’ and 3’ splice sites. The combined RSEM/Bowtie and TopHat alignments were inputted to MISO v2.0 (PMID: 21057496) to quantify isoform expression levels.
Assembly: hg19
Supplementary files format and content: tab-delimited text-files include raw isoform counts for each sample: isoform.expression.1.txt, isoform.expression.2.txt, isoform.expression.3.txt, isoform.expression.4.txt

extract_protocol:
For cell line RNA sequencing (RNA-seq), RNA was extracted from K562 and293Tcells using the Qiagen RNeasy extraction kit, according to the manufacturer’s instructions. A minimum of 500 ng of high-quality RNA (as determined by Agilent Bioanalyzer) per replicate was used as input for library preparation.
Poly(A)-selected, strand-specific (dUTP method) Illumina libraries were prepared by the Integrated Genomics Operation (IGO) at Memorial Sloan Kettering with a modified TruSeq protocol and sequenced on the Illumina HiSeq 2000 to obtain∼60-80M paired-end 100 bp reads per sample.


title: CLIP2

data_processing:
For the analyses of CLIP-seq data, the adaptor sequences were first removed from the reads by Trimmomatic (version 0.36)
Subsequently, Bowtie 2 (version 2.1.0) was applied for mapping of clean reads to the mm10 reference genome with the parameters "-p 10 -L 15 -N 1 -D 50 -R 50 --phred33 --qc-filter --very-sensitive --end-to-end."
CLIP-seq peaks were identified by Piranha (version 1.2.1) with the following parameters: "-s -b 20 -d Zero Truncated Negative Binomial -p 0.05."
Homer (version 4.9.1) was used for peak annotation based on the mm10 genome assembly and for analyses of BCAS2-binding motifs
Assembly: mm10
Supplementary files format and content: bigWig (track)

extract_protocol:
Total cells were isolated from adult WT C57BL/6N mouse testes, and then the cells were cross-linked by ultraviolet light (254 nm) to maintain the covalent binding of RBPs to their cognate RNA. Subsequently, BCAS2 and cross-linked RNAs were immunoprecipitated with an anti-BCAS2 antibody and digested with micrococcal nuclease (EN0181, Thermo Fisher Scientific). An IR800-biotin adapter was ligated to the 3′ ends of the RNA fragments. Then, the BCAS2/RNA complexes were separated by SDS‒PAGE and transferred to a nitrocellulose membrane (HATF00010, Millipore). These RNA and protein complexes from approximately 40 to 60 kDa were extracted from the nitrocellulose membrane, after which proteinase K (9034, Takara) digestion was performed. RNA was isolated with saturated phenol (AM9712, Ambion),
RNA ligated with adaptors, and converted to cDNA with a SuperScript III First-Strand Kit (18080-051, Invitrogen). The cDNA was amplified by PCR to prepare the corresponding libraries and then sequenced on illumina NovaSeq 6000.

tag: clip antibody

value: BCAS2 antibody (PA2466, Abmart)


title: MDA-MB-231, No sEV, Rep 3

tag: cell line

value: No sEV


title: Pa_44228_G


title: mutL* strain, with 100 µM IPTG, replicate 2

value: mutL*


title: cKO3

description: knockout

value: testis

value: Germ cell

value: STRA8+ cell


title: CLIP1


title: CP CML T cells 1

value: Spleen

value: T cells

value: BCR-ABL


title: Pa_37672_B

value: Pancreatic ductal adenocarcinomas (PDAC)

value: tumor


title: MDA-MB-231, No sEV, Rep 2

value: WT


title: 293T-WT-1,sgSUGP1,seqrun1,rep2


title: MDA-MB-231, TIS sEV, Rep 2

value: TIS sEV


title: MDA-MB-231, Cont sEV, Rep 2


title: Pa_43840_B

value: Gland forming


title: 293T-WT-2,sgGPATCH8,seqrun1,rep2


title: Pa_37672_D


title: Pa_30866_H

value: Non-Gland forming


title: IgG1

value: normal mouse IgG (A7016, Beyotime)


title: Pa_30866_G


title: IgG2


title: 293T-WT-1,sgRenilla,seqrun1,rep2


title: Reb1-AA_Rapamycin_PlusTSA

city: Geneva

first: Sevil

last: Zencir

address: 30, quai Ernest-Ansermet

department: Department of Molecular and Cellular Biology

country: Switzerland

institute: University of Geneva

data_processing:
For MNase-seq, adapters were first removed from the paired-end reads using the Trim Galore Tool with default options from the Galaxy server (Afgan et al., 2018). Paired-end reads were aligned to sacCer3 genome assembly using Bowtie2 (Langmead et al., 2012). PCR duplicates were removed from the analysis. Then, deepTools 2.0 (Ramirez et al., 2016) was used through the bamCoverage function with size selection of fragments of 120–200 bp.
For ChEC-seq samples, adapters were first removed from the paired-end reads using the Trim Galore Tool with default options from the Galaxy server (Afgan et al., 2018). Paired-end reads were aligned to sacCer3 genome assembly using Bowtie2 (Langmead et al., 2012). PCR duplicates were removed from the analysis. Then, deepTools 2.0 (Ramirez et al., 2016) was used through the bamCoverage function with size selection of fragments of 0-200 bp.
Assembly: sacCer3
Supplementary files format and content: bigwig files were obtained using Galaxy server (Afgan et al., 2018).

organism: Saccharomyces cerevisiae

growth_protocol:
MNase-seq: Yeast cells were grown at 30 °C in YEPD to mid-log phase before treatment.
ChEC-seq: Yeast cells were grown at 30 °C in YEPD to mid-log phase before treatment.

extract_protocol:
The MNase-seq experiments were performed mainly as described in Gill et al. (2020) with the following modifications; For chromatin extraction, frozen cell pellets were resuspended in 600 mL cell lysis buffer (50 mM HEPES-KOH, pH 7.5, 140mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Sodium Deoxycholate, supplemented with 1 mM PMSF and EDTA-free protease inhibitors) mechanically lysed by bead beating. The cell extract was then centrifuged at 13,000 rpm for 30 min at 4˚C to collect chromatin. The chromatin was resuspended in 600 mL of NP buffer (0.5 mM Spermidine, 50 mM NaCl, 1mM b-mercaptoethanol, 0.075% NP-40, 10 mM Tris-HCl pH 7.4, 5 mM  μgCl2, 1 mM CaCl2) per reaction. The DNA concentration was measured using Qubit dsDNA BR assay kit (Invitrogen). Chromatin was diluted to »20 -30  μg/mL using NP buffer to adjust chromatin density in each reaction. MNase treatment was performed using 0.5 μL of MNase (ThermoScientific 100 units/mL), incubated at 37°C and 100 mL of digestion product was aliquoted for different time points (3, 6, 9 min). The MNase digestion was stopped by adding a stop buffer (20 mM EDTA, 0.5 % SDS, 0.5  μg/mL proteinase-K) in the reaction and incubated first at 42°C for 1 h and then at 65°C for overnight. After reversal of crosslinking, DNA was extracted with phenol- chloroform-iso amyl alcohol (PCI), treated with RNase and visualized on 2.5% agarose gel. The nucleosomal DNA sample for the best MNase digestion time point was purified again with PCI extraction before proceeding further steps.
MNase-seq: NEBnext Ultra DNA library prep kit for Illumina (NEB, E7370L)
NEBnext Ultra DNA library prep kit for Illumina (NEB, E7370L)

treatment_protocol:
MNase-seq: Yeast cells from a fresh plate were grown overnight in YEPD medium at 30°C and diluted to OD600 = 0.3 in YEPD medium next morning. 50 mL of yeast cultures were used for each condition. After one cell cycle, rapamycin (1 μg/ mL, final) was added to corresponding samples at OD600 = 0.6 and incubated for 30 min for anchoring-away of targeted proteins. Nascent DNAs were labelled by addition of 5-Ethynyl-20-deoxyUridine (EdU) at a final concentration of 10 mM for 2 min. After labelling, cells were immediately fixed with formaldehyde at a final concentration of 1% for 15 minutes followed by glycine addition at a final concentration of 125 mM for 5 minutes. For MNase-seq of TSA treated cells, yeast strains were cultured the day before in YEPD medium and next morning they were diluted to OD600 = 0.2 in YEPD. The yeast cells treated with TSA (1 mM, final) for 30 min at OD600 = 0.5.
ChEC-seq: The yeast strains were cultured the day before in YEPD medium and next morning they were diluted to OD600 = 0.2 in YEPD. The 30 min rapamycin treatment (1 μg/ mL, final) was performed for anchoring away of targeted proteins and/or 30 min TSA treatment (1 mM, final) at OD600 = 0.5.

tag: strain

value: HHY221 (MATa tor1-1 fpr1::loxP-LEU2-loxP RPL13A-2x FKBP12::loxP ade 2-1 trp1-1 can1-100)  dBAR1::URA3 BrdU::HIS3(HIS+) Reb1-FRB::KAN

value: treated with rapamycin (1  μg/ml final) and  TSA (1 mM final) for 30 min


title: Pa_30866_F


title: Ino80-AA_Rapamycin_plusTSA_MNase_rep2

value: HHY221 (MATa tor1-1 fpr1::loxP-LEU2-loxP RPL13A-2x FKBP12::loxP ade 2-1 trp1-1 can1-100)  dBAR1::URA3 BrdU::HIS3(HIS+) INO80-FRB::KAN


title: Pa_29919_C


title: diquat, lung (E2_DCL14)

city: Fuzhou

first: Zhimin

last: Chen

address: Chazhong Road NO.20

institute: the First Affiliated Hospital, Fujian Medical University, Fuzhou

description:
E2_DCL14
lung_data_matrix.txt

data_processing:
The data matrix processed by Seurat is output through R language
Assembly: mm10
Supplementary files format and content: tab delimited text file includes data value for each sample

source_name: lung

extract_protocol:
Harvested cells at the required densities were combined with gel beads  containing the barcoded information along with a mixture of cells and  enzymes. Oil surfactant droplets in a microfluidic double-cross system were used for encapsulation to generate Gel Beads-In-Emulsions (GEMs). GEMs were passed through a reservoir and collected while the gel beads were lysed to release the barcode sequence.
The cDNA fragment was then reverse transcribed before the sample was labeled. The gel beads and the oil droplets are ruptured and PCR amplification was performed using the generated cDNA as a template. The products of all GEMs were mixed and a standard sequencing library is constructed. The cDNA was first enzymatically digested into fragments of about 200300 base pairs (bp), together with the library building process of traditional secondgeneration sequencing such as sequencing junction and primers. Finally, the DNA library was generated by PCR amplification

value: lung

value: wild type

value: diquat


title: Ino80-AA_Rapamycin_plusTSA_MNase_rep1


title: 293T-WT-1,sgSUGP1,seqrun1,rep1


title: 293T-WT-2,sgSUGP1,seqrun1,rep1


title: diquat, lung (E1_DCL7)

description:
E1_DCL7
lung_data_matrix.txt


title: Sth1-AA_Rapamycin_plusTSA_MNase_rep1

value: HHY221 (MATa tor1-1 fpr1::loxP-LEU2-loxP RPL13A-2x FKBP12::loxP ade 2-1 trp1-1 can1-100)  dBAR1::URA3 BrdU::HIS3(HIS+) Sth1-FRB::KAN


title: diquat, lung (D3_DVL24)

description:
D3_DVL24
lung_data_matrix.txt


title: 293T-WT-2,sgGPATCH8,seqrun1,rep1


title: 293T-WT-1,sgGPATCH8,seqrun1,rep1


title: Pa_1860_B

city: Milan

first: Pierluigi

last: Di Chiaro

address: Via Adamello 16

institute: European Institute of Oncology (IEO)


title: Sth1-AA_Rapamycin_plusTSA_MNase_rep2


title: Pa_1860_E


title: diquat, lung (D2_DVL23)

description:
D2_DVL23
lung_data_matrix.txt


title: Pa_14_A

data_processing:
Reads were pre-processed (quality trimming and adapter clipping) using Trim Galore v0.6.5, then reads with a minimum of 20 bp were aligned to human genome build GRCh38/hg38 using Kallisto v0.46.0 with default parameters and in the correct orientation (--rf-stranded. Only uniquely mapped reads were retained.
Transcript-level expression were summarized to gene level using tximport v1.14.2 R-package and only protein coding genes were retained.
Differential expression analysis was performed using the DESeq2 R-package v1.26.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file providing raw read count values for each sample

extract_protocol:
FFPE sections (4 μm) were mounted on polyethylene naphthalate membrane (PEN) slides, were deparaffinized in xylene and then partially rehydrated in an ethanol gradient up to 75% EtOH. After that sections were  counterstained with freshly prepared Cresyl Violet for 30 seconds, they were washed twice in 75% EtOH and air dried completely before proceeding to the microdissection using a UV-based LMD7 laser microdissection system (Leica Microsystems) at 20x magnification. Microdissected areas were collected by gravity into strip-tube caps.
Microdissected areas were digested with 10 mU of Proteinase K (ThermoFisher, #AM2546) for 1 hour at 60 C. 1 ml of 5 mM Proteinase K inhibitor (Calbiochem, #539470) was added to stop the reaction and samples were stored at -80 C until library preparation. They were then processed using the SMART-seq Stranded kit (Cat. 634444, protocol version 051018; Takara Bio USA, Inc.) according to the manufacturer’s protocol removing the initial fragmentation step.

value: primary pancreatic ductal adenocarcinoma (PDAC)


title: Ino80-AA_Sth1-ChEC_Rapamycin_rep2

data_processing:
library strategy: ChEC-seq
For MNase-seq, adapters were first removed from the paired-end reads using the Trim Galore Tool with default options from the Galaxy server (Afgan et al., 2018). Paired-end reads were aligned to sacCer3 genome assembly using Bowtie2 (Langmead et al., 2012). PCR duplicates were removed from the analysis. Then, deepTools 2.0 (Ramirez et al., 2016) was used through the bamCoverage function with size selection of fragments of 120–200 bp.
For ChEC-seq samples, adapters were first removed from the paired-end reads using the Trim Galore Tool with default options from the Galaxy server (Afgan et al., 2018). Paired-end reads were aligned to sacCer3 genome assembly using Bowtie2 (Langmead et al., 2012). PCR duplicates were removed from the analysis. Then, deepTools 2.0 (Ramirez et al., 2016) was used through the bamCoverage function with size selection of fragments of 0-200 bp.
Assembly: sacCer3
Supplementary files format and content: bigwig files were obtained using Galaxy server (Afgan et al., 2018).

extract_protocol:
The ChEC-seq experiments were performed mainly as described in Gill et al. (2020) with following modifications; The yeast cells (at OD600 = 0.5-0.6) were washed once in 1 mL Buffer A [15 mM Tris-HCl pH 7.5, 80 mM KCl, 0.1 mM EGTA, 0.2 mM spermine, 0.5 mM spermidine and protease inhibitor tablet (Sigma-Aldrich)]. Cells were resuspended in 693 μL of buffer A and 7 μL of 10% digitonin (0.1% final concentration) were added to facilitate permeabilization of the cells for 5min at 30 °C. CaCl2 was added (final concentration 5 mM) to activate the MNase cleavage. For each samples 100 μL of cells were collected at 30 s after the induction of MNase digestion and and were immediately mixed with 200 mL of 2X Stop solution (400 mM NaCl, 20 mM EDTA, 4 mM EGTA, 1% SDS). The cells were treated with Proteinase K (0.4  μg/mL final concentration) and incubated at 55 °C for 30 min. The DNA was extracted using PCI extraction, and precipitated with Et-OH by adding 30  μg glycogen. Following to RNase treatment, size selection of DNA fragments was performed as follows; 100 μL of AmpureXP beads (Beckman Coulter) were added in 40 μL of RNase treated DNA and the reaction was mixed by pipetting up and down 10 times. The beads were incubated at room temperature for 5 minutes. The tubes then were placed on the magnetic rack and supernatant was transferred to the new tube containing 10 mM Tris and 0.2 M NaCl for each reaction. The DNA was purified by PCI extraction and Et-OH precipitation.
MNase-seq: NEBnext Ultra DNA library prep kit for Illumina (NEB, E7370L)
NEBnext Ultra DNA library prep kit for Illumina (NEB, E7370L)

value: HHY221 (MATa tor1-1 fpr1::loxP-LEU2-loxP RPL13A-2x FKBP12::loxP ade 2-1 trp1-1 can1-100)  dBAR1::URA3 BrdU::HIS3(HIS+) INO80-FRB::KAN Sth1-Flag-MNase::HYG

value: 30 minutes rapamycin (1  μg/ml final)


title: 293T-WT-1,sgGPATCH8,seqrun1,rep2


title: MDA-MB-231, No sEV, Rep 1

city: Singapore

first: Matius

last: Robert

address: 28 Medical Drive

institute: National University of Singapore

value: Human Breast Cancer

value: No sEV


title: diquat, lung (D1_DVL22)

description:
D1_DVL22
lung_data_matrix.txt


title: 293T-WT-1,sgRenilla,seqrun1,rep1


title: Ino80-AA_Sth1-ChEC_Rapamycin_rep1


title: Pa_05_E

value: tumor


title: Ino80-AA_Sth1-ChEC_Vehicle_rep2

value: no rapamycin


title: Pa_44228_H


title: U2AF1-S34F,sgRenilla,seqrun1,rep3


title: control, lung (C2_DCL10)

description:
C2_DCL10
lung_data_matrix.txt

value: control


title: U2AF1-S34F,sgGPATCH8,seqrun1,rep3


title: U2AF1-WT,sgGPATCH8,seqrun1,rep3


title: control, lung (C1_DCL1)

description:
C1_DCL1
lung_data_matrix.txt


title: Pa_44228_F

value: Non-Gland forming


title: Ino80-AA_Sth1-ChEC_Vehicle_rep1


title: U2AF1-WT,sgRenilla,seqrun1,rep3


title: Pa_44228_E


title: U2AF1-S34F,sgGPATCH8,seqrun1,rep2


title: RNA-24S-2

city: Xiamen

first: Huifen

last: Cao

email: hfcao_bnu@163.com, hfcao@hqu.edu.cn

state: Fujian

address: 668 Jimei Road

department: School of Biomedical Sciences

institute: Huaqiao University

description: ncRNAseq

data_processing:
SiNGLe method: The genomic site mapping was performed the same way as in the SSiNGLe-ILM protocol (https://protocolexchange.researchsquare.com/article/pex-920/v2) with the two additional filtering steps. One, PCR duplicates were removed. Two, a read-pair was used only if the first base of the read 2 aligned to the reference sequence. The coordinate of  the first aligning base of the read 2 was assigned as the position of the SSB site. SSiNGLe-AP methods: The analysis is identical with the SSiNGLe method except the coordinate of one base upstream of the first aligning base of the read 2 was assigned as the position of the AP site. RNA analysis: Quality-filtered NGS reads were aligned to the genome using RSEM (version 1.2.28). The TPM values for annotated transcripts were estimated using the “rsem-calculate-expression” function of RSEM (version 1.2.28) with a strand-specific strategy.
Assembly: Mm10 (GRCm38) for the mouse reads mapping
Supplementary files format and content: All BED files contain coordinates of SSB or AP sites mapped to mouse genomes. The 4th columns show the number of reads representing the SSB or AP site.
Supplementary files format and content: TPMs for RNA-seq

source_name: Sperm

extract_protocol:
2 male mice of C57BL/6J strain at 24-month-old were used to extract brains, hearts, livers, bone marrow, PBMCs and sperms. Red cells in bone marrow were removed by Red Blood Cell Lysis Buffer (Beyotime). PBMCs were isolated from blood using Ficoll-Paque PLUS (GE Healthcare). The motile spermatozoa were isolated from the mouse epididymal tail by collecting cells floating in the upper layer of RPMI 1640 (Thermo Fisher Scientific). The isolated tissues were immediately put into liquid nitrogen for quick freezing. The whole organs were cut into small pieces and ground into powder by tissue homogenizer in presence of liquid nitrogen to avoid heating. All ground tissue samples were stored at -80℃ prior to DNA isolation. Genomic DNA from the mouse brain, bone marrow, heart, liver and PBMCs was isolated using TIANamp Genomic DNA kit (Tiangen, DP304) with RNaseA treatment according to the manufacturer’s protocols. Genomic DNA from sperm cells was extracted using Sperm DNA Purification Kit (Simgen, 4202050) following the manufacturer’s instructions. All DNA samples were eluted in UltraPure™ DNase/RNase-Free Distilled Water (Invitrogen), measured the concentration using SMA6000 (Merinton) and stored at -20. Total RNA was isolated with TRNzol (TIANGEN, Beijing).
ncRNAseq:The RNA samples were used for RNA-seq library construction using rRNA depletion and a strand-specific strategy. The library construction and sequencing using the Illumina NovaSeq 6000 platform with the PE150 strategy on the 10-GB scale were outsourced to Novogene Corporation (Beijing).

value: Sperm

tag: development stage

value: 24 months