title: HOU_WT

status: Public on Mar 28 2022

city: Tampa

first: Lindsey

middle: N

last: Shaw

state: FL

address: 4202 E Fowler Avenue

department: CMMB

institute: University of South Florida

data_processing:
Raw data files (.fastq) were exported from the Illumina BaseSpace Server
Raw data files (.fastq) were imported into Qiagen Bioinformatics software platform (version 11) as paired-end reads for analysis and adapter indices trimmed.
Reads corresponding to ribosomal RNA were filtered out and removed
Expression values and fold change for filtered reads were calculated using RNA-Seq Analysis function (v0.1) with experimental fold change feature in Qiagen Bioinformatics software
Expression values and fold change were normalized by quantile normalization, exported in excel format
Assembly: The accession number for the Genbank genome file used as references was NC_010079.1
Supplementary files format and content: RPKM values and fold change for each gene are presented with excel formatting

organism: Staphylococcus aureus

source_name: bacterial cells, pelleted

growth_protocol: Overnight S. aureus cultures were used to inoculate fresh TSB broth and grown for 3 hours. These exponentially growing cultures were subsequently used to seed fresh TSB medium at OD600 0.05. After 15h hour of growth, 5 mL of cells were harvested for RNA isolation.

extract_protocol:
Total bacterial RNA was isolated utilizing the Qiagen RNeasy kit and contaminating DNA was removed by treatment with Ambion TURBO DNA-free kit. Total RNA was enriched for mRNA using MICROBExpress kit and Illumina RiboZero rRNA removal kit for Gram-positive bacteria.
Library construction was performed using the TruSeq Stranded mRNA Kit from Illumina omitting mRNA enrichment steps.

treatment_protocol: Samples were pelleted and stored at -80°C prior to RNA extraction.

value: Wildtype parental strain

tag: growth medium

value: TSB

tag: growth conditions

value: 15h/37 degrees C


title: 147-2 outer

status: Public on Mar 29 2022

type: RNA

city: Evry Cedex

first: Robert

last: Olaso

address: 2 rue Gaston Cremieux

department: CNRGH

country: France

institute: CEA-DRF

description: SAMPLE 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Beadstudio

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Dcx N°147, external stratum pyramidale (SPI) CA3 cells

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification kit for Illumina arrays

extract_protocol: Total RNA was isolated from pooled microdissected material using an RNA isolation kit (Qiagen RNAeasy microkit) according to manufacturer’s instructions. RNA quantity was measured using a nanodrop spectrophotometer. RNA quality was checked using an Agilent 2100 Bioanalyzer with the RNA 6000 Pico LabChip Kit (5065-4473, Agilent Technologies, Palo Alto) according to the manufacturer’s instructions.

tag: genotype

value: Dcx

tag: background strain

tag: developmental stage

value: Adult

tag: tissue

value: Brain

tag: brain region


title: Sorted intestinal blood endothelial cells from Apcfl//fl; Villin-CreERT2 (KO) mice, biological replicate 1.

city: Geneva

first: Isabelle

last: Dupanloup

address: Rue Michel-Servet, 1

country: Switzerland

institute: University of Geneva

description: Transcriptomes of intestinal blood endothelial cells (BEC) from mice with acute epithelial Apc deletion.

hyb_protocol: Biotinylated target cDNA were hybridized, washed and stained according to the protocol described in Affymetrix GeneChip Expression Analysis Manual (Fluidics protocol FS450_0007).

scan_protocol: Affymetrix Mouse Gene 2.0 ST arrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Raw microarray data (CEL files) were processed using the oligo package from Bioconductor. Background subtraction, normalization, and summarization were performed using the RMA algorithm within the oligo package.

source_name: Sorted intestinal blood endothelial cells from Apcfl//fl; Villin-CreERT2 (KO) mice.

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol (Fluidics protocol FS450_0007).

growth_protocol: Control (WT, Apcfl//fl) or Apcfl//fl; Villin-CreERT2 (KO) mice were daily injected subcutaneously with tamoxifen for 5 days.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Plus Micro Kit (Qiagen) and RNA integrity was verified on a Fragment Analyzer (Advanced Analytical). mRNA was amplified using the Ovation Pico WTA System V2 (Nugen).

treatment_protocol: On day 6 the intestine was harvested and digested with Collagenase IV and BECs were sorted as single, live, CD45neg, EpCAMneg, gp38neg, CD31+ cells. Cells were collected in RLT Buffer (Qiagen), vortexed and snap-frozen.

value: mixed C57BL/6 x 129

tag: genotype/variation

value: Apcfl//fl; Villin-CreERT2 (KO)

tag: cell type


title: Ileum_13

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: The data were processed and normalised using RMA normalisation with Expression Console v1.4.1.46

source_name: vancomycin-ileum

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Affymetrix).

extract_protocol: RNA was extracted with QIAGEN miRNeasy mini kit in accordance with the prescribed protocol provided with the kit.

value: FVB

tag: tumor type

value: mammary carcinoma expressing human HER2

value: ileum

tag: treatment

value: vancomycin


title: 145 WT

description: SAMPLE 1

source_name: WT N°145, hippocampal CA3 region

value: WT

value: hippocampal CA3 region


title: Ileum_2

source_name: No antibiotic-ileum

value: No antibiotic


title: HOU_rsp

type: SRA

country: USA

library_source: transcriptomic

tag: strain

value: rsp transposon mutant strain


title: Ileum_1


title: 1107_v1_PBMC

city: Badalona

first: Marta

last: Ruiz-Riol

state: Catalonia/Barcelona

address: Ctra. del Canyet s/n

country: Spain

institute: IrsiCaixa

data_processing:
Mapping was performed with STAR/2.5.3a against GRCh38
Gene quantification was performed with RSEM/1.3.0
Annotation version gencode28
GRCh38
Supplementary_files_format_and_content: COUNTS_genes_IRSIHIV_05.txt and COUNTS_genes_IRSIHIV_06.txt (raw counts)

organism: Homo sapiens

source_name: PBMC

extract_protocol:
AllPrep DNA/RNA Mini Kit
stranded total RNA-seq

tag: timepoint

tag: Sex

value: M

tag: age


title: Ileum_3

source_name: No antibiotic--ileum


title: Colon_5

source_name: No antibiotic-colon

value: colon


title: 1105_v1_CD4


title: Colon_13

source_name: vancomycin-colon


title: Colon_2


title: 1107_v9_PBMC


title: 1107_v1_CD4


title: BV2cells_PBS_24hr_rep3

city: Changsha

first: longyan

last: Li

state: Hunan

address: 87 Xiangya Road

country: China

institute: Xiangya hospital, Central South University

description: Gene expression in pbsTreated BV2 cells human blood for 24hr

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the Agilent Mouse Gene Expression Microarrays V2 (4x44K, Aglient) slide.

scan_protocol: The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Extract data using Agilent Feature Extraction Software，Open the Agilent Feature Extraction (FE) software.Add the images (.tif) to be extracted to the FE Project.Set FE Project Properties. Check the Extraction Set Configuration. Save the FE Project (.fep) by selecting File > Save As and browse for desired location. Select Project > Start Extracting and export data to txt.

source_name: BV2 cells, pbs, 24hr, replicate 3

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol. Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Immortalized murine microglial BV2 cells were obtained from National Infrastructure of Cell Line Resource (Beijing, China), the BV2 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM, Gibco) containing 10% fetal bovine serum (FBS, Gibco) and 1% penicillin/streptomycin and were maintained in a 37°C sterile container in a humidified atmosphere of 5% CO2.

extract_protocol: The collected cells were used to extract the total RNA following the standard protocol, the RNA quantity and quality were tested through NanoDrop ND-1000 Spectrophotometer (Thermo, USA). RNA Integrity and gDNA contamination were tested by denaturing agarose gel electrophoresis.

treatment_protocol: Briefly, BV2 cells were plated onto 6-well plates coated with 0.0005% poly-L-lysine for 24h, 10ng/ml recombinant murine IL-4 (Peprotech, 214-14) or PBS was added to the medium and treated the cells for 24hr.

tag: cell line

value: BV2 cells

value: PBS


title: BV2cells_IL4_24hr_rep3

description: Gene expression in IL-4 Treated BV2 cells human blood for 24hr

source_name: BV2 cells, IL-4, 24hr, replicate 3


title: Colon_11


title: Ileum_14


title: Colon_1


title: Ileum_11

source_name: vancomycin--ileum


title: BV2cells_PBS_24hr_rep2

source_name: BV2 cells, pbs, 24hr, replicate 2


title: BV2cells_PBS_24hr_rep1

source_name: BV2 cells, pbs, 24hr, replicate 1


title: BV2cells_IL4_24hr_rep2

source_name: BV2 cells, IL-4, 24hr, replicate 2


title: 1103_v1_CD4

value: F


title: 1105_v9_CD4


title: Colon_3


title: 1106_v9_CD4


title: BV2cells_IL4_24hr_rep1

source_name: BV2 cells, IL-4, 24hr, replicate 1


title: 1106_v9_PBMC


title: 1106_v1_CD4


title: 1102_v9_CD4


title: 1106_v1_PBMC


title: 1102_v9_PBMC


title: Colon_14


title: 1107_v9_CD4


title: 1103_v9_CD4


title: 1105_v9_PBMC


title: 1105_v1_PBMC


title: 1102_v1_CD4


title: 1101_v9_PBMC


title: 1101_v1_PBMC


title: 1101_v1_CD4


title: B14_w0

description:
MAP_32weeks takes values Yes/No according if they are maintained off cART during the 32 weeks of MAP or not.
If variable Exclusion_MAPandw24 is "Yes" it means the gene expression on MAP and w24 is no valid due to protocol deviation

data_processing:
Mapping was performed with STAR/2.5.3a against GRCh38+HIV genomes
Gene quantification was performed with RSEM/1.3.0
Annotation version gencode28+HIV
Genome_build: GRCh38+HIV
Supplementary_files_format_and_content: COUNTS_genes_IRSIHIV_02.txt (raw counts)

tag: participant id

tag: rebound

value: Early

value: No

value: HC


title: B14_w6


title: B13_MAP

value: MAP

value: Late

value: Yes

value: HUGTIP


title: B13_w1


title: B13_w24


title: 1103_v1_PBMC


title: 1103_v9_PBMC


title: B10_w6


title: 1101_v9_CD4


title: B07_w6


title: B10_w0


title: 1102_v1_PBMC


title: B06_w24


title: B06_w6


title: B14_w24


title: B14_MAP


title: B14_w1


title: B05_w6


title: B03_w24


title: B03_MAP


title: B03_w6


title: B13_w6


title: B03_w1


title: B13_w0


title: B03_w0


title: B10_w24


title: A15_w24


title: B10_MAP


title: B06_MAP


title: B07_w0


title: B07_w1


title: B06_w1


title: A14_w24


title: B06_w0


title: A14_MAP


title: B05_w1


title: A14_w1


title: B05_w24


title: B05_MAP


title: A14_w0


title: B05_w0


title: A13_MAP


title: A15_w6


title: A12_w24


title: B10_w1


title: A15_w1


title: A15_w0


title: A12_w6


title: A12_w0


title: A09_MAP


title: A13_w24


title: A13_w6


title: A15_MAP


title: A09_w6


title: A09_w1


title: A05_w6


title: A05_w1


title: A05_w0


title: A04_w24


title: A04_w0


title: A04_MAP


title: A04_w1


title: A02_w24


title: A14_w6


title: A13_w1


title: A13_w0


title: A02_MAP


title: A02_w1


title: A04_w6


title: A12_MAP


title: A02_w6


title: A12_w1


title: A02_w0


title: A09_w0


title: A05_MAP


title: MRC5-TERC-CHIRP

city: Guangzhou

first: Shu

last: Wu

address: No.601, West Huangpu Avenue

institute: Jinan University

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4.
ChIP-seq reads were aligned to human genome (UCSC, hg38) with Bowtie2 version 2.3.1.
Peaks were called using MACS14, and annotated using CEAS.
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig signal tracks were generated using deepTools (v3.1.3)and normalized to reads per genomic content (RPGC).
Supplementary_files_format_and_content: peaks csv file

molecule: genomic DNA

source_name: MRC5 fibroblast cells

growth_protocol: MRC5 cells were cultured in DMEM medium with 10% fetal bovine serum and 100 U/ml penicillin/ streptomycin

extract_protocol:
40 million MRC5 cells were collected and fixed with 1% glutaraldehyde in PBS for 10 min at room temperature, reflection terminated by 1.25 mM Glycine for 5 min. Cells were resuspended in lysis buffer and sonicate in a 4°C water bath. Supernatant was collected, and diluted with hybridization buffer and appropriate volume of probes (TERC odd probes or Laz-probe), incubate at 37°C for 4 h with shaking. Streptavidin-magnetic C1 beads were blocked with 500ng/ul yeast total RNA and 1mg/ml BSA for 1 hour at room temperature, and resuspended with original volume of lysis buffer and added to the hybridization system, 37°C for 30 min with shaking. Streptavidin-magnetic C1 were washed five times with wash buffer.  For DNA elution, beads were resuspended in 3×original volume DNA elution buffer with RNaseA and RNase H, followed by reverse cross-linking, proteinase K digestion and phenol-chloroform extraction. DNA fragments were precipitated by ethanol in the presence of NaAc and glycogen. Eluted genomic DNA was subject to high-throughput sequencing.
Libraries were prepared according to Illumina's instructions. Briefly, genomic DNA was precisely quantified with Qubit™ dsDNA HS Assay Kit (ThermoFisher, Q32854), fragmented with Covaris and extracted with Hieff NGS™ DNA Selection Beads (Yeasen, 12601ES56). Then, DNA was end-repaired, adapter-ligated and amplified with NEB Next® Ultra™ DNA Library Prep Kit for Illumina® (NEB, E7370), and purified with Hieff NGS™ DNA Selection Beads (Yeasen, 12601ES56). Libraries were sequenced on the Illumina HiSeq following the manufacturer's protocols.
ChIRP-seq

value: fibroblast cells

tag: chirp probe

value: TERC

value: untreated


title: 12H007_GPR56plusCD34-

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

description: sorted on Aria cell sorter

data_processing:
Basecalls performed using Illumina RTA 1.18.64
Samples demultiplexed using bcl2fastq 2.19
Sequenced reads were trimmed for sequencing adapters and low quality extrimities and mapped to the reference genome using STAR version 2.5.1b
Readcounts were computed by STAR during sequence alignment based on annotations from Gencode version 24
Expression values were also computed using RSEM version 1.2.28 based on Gencode version 24 annotations
Genome_build: GRCh38
Supplementary_files_format_and_content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary_files_format_and_content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output (first line identifies the column)

molecule: polyA RNA

source_name: primary human AML cells

extract_protocol:
TriZol + RNeasy mini Kit (Qiagen, #74106)
KAPA Stranded RNA-Seq PolyA (KAPA Biosystems)

treatment_protocol: Cells were thawed, stained for CD34 and GPR56 expression and directly sorted on an Aria cell sorter prior to isolation of RNA.

tag: assay

value: RNA-Seq

tag: sorted fraction


title: 14H007_GPR56plusCD34-

description: sorted on Aria cell sorter


title: 12H007_GPR56plusCD34plus

description: sorted on Aria cell sorter


title: 12H007_GPR56-CD34-

description: sorted on Aria cell sorter


title: 14H007_GPR56-CD34-

description: sorted on Aria cell sorter


title: 10H101_GPR56plusCD34plus

description: sorted on Aria cell sorter


title: 14H007_GPR56plusCD34plus

description: sorted on Aria cell sorter


title: 07H062_GPR56plusCD34-

description: sorted on Aria cell sorter


title: 07H062_GPR56plusCD34plus

description: sorted on Aria cell sorter


title: 07H042_GPR56plusCD34plus

description: sorted on Aria cell sorter


title: 10H101_GPR56plusCD34-

description: sorted on Aria cell sorter


title: PW035-710

city: New York

first: Peter

middle: A

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

data_processing:
12-nt cell barcodes (CBs) and 9-nt unique molecular identifiers (UMIs) were extracted from read 1. Degenerate CBs containing either 'N's or more than four consecutive 'G's were discarded. Synthesis errors, which can result in truncated 11-nt cell barcodes, were corrected.
Read 2 were trimmed to remove poly(A) tails (> dA(7)) from the 3'-ends of each read. Any resulting fragment shorter than 24 nucleotides were discarded.
Trimmed reads were then aligned to GRCh38 (GENCODE v.24) using STAR v.2.5.0 with parameters "-- sjdbOverhang 65 --twopassMode Basic --outSAMtype BAM Unsorted". Only reads with unique, strand-specific alignments to exons were kept for further analysis.
All reads with the same CB, UMI, and gene mapping were collapsed to represent a single molecule. To correct for sequencing errors in UMIs, we further collapsed UMIs that were within Hamming distance 1 of another UMI with the same barcode and gene. To correct for sequencing errors in cell barcodes, we then collapsed CBs that were within Hamming distance one of another cell barcode, had at least 20 unique IMI-gene pairs, and had at least 75% overlap of their UMI-gene pairs. A digital gene expression matrix was then generated from these corrected barcode-UMI-gene triplets.
We estimated the number of cell barcodes corresponding beads associated with cells in our microwell system using the cumulative histogram of reads associated with each barcode
To avoid dead cells and library construction artifacts, we removed cell barcodes that failed to satisfy certain criteria.  We removed all cells where >10% of molecules aligned to genes expressed from the mitochondrial genome or where the ratio of molecules aligning to whole gene bodies (including introns) to molecules aligning exclusively to exons was >1.5. These measures remove cells with compromised plasma membranes, which results in retention of mitochondrial or nuclear transcripts. We also removed cells where the number of reads per molecule (indicative of amplification efficiency) or the number of molecules per gene deviated by more than 2.5 standard deviations from the mean for a given sample.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files that contain the molecular counts of each individual cell. The first two columns contain the gene ID and gene symbol for each gene and all subsequent columns correspond to profiles of individual cells. There is a header contain the cell-identifying barcode sequence for each cell.

source_name: glioma surgical specimen

extract_protocol:
mRNA molecues were captured using bead-bound oligo dT(30).
Captured mRNA molecues were reverse transcriped to obtain cDNA which is then amplified by PCR reactions. The cDNA PCR reaction product was then purified with AMPure XP beads. The purified cDNA PCR product was used as the input for Nextera XT reactions to generate sequencing library.

value: male

tag: idh1 status

value: IDH1 wildtype

tag: diagnosis

value: WHO Grade IV Glioblastoma

tag: primary/recurrent

value: primary

value: glioma surgical specimen


title: 09H002_GPR56plusCD34plus

description: sorted on Aria cell sorter


title: 09H002_GPR56-CD34-

description: sorted on Aria cell sorter


title: 08H053_GPR56plusCD34-

description: sorted on Aria cell sorter


title: 10H101_GPR56-CD34-

description: sorted on Aria cell sorter


title: 08H053_GPR56-CD34-

description: sorted on Aria cell sorter


title: 09H002_GPR56plusCD34-

description: sorted on Aria cell sorter


title: 07H062_GPR56-CD34-

description: sorted on Aria cell sorter


title: 07H042_GPR56plusCD34-

description: sorted on Aria cell sorter


title: Healthy pooled plasma_hybrid capture_whole exome+lincRNA enrichment_Rep 4

city: Waltham

first: Johan

last: Skog

state: MA

address: 266 Second Avenue, Suite 200

institute: ExosomeDx

data_processing:
Alignment by STAR
Gene expression quantification by Salmon
Differential expression analysis by DESeq2
Assembly: hg38
Supplementary files format and content: salmon quantification

source_name: plasma

extract_protocol:
Exolution RNA (Exosome Diagnostics)
ExoDx long RNASeq protocol. Briefly, isolated RNA samples from whole blood, plasma, CSF, and urine were first treated with DNase to remove any trace of amounts of co-purified DNA present in the sample. Post DNA digestion, synthetic RNA spike-in controls (ERCC spike-in mix, Thermo Fisher Scientific) were added to each sample. The exoRNA/ERCC blend was then reverse transcribed using a combination of random hexamers and oligo-dT primers. Second strand synthesis and adapter addition were performed using a PCR-based approach. Libraries were purified via two rounds of AMPureXP beads (Beckman Coulter), and ribosomal cDNA was depleted enzymatically. The final libraries were then amplified to desired concentration for sequencing and purified using AMPureXP. Libraries were quantified using the Agilent Bioanalyzer High Sensitivity Assay (Agilent) and Qubit 1X dsDNA HS Assay Kit (Thermo Fisher Scientific). Libraries were pooled and sequenced on Illumina NextSeq500 using 2x150 cycles read length chemistry.

tag: tissue

value: plasma

tag: rna population

value: Exosomes

tag: health status

value: Healthy

tag: pooling status

value: Pooled

tag: treatment statusstage

value: Not applicable


title: Healthy pooled plasma_hybrid capture_whole exome+lincRNA enrichment_Rep 3


title: Healthy individuals_pooled urine_pool 6

source_name: Urine

value: Urine


title: PW039-705


title: PDC001


title: Healthy individuals_pooled urine_pool 2


title: Healthy individuals_pooled CSF_pool 6

source_name: CSF

value: CSF


title: Healthy individuals_pooled CSF_pool 5


title: Healthy individual 7 urine_hybrid capture_whole exome+lincRNA enrichment_Rep 2

value: Individual


title: MRC5-INPUT

tag: cell type

value: fibroblast cells

value: Input

tag: treatment


title: 07H042_GPR56-CD34-

description: sorted on Aria cell sorter


title: Healthy individual urine_hybrid capture_whole exome+lincRNA enrichment_sample 1


title: Healthy individual 7 urine_hybrid capture_whole exome+lincRNA enrichment_Rep 1


title: Healthy pooled urine_hybrid capture_whole exome+lincRNA enrichment_sample 2


title: Healthy pooled plasma_hybrid capture_whole exome+lincRNA enrichment_Rep 2


title: Healthy individuals_pooled urine_pool 1


title: Healthy individuals_pooled urine_pool 5


title: Healthy individual urine exosome_Collipee_Rep 2


title: Healthy individuals_pooled urine_pool 3


title: Urine exosomes_Low ICP_post-treatment_Sample 6_post 1 month preservation_FTAEluate

value: High ICP Patient

value: Post treatment


title: Healthy pooled plasma_hybrid capture_whole exome+lincRNA enrichment_Rep 1


title: Healthy individuals_pooled CSF_pool 4


title: Urine exosomes_Low ICP_post-treatment_Sample 6


title: Healthy individuals_pooled urine_pool 4


title: Healthy individual urine exosome_Sarstedt_Rep 2


title: CSF exosomes_High ICP_pre-treatment_Sample 1

value: Pre-treatment


title: Whole blood_High ICP_pre-treatment_Sample 3_sequencing Re-run data

source_name: Whole blood

value: Whole blood

value: Whole blood RNA


title: Healthy individual urine exosome_Collipee_Rep 1


title: Healthy individual urine exosome_Sarstedt_Rep 3


title: Plasma exosomes_Low ICP_post-treatment_Sample 1


title: Healthy individuals_pooled CSF_pool 3


title: Urine exosomes_Low ICP_post-treatment_Sample 5_post 1 month preservation_Gentegra


title: Urine exosomes_Low ICP_post-treatment_Sample 4_post 1 month preservation_DNAStable


title: Whole blood_Low ICP_post-treatment_Sample 3


title: Plasma exosomes_High ICP_pre-treatment_Sample 1


title: Whole blood_Low ICP_post-treatment_Sample 2


title: CSF exosomes_High ICP_pre-treatment_Sample 3


title: Healthy individual urine exosome_Sarstedt_Rep 1


title: CSF exosomes_High ICP_pre-treatment_Sample 2


title: Urine exosomes_Low ICP_post-treatment_Sample 4


title: Urine exosomes_Low ICP_post-treatment_Sample 5


title: Plasma exosomes_Low ICP_post-treatment_Sample 3


title: Plasma exosomes_High ICP_pre-treatment_Sample 3


title: Plasma exosomes_Low ICP_post-treatment_Sample 2


title: Healthy individual urine exosome_Collipee_Rep 3


title: TZ47 CAR only

city: Lebanon

first: Yina

last: Huang

state: NH

address: 1 Medical Center Drive

department: Microbiology and Immunology

institute: Dartmouth College

data_processing:
Basecall software: Illumina RTA 2.0 on-instrument
Basecalls converted to FASTQ files using bcl2fastq
Alignment, filtering, barcode counting, and UMI counting performed on cellranger 6.0.1
filtered-feature-barcode-matrices used to generate Seurat objects (4.0)
Assembly: GrCh38 modified with mCD19 and B7H6 CAR sequence

source_name: Healthy donor PBMC's

extract_protocol:
RNA extraction and library construction from sorted cells was performed using 10X Genomics Chromium Next GEM Single Cell 3ʹ v3.1 platform.
10X Genomics Chromium Next GEM Single Cell 3ʹ v3.1 platform

treatment_protocol: CAR-T cells were isolated by FACS: Super2+IL33 CAR T cells were isolated by surface expression of mCD19 and GFP fluorescence; CAR only T cells were isolated by surface expression of mCD19.

value: Human CAR T cells

tag: dna construct(s)


title: TZ47 CAR + Super2+IL-33

value: pSFG-TZ47-CAR and pCigar-Super2-IL33


title: Plasma exosomes_High ICP_pre-treatment_Sample 2

value: plasma


title: Whole blood_Low ICP_post-treatment_Sample 1


title: Whole blood_High ICP_pre-treatment_Sample 3


title: DHT_Bicalutamide 5h

city: Iwaki

first: Takahiro

last: Sawada

state: Fukushima

address: Jobankamiyunagayamachi Kaminodai57

country: Japan

institute: Research Institute of Innovative Medicine

data_processing:
Paired-end sequencing were performed on the Illumina NextSeq 500 sequencer . Reads were mapped to the  hg19 reference sequence using Burrows-Wheeler Aligner (BWA-MEM: ver. 0.7.17-r1188), and duplicate  reads were removed with Picard (ver. 2.18.16).
Mapping by Bowtie2
Peak calling was performed using MACS2 (ver. 2.1.2) and PePr  (ver. 1.1.24) with default parameters respectively. Peak annotation were conducted by HOMER (ver.4.9.1) with default settings.
Assembly: GRch38
Supplementary files format and content: tab-delimited text files include CPM  (FPKM, peak) values for each sample.

source_name: Prostate cancer cell line

growth_protocol: For treatment of the human cancer cell line LNCaP, 1.0 x 106 cells were seeded in a 10 cm dish, cultured in conditioned RPMI1640 medium for 48 h, and subsequently with charcoal-treated medium for 72h.

extract_protocol:
Approximately 50,000 cells were lysed and the rearrangement reaction was performed using Tn5 Transposase (Illumina Catalog #FC121-1030) for 30 min at 37°C.
The reaction solution was purified with Qiagen MinElute PCR Purification Kit. Next, five cycles of PCR with custom Nextera PCR primers were performed using NEBNext Q5 Hot Start HiFi PCR Master Mix. The number of additional PCR cycles was determined by qPCR of the partially amplified product. PCR products were prepared using Agencourt AMPure XP beads using the manufacturer's The PCR products were purified using Agencourt AMPure XP beads by double size selection (left ratio: 1.4X, right ratio: 0.5X) according to the manufacturer's protocol.

treatment_protocol: 24 h after addition of 10 nM DHT to the culture medium, cells were collected. The antagonistic action of bicalutamide (10 µM), Enzalutamide (10 µM) were tested in LNCaP cells treated for the indicated times.

tag: cell line

value: LNCaP

tag: transposase

value: Tn5 Transposase

tag: agent

tag: time point


title: S516_day 80_1

city: Kyoto

first: Hidetoshi

last: Sakurai

address: 53 Shogoin-Kawahara-cho, Sakyo-ku

institute: Center for iPS Cell Research and Application

data_processing:
The 10X Genomics Cell Ranger pipeline (version 4.0.0) was used to perform sample demultiplexing, alignment to the mm10 mouse reference genome or hg38 human reference genome and the reporter sequences (mCherry or mCherry and zsGreenDR), barcode/UMI processing, and gene counting for each cell.
Scrublet (v.0.2.3) was used to exclude doublet cells (scrublet score >= mean + 1SD) from further analysis.
Assembly: hg38
Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample, mtx files count gene UMI couns for each sample

source_name: Differentiated muscle cells from hiPSC

growth_protocol: hiPSC were differentiated into myogenic linage by using a step wise protocol as previously described (Stem Cell Reports, 2020 Jul 14;15(1):80-94)

extract_protocol:
Differentiated cells were incubated with Collagenase G and H for 1 hour and for 10 minutes with accutase. Single cells were dissociated by pipeting and filtered by a 50 nm mesh.
For scRNAseq, RNA from the barcoded cells for each sample was subsequently reverse-transcribed and sequencing libraries were constructed with reagents from a Chromium Single Cell v3.1 reagent kit (10x Genomics). Sequencing was performed with Illumina NextSeq 500 and HiSeq 4000.

tag: hipsc establishment

value: hiPSC cell line established from cord blood cells using an episomal vector system

tag: derived cell type

value: Differentiated muscle cells from hiPSC

tag: disease state

value: Healthy

tag: differentiation duration

value: HiPSC-MuPCs differentiated for 80 days


title: Vehicle 5day

value: Vehicle


title: S516_day 80_2


title: DHT 5h

value: DHT


title: DHT 5day


title: Vehicle 5h


title: Whole blood_High ICP_pre-treatment_Sample 2

value: Individual


title: Whole blood_High ICP_pre-treatment_Sample 1

value: High ICP Patient


title: stromal CD3+ T cell in patient 709

city: Farmington

first: Jianan

last: Lin

state: CT

address: 10 discovery dr

institute: The Jackson Laboratory

description:
709-sCD3
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv

data_processing:
bases with quality value lower than 30 were trimmed from the 3’ end of the read, and only reads with more than 50% bases of good quality were kept.
the reads were aligned to the human genome using RSEM with the following parameters, --phred33-quals --seed-length 25 --forward-prob 0.5 --time --output-genome-bam --bowtie2.
protein-coding genes and lincRNAs were kept in the downstream analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: the processed data (raw counts/TPM values from RSEM) is in tab-separated values (.tsv) format. The first row is the sample names and the last column is the gene names.

source_name: T cells

extract_protocol:
PicoPure RNA isolation kit following manufacturer protocol
SMART-Seq V4 Ultra Low Input RNA kit

treatment_protocol: Laser capture microdissection

value: CD3+ T cell

tag: location

value: stroma

tag: patient


title: stromal CD3+ T cell in patient 626

description:
626-sCD3
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: Bicalutamide 5day

value: Bicalutamide


title: DHT_Bicalutamide 5day


title: stromal CD3+ T cell in patient 130

description:
130-sCD3
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: stromal CD3+ T cell in patient 997

description:
997-sCD3
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: intratumoral CD3+ T cell in patient 898

description:
898-iCD3
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv

value: intratumoral


title: stromal CD3+ T cell in patient 562

description:
562-sCD3
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: stromal CD3+ T cell in patient 898

description:
898-sCD3
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: Bicalutamide 5h


title: stromal CD3+ T cell in patient 447

description:
447-sCD3
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: intratumoral CD3+ T cell in patient 997

description:
997-iCD3
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: intratumoral CD3+ T cell in patient 130

description:
130-iCD3
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: cancer cell in patient 898 section 1

description:
898-Cancer-1
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv

source_name: melanoma

value: Cancer cell

value: melanoma


title: cancer cell in patient 898 section 2

description:
898-Cancer-2
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: intratumoral CD3+ T cell in patient 577

description:
577-iCD3
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: cancer cell in patient 709 section 1

description:
709-Cancer-1
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: cancer cell in patient 626 section 1

description:
626-Cancer-1
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: intratumoral CD3+ T cell in patient 626

description:
626-iCD3
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: cancer cell in patient 562 section 2

description:
562-Cancer-2
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: intratumoral CD3+ T cell in patient 709

description:
709-iCD3
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: cancer cell in patient 577 section 1

description:
577-Cancer-1
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: intratumoral CD3+ T cell in patient 562

description:
562-iCD3
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: cancer cell in patient 447 section 1

description:
447-Cancer-1
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: cancer cell in patient 130 section 2

description:
130-Cancer-2
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: cancer cell in patient 709 section 2

description:
709-Cancer-2
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: cancer cell in patient 997 section 2

description:
997-Cancer-2
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: stromal CD14+  cell in patient 997 section 1

description:
997-sCD14-1
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv

source_name: Myeloid cells

value: CD14+ cells


title: cancer cell in patient 997 section 1

description:
997-Cancer-1
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: stromal CD14+  cell in patient 898 section 1

description:
898-sCD14-1
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: stromal CD14+  cell in patient 709 section 2

description:
709-sCD14-2
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: intratumoral CD3+ T cell in patient 447

description:
447-iCD3
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: cancer cell in patient 577 section 2

description:
577-Cancer-2
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: cancer cell in patient 626 section 2

description:
626-Cancer-2
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: cancer cell in patient 447 section 2

description:
447-Cancer-2
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: stromal CD14+  cell in patient 577 section 1

description:
577-sCD14-1
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: stromal CD14+  cell in patient 562 section 2

description:
562-sCD14-2
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: stromal CD14+  cell in patient 562 section 1

description:
562-sCD14-1
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: stromal CD3+ T cell in patient 577

description:
577-sCD3
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: cancer cell in patient 562 section 1

description:
562-Cancer-1
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: cancer cell in patient 130 section 1

description:
130-Cancer-1
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: stromal CD14+  cell in patient 997 section 2

description:
997-sCD14-2
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: stromal CD14+ cell in patient 130 section 1

description:
130-sCD14-1
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: stromal CD14+  cell in patient 130 section 2

description:
130-sCD14-2
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: intratumoral CD14+  cell in patient 997 section 1

description:
997-iCD14-1
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: stromal CD14+  cell in patient 709 section 1

description:
709-sCD14-1
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: intratumoral CD14+  cell in patient 898 section 1

description:
898-iCD14-1
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: stromal CD14+  cell in patient 626 section 2

description:
626-sCD14-2
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: stromal CD14+  cell in patient 898 section 2

description:
898-sCD14-2
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: intratumoral CD14+  cell in patient 709 section 1

description:
709-iCD14-1
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: stromal CD14+  cell in patient 577 section 2

description:
577-sCD14-2
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: intratumoral CD14+  cell in patient 626 section 1

description:
626-iCD14-1
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: stromal CD14+  cell in patient 447 section 2

description:
447-sCD14-2
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: intratumoral CD14+  cell in patient 577 section 1

description:
577-iCD14-1
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: stromal CD14+  cell in patient 626 section 1

description:
626-sCD14-1
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: stromal CD14+  cell in patient 447 section 1

description:
447-sCD14-1
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: intratumoral CD14+  cell in patient 447 section 2

description:
447-iCD14-2
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: intratumoral CD14+  cell in patient 447 section 1

description:
447-iCD14-1
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: intratumoral CD14+  cell in patient 898 section 2

description:
898-iCD14-2
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: intratumoral CD14+  cell in patient 997 section 2

description:
997-iCD14-2
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: intratumoral CD14+ cell in patient 130 section 1

description:
130-iCD14-1
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: GLOE HCT116 CAD-/- 24h R1

city: Solna

first: Simon

middle: J

last: Elsässer

address: Tomtebodavägen 23A

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
Library strategy: GLOE-seq
read alignment: Filtered paired-end FASTQ files were then mapped to hg19 genome using bowtie2 --fast option. BAM files were filtered for amplification and optical duplicates using Picard MarkDuplicates function, taking into account paired-end mapping information to define unique ligation events.
read coverage: First-in-pair reads were extracted from BAM file separately for plus and minus strand using deepTools bamCoverage --samFlagInclude 64 --samFlagExclude 16 and --samFlagInclude 80, respectively. BigWig output coverage was normalized using --normalizeUsing RPGC parameter
Genome_build: hg38
Supplementary_files_format_and_content: Two BigWig files are provided per sample showing nornalized coverage of first-in-pair reads mapping to positive and negative strand, respectively

source_name: HCT116 CAD-/-

growth_protocol: HCT116 cells were culture in McCoy’s 5A media (Life Tech 16600082) supplemented with 10%fetal Bovine Serum (GE Healthcare SV30160.03) and 1X Penicillin-Streptomycin (Gibco 15140-122). Standard culture conditions 5%CO2, 37 °C.

extract_protocol:
GLOE-seq was performed according to the published protocol (Sriramachandran et al., 2020; doi:10.1016/j.molcel.2020.03.027) with minor modifications as described below. Briefly 5x10^6  of each HTC116 cells under different treatment conditions were harvested and individually embedded in an agarose plug for genome DNA extraction. After splinter adaptor ligation, sonication and clean-up of genomic DNA, each HCT116 sample was adjusted and normalized to 15.5ug input DNA amount. Genomic DNA from mouse embryonic stem cells (E14, 129/Ola) prepared in the same manner was added as a spike-in at 5% (w/w) final concentration before affinity capture by streptavidin magnetic beads.
GLOE-seq libraries were prepared as described (Sriramachandran et al., 2020' doi: 10.1016/j.molcel.2020.03.027) and double size-selected with AMPure XP SPRI beads at 0.4X-0.8X before sequencing on the Illumina NextSeq 500 platform.

treatment_protocol: Cell were irradiated with a Faxitron X-ray apparatus at a dosage rate of 1Gy/min for a total of 8Gy of radiation.

value: 24 hr post-IR (8Gy)

tag: genotype

value: CAD-/-

value: colorectal carcinoma

tag: assay

value: GLOE-Seq


title: intratumoral CD14+  cell in patient 709 section 2

description:
709-iCD14-2
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: GLOE HCT116 CAD-/- 24h R2


title: intratumoral CD14+  cell in patient 577 section 2

description:
577-iCD14-2
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: GLOE HCT116 CAD-/- 20m R3

value: 20 min post-IR (8Gy)


title: GLOE HCT116 CAD-/- UT R3

value: untreated


title: GLOE HCT116 CAD-/- 20m R2


title: intratumoral CD14+  cell in patient 562 section 2

description:
562-iCD14-2
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: intratumoral CD14+  cell in patient 562 section 1

description:
562-iCD14-1
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: GLOE HCT116 CAD-/- 24h R3


title: GLOE HCT116 CAD-/- 20m R1


title: intratumoral CD14+  cell in patient 626 section 2

description:
626-iCD14-2
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: GLOE HCT116 WT UT R3

value: wildtype


title: GLOE HCT116 WT 20m R1


title: Zcchc8_KO3_MPP8_ChIPseq

city: Aarhus C

first: William

last: Garland

address: C.F. Møllers Allé 3

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

description: ChIP-seq

data_processing:
MPP8 ChIP-seq was performed in 2 batches, with each comprised 1 independent biological replicate of WT and Zcchc8-/- cells. Input samples were sequenced for WT of batch 1 (b1) and both WT and Zcchc8-/- for batch 2 (b2).
Raw reads were trimmed using Trim Galore to remove Illumina adaptors, low-quality bases with Phred score lower than 20, and reads shorter than 25 bp; reads were further trimmed using parameters --clip_R1 13 --clip_R2 13 --three_prime_clip_R1 1 --three_prime_clip_R2 1. Trimmed reads were mapped to mouse genome mm10, using bowtie2 with default settings.
genome build: mm10
processed data files format and content: For visualisation, the genomic coverage was calculated and normalised to library size using bamCoverage from deepTools (v2.5.3). Bigwig files were generated using bedGraphToBigwig function from UCSC tools (v357)

source_name: Embryonic stem cells

growth_protocol: ES cells were culturered on 0.2% gelatin coated plates in 2i/LIF containing medium

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes at RT before quenching with glycine. DNA was sheared to ~ 200 bp using a Bioruptor (Diagenode). ChIPs were carried out using using 300 µg of chromatin and 5 µg of MPP8 antibody (Proteintech, 16796-1-AP)
ChIPseq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (NEB) using AmpureXP beads (Beckman) for size selection.

tag: epap treatment

tag: chip antibody


title: GLOE HCT116 WT 20m R3

tag: cell type


title: GLOE HCT116 CAD-/- UT R2

tag: treatment


title: GLOE HCT116 WT UT R1


title: WT_2_input

description: ChIP-seq

value: Wildtype


title: GLOE HCT116 WT 24h R3


title: Zcchc8_KO2_MPP8_ChIPseq

description: ChIP-seq


title: GLOE HCT116 WT 20m R2


title: GLOE HCT116 WT UT R2


title: intratumoral CD14+  cell in patient 130 section 2

description:
130-iCD14-2
LCM_all_expression_tpm.tsv
LCM_all_expression_cnt.tsv


title: Zcchc8_KO3_input

description: ChIP-seq


title: WT_1_MPP8_ChIPseq

description: ChIP-seq


title: GLOE HCT116 WT 24h R2


title: WT_2_MPP8_ChIPseq

description: ChIP-seq


title: WT_1_input

description: ChIP-seq


title: Zfc3h1_KO_1_ESC_RNAseq

description:
Re-analysis of GSM4080125
Stranded RNA-seq

data_processing:
Raw reads were trimmed using Trim Galore to remove Illumina adaptors, low-quality bases with Phred score lower than 20, and reads shorter than 25 bp; reads were further trimmed using parameters --clip_R1 13 --clip_R2 13 --three_prime_clip_R1 1 --three_prime_clip_R2 1.
Trimmed reads were mapped to mouse genome mm10 using STAR (v2.7.3a) in which reads with maximum multiple alignment of no more than 100 were kept using parameters --winAnchorMultimapNmax 100 --outFilterMultimapNmax 100.
Mapped reads, overlapping with genes and TEs, were counted using TElocal (v0.1.0). For genes, GENCODE M22 annotation was used; and for TEs, the pre-built annotation provided by TElocal was used. Differential expression analysis was performed using edgeR with default parameters.
genome build: mm10
processed data files format and content: To generate visualisation, the strand specific genomic coverage was calculated and normalised to library size using bamCoverage from deepTools (v2.5.3). Bigwig files were generated using bedGraphToBigwig function from UCSC tools (v357)

extract_protocol:
Total RNA for RNA-seq was isolated using the RNeasy Mini Kit (Qiagen)
RNAseq libraries were prepared from 1 µg RNA using the TruSeq Stranded Total RNA library prep kit (Illumina) following rRNA depletion using Ribozero Gold (Illumina)


title: Zfc3h1_KO_2_ESC_RNAseq

description:
Re-analysis of GSM4080126
Stranded RNA-seq


title: RKO_siCtrl#1_3

city: Warsaw

first: Michal

last: Mikula

address: Roentgena 5

department: Experimental Oncology

country: Poland

institute: Maria Skłodowska-Curie National Research Institute of Oncology

data_processing:
torrent mapper, version 5.0.4
htseq-count, version 0.6.0, default parameters
DESeq2, version 1.18.1, normalization
removal of features with less then 10 counts based on the sum of normalized counts across all samples, removal of non-protein coding features
Genome_build: hg19
Supplementary_files_format_and_content: DESeq2 normalized count matrix

source_name: colorectal carcinoma RKO cell line

growth_protocol: Human colorectal carcinoma cell line RKO was obtained fom ATCC (Cat# CRL-2577). Cells were grown in EMEM medium (ATCC, 30-2003) supplemented according to ATCC recommendation with 10% (v/v) non-heat inactivated fetal bovine serum (FBS, Sigma-Aldrich, F7524). Cells were splited 1:8-1:10 twice a week. During the study, cells were regularly tested for mycoplasma and the identity of  RKO cell line was confirmed by short tandem repeat (STR) profiling performed by the ATCC Cell Authentication Service.

extract_protocol:
Total RNA was isolated with RNeasy Mini Kit (Qiagen) according to manufacturer protocol.
Library was prepared with the Ion AmpliSeq Transcriptome Human Gene Expression Panel (Thermo Fisher, USA)

treatment_protocol: 2x105 of RKO were seeded per well of 6-well plate. Next day, cells were transfected with siRNA using Lipofectamine RNAiMAX transfection reagent (ThermoFisher Scientific, 13778150) according the protocol provided by the manufacturer. Control cells were transfected with 30 nM of non-targeting siRNA siCtrl#1 or #2. For Tsg101 or Vps28 depletion 30 nM of siTsg101#1 or #2, or siVps28#1 or #2 was used. The following Pre-Design or Validated Ambion Silencer Select siRNAs (ThermoFisher Scientific) were applied: non-targeting siCtrl#1 (4390843), siCtrl#2 (4390846); on-target siTsg101#1 (s14439), siTsg101#2 (s14440), siVps28#1 (s27577), siVps28#2 (s27579). Cells were harvested 72 h after transfection.

value: RKO

tag: sirna

tag: batch


title: RKO_siVps28#1_3

tag: cell line


title: RKO_siVps28#2_3


title: RKO_siTsg101#1_3


title: RKO_siTsg101#2_3


title: Zcchc8_KO_3_ESC_RNAseq

description: Stranded RNA-seq


title: GLOE HCT116 WT 24h R1


title: RKO_siCtrl#2_3


title: RKO_siVps28#1_2


title: RKO_siTsg101#2_2


title: WT_3_ESC_RNAseq

description:
Re-analysis of GSM4080124
Stranded RNA-seq


title: GLOE HCT116 CAD-/- UT R1


title: Zcchc8_KO_2_ESC_RNAseq

description: Stranded RNA-seq


title: Zcchc8_KO_1_ESC_RNAseq

description: Stranded RNA-seq


title: RKO_siVps28#2_2


title: RKO_siTsg101#1_2


title: RKO_siCtrl#2_2


title: WT_2_ESC_RNAseq

description:
Re-analysis of GSM4080123
Stranded RNA-seq


title: RKO_siCtrl#1_2


title: WT_1_ESC_RNAseq

description:
Re-analysis of GSM4080122
Stranded RNA-seq


title: Zr2110-2

city: new haven

first: Yuping

last: Zhou

address: 310 cedar street

department: OB/GYN

institute: Yale

description:
901
CHH_result_table.xls
CHH_result_table.txt.gz

data_processing:
Library strategy: Methylation mini-Sequencing
Sequence reads from bisulfite-treated Methyl-MiniSeq® libraries were identified using standard Illumina base calling software and then raw FASTQ files were adapter, filled-in nucleotides, and quality trimmed using TrimGalore0.6.4.FastQC0.11.8 was used to assess the effect of trimming and overall quality distributions of the data. Alignment to the mm10 reference genome was performed using Bismark0.19.0. Methylated and unmethylated read totals for each CpG site were called using MethylDackel0.4.0. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. Fisher’s exact test was performed on each CpG, CHG and CHH site that has at least 5x coverage.10% difference in methylation value between groups and a p-value (unadjusted) of < 0.05 was used to identify significantly differentially methylated cytosines. Promoter, gene body, and CpG island annotations were added for each CpG included in the comparison where available.
Assembly: mm10
Supplementary files format and content: Excel, CSV and gz files for each Sample

source_name: Brain

growth_protocol: Eight-week-old CD-1 female mice were bred to male mice of the same strain and examined every 12 hours until the presence of a vaginal plug was detected. Detection of a vaginal plug was considered day 0.5 of pregnancy.

extract_protocol:
Mouse hippocampus and frontal cortexes were removed and DNA was extracted using the Quick-DNA Microprep Kit (Cat#D3020) from Zymo research
Samples were sent to Zymo Research to process and analyze using the Methyl-MiniSeq Full Service library preparation. Briefly, libraries were prepared from 200-500 ng of genomic DNA digested with 60 units of TaqαI and 30 units of MspI (NEB) sequentially and then extracted with Zymo Research (ZR) DNA Clean & Concentrator TM-5 kit (Cat#: D4003). Fragments were ligated to pre-annealed adapters containing 5’-methyl-cytosine instead of cytosine according to Illumina’s specified guidelines (www.illumina.com). Adaptor-ligated fragments of 150–250 bp and 250–350 bp in size were recovered from a 2.5% NuSieve 1:1 agarose gel (ZymocleanTM Gel DNA Recovery Kit, ZR Cat#: D4001). The fragments were then bisulfite-treated using the EZ DNA Methylation-Lightning TM Kit (ZR, Cat#: D5020). Preparative-scale PCR was performed and the resulting products were purified (DNA Clean & ConcentratorTM - ZR, Cat#D4005) for sequencing on an Illumina HiSeq. Sequence alignments and data analysis

treatment_protocol: Detection of a vaginal plug was considered day 0.5 of pregnancy.  Pregnant CD-1 mice were then housed individually and continuously treated with E3 (50µl of 0.46mg/ml in DMSO to approximate human exposure) or vehicle control (DMSO) via a mini-osmotic pump (Alzet model # 1002) beginning on Day 9 of gestation for 7 days.We began each experiment by treating pregnant mice with E3, and ended by analyzing their offspring.

tag: strain

tag: Sex

value: Female

value: vehicle control

tag: age

value: 8 weeks

tag: tissue

value: hippocampus

value: wild type


title: Zfc3h1_KO_3_ESC_RNAseq

description:
Re-analysis of GSM4080127
Stranded RNA-seq


title: Zr3002-2

description:
FCT14
FE311_vs_FCT14_CHG_top3000.xlsx
FE311_vs_FCT14.CHH.csv

value: frontal cortexes


title: BV2cells_PBS_24hr_rep1

description: CircRNA expression in pbs treated BV2 cells human blood for 24hr

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Mouse circRNA Arrays V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software limma package. The circRNAs that at least 3 out of 6 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses.

source_name: BV2 cells, pbs, 24hr, replicate 1

label_protocol: The enriched circular RNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

extract_protocol: The collected cells were used to extract the total RNA following the standard protocol, the RNA quantity and quality were tested through NanoDrop ND-1000 Spectrophotometer (Thermo, USA). RNA Integrity and gDNA contamination were tested by denaturing agarose gel electrophoresis. The total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circRNAs.

value: BV2 cells

value: PBS


title: Zr2110-1

description:
969
CHG_result_table.xls
CpG_result_table.xls
CHG_result_table.txt.gz
CpG_result_table.txt.gz

value: Estriol


title: RKO_siVps28#2_1


title: RNAseq_sgNSD1

city: Santiago de Compostela

first: Carmen

last: Rivas

address: Avda Barcelona

department: CIMUS

institute: Universidad de Santiago de Compostela

description: According to manufacturer's protocol

data_processing:
Raw ChIP sequencing reads were aligned using BWA version 0.7.17 with default parameters
Raw RNA sequencing reads were aligned using STAR version 2.5.3a with default parameters
Whole-Genome Bisulfite Sequencing (WGBS) raw reads were submitted to Bismark(version 0.22.3) for mapping and methylation calling, against mouse genome version mm10/GRCm38, discarding duplicate reads. Briefly, the methylation level at a CpG (similarly for CHH) site was the number of reads with that site methylated divided by the total number of reads covering the site. To ensure comparability of region DNA methylation levels across all samples, CpGs that overlapped with SNPs from dbSNPs or were located within the ENCODE blacklisted regions, termed DER (Duke excluded regions) were excluded and only CpGs covered by ≥ 5x in all samples were retained for the computation of DNA methylation levels. We defined the average methylation for a genomic region as the coverage-weighted mean of the methylation levels of the individual CpGs within the region.
Genome_build: mm10 and dm6 for mouse and drosophila data, respectively
Supplementary_files_format_and_content: bigWig, tdf

source_name: Mouse embryonic stem cells

growth_protocol: Mouse embryonic stem cells were maintained on gelatin-coated plates in Knockout DMEM (Gibco) supplemented with 15% ES-cell-qualified FBS (Gemini), 0.1 mM 2-mercapoethanol, 2mM L-glutamine (Life technologies) and LIF. Drosophila S2 cells were cultured in Schneider’s Drosophila Medium (Invitrogen) containing 10% heat-inactivated FBS.

extract_protocol:
RNA was extracted from 1M cell pelet using miRNeasy Mini Kit (QIAGEN) adding the DNase digest using Rnase-free Dnase Set (QIAGEN). RNA Integrity Number and concentration were determined by Agilent RNA Bioanalyzer Nano assay.
TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat

value: ESC line V6.5 1A

value: C57BL/6 x 129S4/SvJae F1 embryo-derived embryonic stem cells


title: BV2cells_IL4_24hr_rep3

description: CircRNA expression in IL-4 treated BV2 cells human blood for 24hr

source_name: BV2 cells, IL-4, 24hr, replicate 3


title: BV2cells_PBS_24hr_rep2

source_name: BV2 cells, pbs, 24hr, replicate 2


title: Zr3002-1

description:
FE311
FE311_vs_FCT14_CG_top3000.xlsx
FE311_vs_FCT14_CHH_top3000.xlsx
FE311_vs_FCT14.CG (1).csv
FE311_vs_FCT14.CHG.csv


title: BV2cells_IL4_24hr_rep1

source_name: BV2 cells, IL-4, 24hr, replicate 1


title: BV2cells_IL4_24hr_rep2

source_name: BV2 cells, IL-4, 24hr, replicate 2


title: RKO_siVps28#1_1

value: colorectal carcinoma


title: RKO_siTsg101#1_1


title: RNAseq_Parental

description: According to manufacturer's protocol

value: wild-type


title: BV2cells_PBS_24hr_rep3

source_name: BV2 cells, pbs, 24hr, replicate 3


title: H3K27me3_ChIP-seq_mESC_DNMT_TKO_rep2

description: According to manufacturer's protocol

growth_protocol: Cells were cultured in Knockout-DMEM (Gibco) with 15% ES qualified FBS (Gibco), ESGRO mouse LIF 1000U/mL (Millipore), 1X PenStrep (Invitrogen), 1X Glutamax (Invitrogen), 55µM b-merceptoethanol (Invitrogen), 1X non-essential amino acids (Invitrogen) and 1X Primocin (Invivogen). Cells were maintained at 37 °C and 5% CO2 on a layer of murine embryonic feeders (MEFs). Prior to collection for ChIP experiments, cells were passaged once on plates pretreated with 0.1% gelatin but without feeders. The day of collection, cells were washed with PBS followed by digestion with TrypLE 30% (for A1 lines) or trypsin 0.25% (for J1 lines) for 7 minutes at 37 °C. Trypsinizaton was terminated by addition of 1X SoyBean Trypsin inhibitor (for A1 lines) or of media (for J1 lines).

extract_protocol:
5 million cells per condition were collected by 300xg centrifugation and resuspended in 900µl 1X PBS at room temperature. Cells were fixed by the addition of 60µl of 16% fresh formaldehyde (1% final conc., Pierce) followed by an incubation of 10 minutes at room temperature, with rotation. The reaction was stopped by adding glycine 1M to a final concentration of 0.14M, followed by another incubation of 10 minutes at room temperature, with rotation. Cells were collected by centrifugation at 3000 rpm for 5 minutes at 4°C and washed once with 1X PBS. Aliquots of 1 million cells were flash frozen and stored at -80°C. To lyse the cells for ChIP, cells were thawed and resuspended with 1mL of lysis buffer 1 (10mM Tris-HCl pH 8.0, 0.25% Triton X-100, 10mM EDTA, 0.5mM EGTA, 1x Protease inhibitors, and 1mM PMSF), then incubated with rotation for 15 minutes at room temperature. Nuclei were pelleted by centrifugation at 1465 g for 5 minutes at 4°C. Nuclei were then resuspended with 1mL of lysis buffer 2 (10mM Tris-HCl pH 8.0, 200mM NaCl, 10mM EDTA, 0.5mM EGTA, 1x Protease inhibitors, and 1mM PMSF), then incubated with rotation for 10 minutes at 4°C. Nuclei were pelleted by centrifugation at 1465 g for 5 minutes at 4°C. Nuclei were then resuspended in 900uL of lysis buffer 3 (10mM Tris-HCl pH 8.0, 10mM EDTA, 0.5mM EGTA, 0.1% SDS, 1x Protease inhibitors, and 1mM PMSF) and sonicated in a Covaris M220 instrument (PIP = 75; CPB = 200; Duty Factor = 20%; Time = 10 minutes; Setpoint temperature = 7°C) using a 1mL AFA Fiber milliTube (Covaris). The sonicated lysate was centrifuged at max. speed for 10 minutes at 4°C, and the supernatant was retained.    30uL of Protein A Dynabeads (Invitrogen 10001D) were washed three times with ChIP dilution buffer (16.7mM Tris-HCl pH 8.0, 0.01% SDS, 1.1% Triton X-100, 1.2mM EDTA, and 167mM NaCl), each wash consisting of addition of 1mL of buffer and collection of the beads on a magnetic rack. The 30uL beads were then resuspended in 900uL of dilution buffer and combined with the ChIP sample to pre-clear the sample. Beads and chromatin were incubated with rotation for 2 hours at 4°C. Beads were then collected on a magnetic rack and the supernatant was retained.     2uL of SNAP-ChIP K-MetStat panel (EpiCypher, 19-1001) was added to the sample chromatin.  SNAP-ChIP K-MetStats are barcoded recombinant nucleosomes bearing distinct methyl-lysine modifications and was used as spike-in controls for ChIP reactions. 1% of the sample was saved as Input, the rest was used for ChIP. 2uL of antibody (Cell Signaling; anti-H3K27me3 (9733S), (Cell Singaling; anti-H3K36me2 (2901S)) was added to the ChIP sample. The samples were then rotated overnight at 4°C.    60uL of Protein A Dynabeads were washed three times with 1mL of ChIP dilution buffer and resuspended in 60uLof dilution buffer. Beads were then added to the ChIP sample and rotated for 2 hours at 4°C. The beads were then washed twice with Wash buffer A (50mM HEPES pH 7.9, 1% Triton X-100, 0.1% Deoxycholate, 1mM EDTA, and 140mM NaCl), with Wash buffer B (50mM HEPES pH 7.9, 0.1% SDS, 1% Triton X-100, 0.1% Deoxycholate, 1mM EDTA, and 500mM NaCl), and with TE buffer (10mM TrisHCl pH 8.0, 1mM EDTA). Each wash consists of resuspension in 500μL buffer and rotation for 4 minutes, followed by collection of beads and removal of supernatant.     DNA was eluted in 100μL elution buffer (50mM TrisHCl pH 8.0, 1mM EDTA, and 1% SDS) at 65°C for 10 minutes shaking at 1400RPM on orbital shaker. The eluent was collected and the beads were subjected to a second round of elution with 150μL elution buffer. The ChIP eluants were pooled, and the input sample was diluted to 250μL with elution buffer. These samples were incubated at 65°C overnight to promote decrosslinking. The samples were then allowed to cool to room temperature, 15μg of RNAse A (PureLink, Invitrogen) was added, and the samples were incubated at 37°C for 30 minutes to degrade RNA. 100μg Proteinase K was then added and the samples were incubated at 56°C for two hours. DNA was purified using a MinElute PCR Purification kit (Qiagen).  DNA was sonicated again to 150bp average fragment size with a Covaris M220 instrument (PIP = 75; CPB = 200; Duty Factor = 20%; Time = 10 minutes; Setpoint temperature = 20°C) and libraries were generated using the Accel-NGS 2S Plus DNA Library Kit (Swift).
Accel-NGS 2S Plus DNA Library Kit

value: H3K27me3 (Cell Signaling Technologies #9733)

value: ESC line J1

value: 129S4/SvJa embryo-derived embryonic stem cells


title: RKO_siTsg101#2_1

value: RKO


title: RKO_siCtrl#2_1


title: RKO_siCtrl#1_1


title: 3230__WT-TLR-1

city: Charleston

first: Melissa

last: Cunningham

state: SC

address: 96 Jonathan Lucas Street

institute: Medical University of South Carolina

description: Raw data files were corrupted thus there are no raw data available for this sample.

data_processing:
Illumina Casava1.8 software used for base calling
Reads were trimmed using cutadapt. Quality scores were assessed using FastQC. Reads were aligned to the Mus musculus genome build mm10 using STAR.
Individual sample reads were quantified using HTseq and normalized via Relative Log Expression (RLE) using DESeq2 R library.
Assembly: mm10
Supplementary files format and content: Matrix table with raw abundance values for every gene and every sample

source_name: WT-Treat / WT.TLR

extract_protocol:
Bone marrow (BM) was flushed from the femurs and tibias of mice, dissociated through a 70μm strainer, and depleted of red blood cells using red blood cell lysis buffer (144mM NH4Cl and 17M Tris, pH 7.6). Cells were spun immediately (3min low speed spin) and resuspended in cold PBS. To generate bone marrow-derived dendritic cells (BM-DC) for RNA-seq, total BM was plated at a concentration of 1.5x106 cells/ml in RPMI 1640 media containing 10% FBS, 1% penicillin/streptomycin/ampicillin, and L-glutamine with 20 ng/ml GM-CSF and 10 ng/ml IL-4. Media and cytokines were replenished on day 3 and BM-DCs were harvested on day 7, and washed with PBS prior to staining.
RNA-Seq libraries were prepared using the TruSeq RNA Sample Prep Kit (Illumina, CA, USA), following the protocol described by the manufacturer. Paired-end RNA sequencing was performed using an Illumina HiSeq2500 in the MUSC Center for Genomic Medicine (CGM), with each sample sequenced to a minimum depth of ∼50 million reads.

treatment_protocol:
surgery protocol: ovariectomized (OVX) pre-disease at 4-8 weeks of age (peri-puberty) in order to combat hypergonadism (high testosterone, high estrogen) that results from loss of normal endocrine feedback. subsequently received 0.25 mg, 90-day sustained release 17β-estradiol pellet (Innovative Research of America, Sarasota, FL, USA) implanted sub-dermally to replete physiologic E2 levels.
Experimental triplicates were treated with vehicle or loxoribine (200 μmol/ml), a TLR7 agonist, and CpG (1 μg/ml), a TLR9 agonist (Invivogen, San Diego, CA) for 24 hours

tag: cell tpye

value: bone marrow-derived dendritic cells

value: NZM2410 mice

value: WT

tag: surgery

value: no surgery

value: treated


title: 3232__WT-TLR-2


title: H3K36me2_ChIP-seq_mESC_DNMT_TKO_rep2

description: According to manufacturer's protocol

value: H3K36me2 (Cell Signaling Technologies #2901)


title: H3K27me3_ChIP-seq_mESC_EZH2_KO

description: According to manufacturer's protocol


title: 3228__WT-phi-2

source_name: WT-Control / WT.phi

value: untreated


title: PMBC_FastRebound_week10_B14

type: genomic

first: IJC

last: Bioinformatics

state: Catalonia

address: Josep Carreras Building, Ctra de Can Ruti, Camí de les Escoles, s/n

institute: Josep Carreras Leukemia Research Institute

description:
200999740145_R06C02_Red.idat
200999740145_R06C02_Grn.idat
BCN02 clinical trial
Sample_117

hyb_protocol: Genomic DNA was bisulfite converted using EZ DNA Methylation Kit (Zymo) following manufacturer’s protocol. 4uL of bisulfite-converted DNA were hybridized to Infinium HumanMethylationEPIC BeadChip following Illumina Infinium HD Methylation protocol

scan_protocol: Chip analysis was performed using Illumina HiScan SQ fluorescent scanner and the intensities of the images were extracted using GenomeStudio (2010.3) Methylation module (1.8.5) software

data_processing: Quality control, background correction and quantile normalization across arrays was performed using ChAMP R/Bioconductor package with functions extracted from Minfi R/Bioconductor package

label: Cy5 and Cy3

label_protocol: Standard Illumina labelling protocol.

extract_protocol: DNA and RNA were isolated simultaneously from the same sample using AllPrep DNA/RNA Mini Kit (Qiagen) and were frozen until use.

treatment_protocol: Blood samples were processed using Lymphoprep (STEMCELL technologies) and 2M dry pelleted PBMCs were frozen until use

value: PBMC

tag: rebound

value: Fast

tag: time

tag: individual

value: male


title: 3226__WT-phi-1

description: The raw data were originally paired-end but the R2 file was corrupted and not included. Only R1 is available.

tag: genotype


title: H3K27me3_ChIP-seq_mESC_NSD1_KO

description: According to manufacturer's protocol

value: ESC line V6.5 1A

value: C57BL/6 x 129S4/SvJae F1 embryo-derived embryonic stem cells


title: PMBC_FastRebound_week0_B14

description:
200999740145_R03C02_Red.idat
200999740145_R03C02_Grn.idat
BCN02 clinical trial
Sample_114


title: PMBC_LateRebound_week1_B13

description:
200999740145_R06C01_Red.idat
200999740145_R06C01_Grn.idat
BCN02 clinical trial
Sample_107

value: Late


title: PMBC_FastRebound_week1_B14

description:
200999740145_R04C02_Red.idat
200999740145_R04C02_Grn.idat
BCN02 clinical trial
Sample_115


title: H3K36me2_ChIP-seq_mESC_NSD1_KO

description: According to manufacturer's protocol


title: H3K36me2_ChIP-seq_mESC_EZH2_KO

description: According to manufacturer's protocol


title: PMBC_FastRebound_week6_B14

description:
200999740145_R05C02_Red.idat
200999740145_R05C02_Grn.idat
BCN02 clinical trial
Sample_116


title: H3K27me3_ChIP-seq_mESC_WT_J1

description: According to manufacturer's protocol

value: H3K27me3 (Cell Signaling Technologies #9733)

value: wild-type


title: PMBC_LateRebound_week10_B13

description:
200999740145_R02C02_Red.idat
200999740145_R02C02_Grn.idat
BCN02 clinical trial
Sample_109


title: PMBC_LateRebound_week0_B13

description:
200999740145_R05C01_Red.idat
200999740145_R05C01_Grn.idat
BCN02 clinical trial
Sample_106


title: PMBC_LateRebound_week6_B13

description:
200999740145_R01C02_Red.idat
200999740145_R01C02_Grn.idat
BCN02 clinical trial
Sample_108


title: 3229__KO-TLR-1

description: these express a truncated form of Eralpha (Eralpha short) and have residual estrogen responsivity

source_name: ERKO (ERKO Shrt) Treat / KO.TLR

value: Esr1(tm1Ksk) allele


title: 3231__KO-TLR-2

description:
these express a truncated form of Eralpha (Eralpha short) and have residual estrogen responsivity
The raw data were originally paired-end but the R1 file was corrupted and not included. Only R2 is available.


title: 3227__KO-phi-2

description:
these have no tissue responses to estrogen or estrogen resceptor alpha activity
The raw data were originally paired-end but the R1 file was corrupted and not included. Only R2 is available.

source_name: ERKO (ERKO Shrt) Control / KO.phi

value: Esr1(tm4.2Ksk) allele


title: PMBC_FastRebound_week10_B10

description:
200999740145_R04C01_Red.idat
200999740145_R04C01_Grn.idat
BCN02 clinical trial
Sample_101


title: H3K36me2_ChIP-seq_mESC_WT_J1

description: According to manufacturer's protocol

value: ESC line J1

value: 129S4/SvJa embryo-derived embryonic stem cells


title: 3225__KO-phi-1

description: these have no tissue responses to estrogen or estrogen resceptor alpha activity

value: bone marrow-derived dendritic cells

value: NZM2410 mice


title: PMBC_LateRebound_week10_A09

description:
200999740180_R02C02_Red.idat
200999740180_R02C02_Grn.idat
BCN02 clinical trial
Sample_29


title: PMBC_FastRebound_week10_B07

description:
200999740180_R06C02_Red.idat
200999740180_R06C02_Grn.idat
BCN02 clinical trial
Sample_93


title: H3K27me3_ChIP-seq_mESC_WT_A1

description: According to manufacturer's protocol


title: PMBC_FastRebound_week10_B05

description:
200999740180_R05C02_Red.idat
200999740180_R05C02_Grn.idat
BCN02 clinical trial
Sample_77


title: 3224__Ex3a-tLr2

source_name: Ex3a (ERKO NULL OVX) -Treat / Ex3a.tLr

value: surgery

value: treated


title: PMBC_FastRebound_week0_B10

description:
200999740145_R01C01_Red.idat
200999740145_R01C01_Grn.idat
BCN02 clinical trial
Sample_98


title: PMBC_FastRebound_week10_A13

description:
200999740180_R03C02_Red.idat
200999740180_R03C02_Grn.idat
BCN02 clinical trial
Sample_45


title: 3223__Ex3a-tLr1


title: PMBC_FastRebound_week1_B10

description:
200999740145_R02C01_Red.idat
200999740145_R02C01_Grn.idat
BCN02 clinical trial
Sample_99


title: LNCaP_YAP-FOSL1-Rep2

first: Ekta

last: Khurana

address: 1305 York Ave

institute: Weill Cornell Medicine

data_processing:
The raw data were processed with the ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline)
bigwig files were generated using bamCoverage from Deeptools (PMID: 27079975)
Assembly: GRCh37.p13
Supplementary files format and content: bigwig

source_name: prostate cancer cell line

growth_protocol: LNCaP prostate cancer cells (ATCC CRL-1740) were maintained in RPMI medium supplemented with 10% fetal bovine serum and 1% pen/strep.

extract_protocol: The libraries were generated using the OMNI-ATAC protocol (PMID: 28846090), and the final library was purified with AMPure beads (Beckman Coulter, A63880).

treatment_protocol: LNCaP cells were transduced with retroviruses to stably express FOSL1, YAP, YAP/FOSL1, TAZ, or TAZ/FOSL1.

value: LNCaP

tag: primary site

value: Prostate

tag: overexpressed gene

value: YAP and FOSL1

tag: replicate


title: H3K36me2_ChIP-seq_mESC_WT_A1

description: According to manufacturer's protocol

tag: chip antibody

value: H3K36me2 (Cell Signaling Technologies #2901)

tag: cell type


title: PMBC_FastRebound_week6_A15

description:
200999740180_R04C01_Red.idat
200999740180_R04C01_Grn.idat
BCN02 clinical trial
Sample_60

value: PBMC

value: Fast

value: male


title: PMBC_FastRebound_week6_B05

description:
200999740180_R05C01_Red.idat
200999740180_R05C01_Grn.idat
BCN02 clinical trial
Sample_76


title: LNCaP_YAP-FOSL1-Rep1


title: PMBC_FastRebound_week10_A15

description:
200999740180_R04C02_Red.idat
200999740180_R04C02_Grn.idat
BCN02 clinical trial
Sample_61


title: PMBC_FastRebound_week10_A04

description:
200999740180_R01C02_Red.idat
200999740180_R01C02_Grn.idat
BCN02 clinical trial
Sample_13


title: 3221__Ex3a-Ctl1

source_name: Ex3a (ERKO NULL OVX) - Control / Ex3a.Ctl

tag: treatment

value: untreated


title: LNCaP_YAP-Rep2

tag: cell line

value: YAP


title: 3222__Ex3a-Ctl2

tag: strain

value: Esr1(tm1Ksk) allele


title: PMBC_FastRebound_week6_B07

description:
200999740180_R06C01_Red.idat
200999740180_R06C01_Grn.idat
BCN02 clinical trial
Sample_92

tag: Sex


title: PMBC_FastRebound_week6_B10

description:
200999740145_R03C01_Red.idat
200999740145_R03C01_Grn.idat
BCN02 clinical trial
Sample_100

tag: age


title: LNCaP_YAP-Rep1


title: PMBC_FastRebound_week1_B07

description:
200999740160_R06C02_Red.idat
200999740160_R06C02_Grn.idat
BCN02 clinical trial
Sample_91


title: 3220__Erko-Ctl2

source_name: ERKO (ERKO Shrt OVX) Control / Erko.Ctl

value: Esr1(tm4.2Ksk) allele


title: LNCaP_TAZ-FOSL1-Rep2

value: TAZ and FOSL1


title: 3218__Erko-cp6-lox2

description:
these express a truncated form of Eralpha (Eralpha short) and have residual estrogen responsivity
The raw data were originally paired-end but the R2 file was corrupted and not included. Only R1 is available.

source_name: ERKO (ERKO Shrt OVX) Treat / Erko.cp6.lox


title: PMBC_FastRebound_week1_A15

description:
200999740160_R04C02_Red.idat
200999740160_R04C02_Grn.idat
BCN02 clinical trial
Sample_59


title: LNCaP_TAZ-FOSL1-Rep1


title: PMBC_FastRebound_week6_A13

description:
200999740180_R03C01_Red.idat
200999740180_R03C01_Grn.idat
BCN02 clinical trial
Sample_44


title: PMBC_FastRebound_week0_B07

description:
200999740160_R06C01_Red.idat
200999740160_R06C01_Grn.idat
BCN02 clinical trial
Sample_90


title: LNCaP_TAZ-Rep2

value: TAZ


title: 3217__Erko-cp6-lox1

description: these express a truncated form of Eralpha (Eralpha short) and have residual estrogen responsivity

value: bone marrow-derived dendritic cells


title: PMBC_FastRebound_week6_A04

description:
200999740180_R01C01_Red.idat
200999740180_R01C01_Grn.idat
BCN02 clinical trial
Sample_12


title: PMBC_LateRebound_week1_A09

description:
200999740160_R02C02_Red.idat
200999740160_R02C02_Grn.idat
BCN02 clinical trial
Sample_27

value: Late


title: 3219__Erko-Ctl1

description: these have no tissue responses to estrogen or estrogen resceptor alpha activity

value: NZM2410 mice

value: surgery


title: LNCaP_TAZ-Rep1

value: LNCaP


title: mutant_RNAseq_Rep2

city: Iowa City

first: Eric

last: Van Otterloo

state: Iowa

address: 801 Newton Rd

institute: University of Iowa

data_processing:
Raw sequencing reads were demultiplexed and fastq files subsequently processed, as previously described (Van Otterloo et al., 2018). Briefly, reads were trimmed using the Java software package Trim Galore! (Babraham Bioinformatics, Babraham Institute, Cambridge, UK) and subsequently mapped to the Mm10 genome using the HISAT2 software package (Pertea, Kim, Pertea, Leek, & Salzberg, 2016) (both with default settings). Following mapping, RNA expression levels were generated using StringTie (Pertea et al., 2016) and differential expression computed between genotypes using CuffDiff2 (Trapnell et al., 2012), with a significance cut-off value of Q<0.05 (FDR-corrected P-value).
Assembly: Mm10

source_name: E10.5 facial prominences

extract_protocol: RNA-sequencing:   For RNA-sequencing E10.5 facial prominences encompassing ectoderm and mesenchyme of the mandibular, maxillary, and nasal prominences were micro-dissected in ice cold PBS using insulin syringes and stored in RNA-later at -20°C.  Once sufficient EDKO (Crect; Tfap2aflox/null; Tfap2bflox/null) and control littermate samples lacking Crect (e.g. Tfap2aflox/+; Tfap2bflox/+) were identified for 3 biological replicates of each, tissue was removed from RNA-later and RNA harvested as previously described using the microRNA Purification Kit (Norgen Biotek) and following manufacturer's protocol (Van Otterloo et al., 2018).  Following elution, mRNA was further purified using the Qiagen RNAeasy Kit according to the manufacturer's protocol. The quality of extracted mRNA was assessed using DNA Analysis ScreenTape (Agilent Technologies) prior to library production. Following validation of extracted mRNA, cDNA libraries were generated using the Illumina TruSeq Stranded mRNA Sample Prep Kit. All libraries passed quality control guidelines and were then sequenced using the Illumina HiSeq2500 platform and single-end reads (1×150) to a depth of ~15-25x106 reads per sample. To identify differentially expressed genes between control and mutant groups, we next utilized a standard bioinformatic pipeline for read filtering, mapping, gene expression quantification, and differential expression between groups (see below). Library construction and sequencing was carried out by the University of Colorado, Anschutz Medical Campus, Genomics and Microarray Core.

tag: Stage

value: embryonic day 10.5


title: mutant_RNAseq_Rep3


title: PMBC_FastRebound_week0_A13

city: Badalona

description:
200999740160_R03C01_Red.idat
200999740160_R03C01_Grn.idat
BCN02 clinical trial
Sample_42


title: PMBC_LateRebound_week6_A09

description:
200999740180_R02C01_Red.idat
200999740180_R02C01_Grn.idat
BCN02 clinical trial
Sample_28


title: wt-GMP 2

city: Copenhagen

first: Kim

last: Theilgaard-Mönch

address: Ole Maaløes Vej 5

institute: Rigshospitalet/National Univ. Hospital and Biotech Research and Innovation Centre

description: Granulocyte-Monocyte Progenitor (GMP)

hyb_protocol: The arrays were washed and stained with phycoerytrin conjugated streptavidin using the Affymetrix/ThermoFisher Fluidics Station 450, and the arrays were scanned in the Affymetrix GeneArray 3000 7G scanner to generate fluorescent images

scan_protocol: Cell intensity files (.CEL files) were generated in the GeneChip Command Console Software (AGCC; Affymetrix).

data_processing: As described in Reckzeh et al. 2020, TET2 deficiency cooperates with CBFB-MYH11 to induce acute myeloid leukemia and represents an early leukemogenic event.

source_name: Bone marrow

label_protocol: Purified RNA was analyzed on expression arrays. RNA was processed using Mouse Gene 1.0 ST Reagent Kit. RNA was reverse transcribed and used for cRNA synthesis, labelling and hybridization with Mouse Gene 1.0 ST Array (ThermoFisher) according to the manufacturer’s protocol.

growth_protocol: FACs-sorted GMPs from freshly isolated BM cells

extract_protocol: RNA was extracted from 200000 sorted GMPs using miRNeasy KIT (Qiagen) according to the manufacturer's instructions

value: WT C57BL6

value: granulocyte macrophage progenitor (GMP) cells

tag: cell markers

value: Lin- IL7R- Sca1- ckit+ FcgRhiCD34+


title: PMBC_LateRebound_week0_A09

description:
200999740160_R02C01_Red.idat
200999740160_R02C01_Grn.idat
BCN02 clinical trial
Sample_26

value: PBMC


title: PMBC_FastRebound_week1_A13

description:
200999740160_R03C02_Red.idat
200999740160_R03C02_Grn.idat
BCN02 clinical trial
Sample_43

value: Fast

value: male


title: LNCaP_FOSL1-Rep2

value: Prostate


title: LNCaP_EV-Rep2

value: Empty Vector


title: PMBC_FastRebound_week1_B05

description:
200999740160_R05C02_Red.idat
200999740160_R05C02_Grn.idat
BCN02 clinical trial
Sample_75


title: PMBC_FastRebound_week6_B06

description:
200999740179_R06C01_Red.idat
200999740179_R06C01_Grn.idat
BCN02 clinical trial
Sample_84


title: control_RNAseq_Rep3

value: control


title: mutant_RNAseq_Rep1


title: PMBC_FastRebound_week10_B06

description:
200999740179_R06C02_Red.idat
200999740179_R06C02_Grn.idat
BCN02 clinical trial
Sample_85


title: PMBC_FastRebound_week0_A04

description:
200999740160_R01C01_Red.idat
200999740160_R01C01_Grn.idat
BCN02 clinical trial
Sample_10


title: wt-GMP 1

description: Granulocyte-Monocyte Progenitor (GMP)


title: PMBC_FastRebound_week0_B05

description:
200999740160_R05C01_Red.idat
200999740160_R05C01_Grn.idat
BCN02 clinical trial
Sample_74


title: wt-GMP 3

description: Granulocyte-Monocyte Progenitor (GMP)


title: LNCaP_FOSL1-Rep1


title: PMBC_LateRebound_week6_A02

description:
200999740179_R01C01_Red.idat
200999740179_R01C01_Grn.idat
BCN02 clinical trial
Sample_4


title: control_RNAseq_Rep2


title: inv(16):TET2ko L-GMP 3

description: Granulocyte-Monocyte Progenitor (GMP)

value: Lin- Sca1- ckit+ CD41- FcgR+ CD150-


title: PMBC_FastRebound_week0_A15

description:
200999740160_R04C01_Red.idat
200999740160_R04C01_Grn.idat
BCN02 clinical trial
Sample_58


title: PMBC_FastRebound_week10_A12

description:
200999740179_R03C02_Red.idat
200999740179_R03C02_Grn.idat
BCN02 clinical trial
Sample_37


title: PMBC_LateRebound_week10_B03

description:
200999740179_R05C02_Red.idat
200999740179_R05C02_Grn.idat
BCN02 clinical trial
Sample_69


title: C3KO MT 3

city: Toledo

first: Jennifer

middle: M

last: Peterson

state: OH

address: 2801 W Bancroft St

department: SERS

institute: The University of Toledo

description: replicate 3

data_processing:
data were extracted using Genome Studio (software provided by Illumina), with no background subtraction, then normalized using the “quantiles” function.
Processed data are available only as fold-change values.

source_name: Differentiated myotubes

label_protocol: Biotinylated cRNA were prepared from 250 ng of total RNA using an Illumina Totalprep RNA amplification kit according to manufacturer’s protocol.

growth_protocol: Conditionally immortalized control C57BL/6 and Capn3-deficient myoblast clones contain a temperature-sensitive immortalizing gene, the tsA58 mutation of the SV40 large T antigen, under the control of the H-2Kb inducible promoter. When induced with interferon-gamma (IFN-γ), the tsA58 protein is expressed, allowing the cells to proliferate at 33 °C. Myoblasts were plated and maintained on gelatin-coated dishes (0.01% gelatin) in H2KPM at 33 °C and 10% CO2 in a humidified incubator. Cultures were fed every 2–3 days with H2KPM, and fresh IFN-γ (20 U/ml) was added to the culture medium at each feeding. Cells were grown to near confluence, harvested with trypsin/EDTA (0.5/0.2 g/l), and centrifuged at 800g for 3 min. Under these conditions, the cells doubled every 24–30 h at 33 °C and fused with > 50% efficiency into multinucleated sarcomeric tropomyosin-positive muscle fibers when switched to 37 °C in the absence of IFN-γ.

extract_protocol: RNA was extracted with TRIzol Reagent followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

value: Differentiated myotubes

value: Calpain-3 deficient


title: PCa3_siYAPTAZ_1

growth_protocol: MSK-PCa3 prostate cancer organoid cells were maintained in human organoid media as described previously (PMID: 25201529, 26797458).

treatment_protocol: MSK-PCa3 cells were transfected with a pooled ON-TARGETplus siRNAs targeting FOSL1, YAP, TAZ, or YAP/TAZ (Dharmacon) using RNAiMAX (Thermo Fisher Scientific #13778075) for 48 hours

tag: knockdown

value: TAZ/YAP


title: inv(16):TET2ko L-GMP 2

description: Granulocyte-Monocyte Progenitor (GMP)


title: PMBC_LateRebound_week10_A05

description:
200999740179_R02C02_Red.idat
200999740179_R02C02_Grn.idat
BCN02 clinical trial
Sample_21

tag: rebound

value: Late


title: PMBC_FastRebound_week1_A04

description:
200999740160_R01C02_Red.idat
200999740160_R01C02_Grn.idat
BCN02 clinical trial
Sample_11

tag: time


title: PCa3_siYAP_2

value: YAP


title: C3KO MT 2

description: replicate 2


title: PCa3_siYAPTAZ_2


title: NC_1

city: Taigu

first: Lijun

last: Zhao

state: Shanxi

address: No. 1 Mingxian South Road,Taigu,  Shanxi Province, China

department: College of Veterinary Medicine

institute: Shanxi Agricultural University

data_processing:
Raw data processing and quality control.
The filtered Reads were compared to the reference genome using HISAT2 software.
Comparison results quality control:
Expression analysis:HTSeq statistics were used to compare the Read Count value of each gene as the original expression amount of the gene.
Expression difference analysis:using DESeq for differences in gene expression analysis, screening of differentially expressed genes conditions as follows: multiple expression differences | log2FoldChange | >1, significance p-value<0.05.
Assembly: mm9
Supplementary files format and content: Format:txt
Supplementary files format and content: rawdata_info.txt：Raw data statistics for sequencing.
Supplementary files format and content: cleandata_info.txt:The sequencing data were further filtered.
Supplementary files format and content: expression.txt:The expression levels of different gene types in annotated files of the genome were counted.
Supplementary files format and content: origin.txt：Results of differential expression analysis were obtained.

source_name: keratinocyte

growth_protocol: PAM212 cells and miR-28-3p overexpression PAM212 were cultured in medium DMEM +10%FBS.

extract_protocol:
PAM212 cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: miR-28-3p-overexpression PAM212 cells were that \ were infected with lentivirus including mice miR-28-3p gene.

value: not treated


title: LNCaP_EV-Rep1

city: New York

value: LNCaP


title: PMBC_FastRebound_week1_B06

description:
200999740198_R06C02_Red.idat
200999740198_R06C02_Grn.idat
BCN02 clinical trial
Sample_83

tag: individual


title: PMBC_LateRebound_week6_B03

description:
200999740179_R05C01_Red.idat
200999740179_R05C01_Grn.idat
BCN02 clinical trial
Sample_68


title: PMBC_FastRebound_week6_A12

description:
200999740179_R03C01_Red.idat
200999740179_R03C01_Grn.idat
BCN02 clinical trial
Sample_36


title: PMBC_LateRebound_week1_B03

description:
200999740198_R05C02_Red.idat
200999740198_R05C02_Grn.idat
BCN02 clinical trial
Sample_67


title: PMBC_LateRebound_week6_A05

description:
200999740179_R02C01_Red.idat
200999740179_R02C01_Grn.idat
BCN02 clinical trial
Sample_20


title: NC_2


title: control_RNAseq_Rep1

tag: genotype

value: embryonic day 10.5


title: PMBC_LateRebound_week10_A02

description:
200999740179_R01C02_Red.idat
200999740179_R01C02_Grn.idat
BCN02 clinical trial
Sample_5


title: PCa3_siTAZ_1

tag: primary site

value: TAZ


title: miR28_2

value: overexpression miR-28-3p


title: inv(16):TET2ko L-GMP 1

description: Granulocyte-Monocyte Progenitor (GMP)

value: granulocyte macrophage progenitor (GMP) cells


title: WT MT 2

description: replicate 2

value: wild type


title: miR28_3


title: PCa3_siFOSL1_2


title: NC_3


title: WT_72h_3

city: Beijing

first: Fuliang

last: Zong

state: China

address: Feitai region Dongda road

institute: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology

description: treated with ricin

data_processing:
removing reads containing the sequencing adapter
removing reads with >15% low-quality base ratio (base quality ≤5)
removing reads whose unknown base ('N' base) ratio was >5%.
Clean reads were mapped to the reference genome using HISAT2 (v2.1.0). Bowtie2 (v2.2.3) was applied to align the clean reads to the reference coding gene set.
Assembly: mm9
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung tissue cells

extract_protocol:
RNAprep Pure Tissue Kit
using NovaSeq 6000 S4 Reagent kit V1.5

treatment_protocol: The ricin dose was 1.5*LD50.

tag: tissue

value: lung

value: female

value: treated with ricin

tag: time (h)


title: PCa3_siTAZ_2

value: Prostate

tag: replicate


title: C3KO MB 3

description: replicate 3

data_processing:
data were extracted using Genome Studio (software provided by Illumina), with no background subtraction, then normalized using the “quantiles” function.
Processed data are available only as fold-change values and p-values.

source_name: Prolfierating myoblasts

tag: cell type

value: myoblasts


title: MMP13KO rep6 (S6)

city: Dublin

first: Henry

middle: Fergus

last: Duncan

address: Lincoln Place

department: Restorative Dentistry

country: Ireland

institute: Dublin Dental University Hospital, Trinity College Dublin

description: MMP13KO rep6 (S6)

data_processing:
StrandNGS 4.0 (Strand Life Sciences, Bengaluru, India) software used for basecalling.
StrandNGS assessed for quality in Stand-NGS, before the reads were thereafter trimmed to remove adapter sequences, the software mapped to mm10 whole genome using v4.0 Strand NGS with parameters
Prior to differential expression analysis the RNAseq sample results was normalised using DEseq
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw and noarmalised gene counts for every gene and all 6 samples

source_name: dental pulp tissue

growth_protocol: 3 month old WT andMMP13KO mouse molars, teteh extracted and dental pulp tissue removed

extract_protocol:
Total RNA was extracted using the RNeasy mini kit (Qiagen, West Sussex, UK). mRNA was isolated on the RNAeasy mini-column  assembly (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: dental pulp


title: WT MT 3

description: replicate 3

value: Differentiated myotubes


title: PCa3_siFOSL1_1


title: PMBC_LateRebound_week0_A05

description:
200999740198_R02C01_Red.idat
200999740198_R02C01_Grn.idat
BCN02 clinical trial
Sample_18

value: PBMC

value: male


title: MMP13KO rep1 (S1)

description: MMP13KO rep1 (S1)


title: PCa3_sictrl_1

value: control


title: WT_72h_2

description: treated with ricin

tag: treatment


title: C3KO MB 2

description: replicate 2

value: Calpain-3 deficient


title: PCa3_sictrl_2


title: PCa3_siYAP_1

value: YAP


title: Molar WT rep5 (S5)

description: Molar WT rep5 (S5)

value: WT


title: C3KO MT 1

description: replicate 1


title: WT_72h_1

description: treated with ricin


title: C3KO MB 1

description: replicate 1


title: WT MB 3

description: replicate 3


title: WT MT 1

description: replicate 1


title: PMBC_FastRebound_week0_B06

description:
200999740198_R06C01_Red.idat
200999740198_R06C01_Grn.idat
BCN02 clinical trial
Sample_82

value: Fast


title: DU145_YAP_TAZ

growth_protocol: DU145 cells were maintained in human organoid media as described previously (PMID: 25201529, 26797458).

treatment_protocol: DU145 cells were transfected with a pooled ON-TARGETplus siRNAs targeting YAP, TAZ, or YAP/TAZ (Dharmacon) using RNAiMAX (Thermo Fisher Scientific #13778075) for 48 hours

value: YAP/TAZ

value: merged


title: PMBC_LateRebound_week1_A02

description:
200999740198_R01C02_Red.idat
200999740198_R01C02_Grn.idat
BCN02 clinical trial
Sample_3

value: Late


title: Molar WT rep2 (S2)

description: Molar WT rep2 (S2)


title: KO_72h_3

description: treated with ricin

value: lung


title: KO_72h_2

description: treated with ricin

value: female


title: DU145_scr

value: Scrambled


title: WT_12h_1

description: treated with ricin

value: treated with ricin

value: wild type


title: H3K27ac_ChIP-seq_mESC_sgNSD1

description: According to manufacturer's protocol

organism:
Drosophila melanogaster
Mus musculus

source_name: Mouse embryonic stem cells & S2 cells

extract_protocol:
To obtain a soluble chromatin extract, ~2x10^7 cells were resuspended in 1 mL LB1 (50 mM HEPES, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1x Complete protease inhibitor) and incubated rotating at 4°C for 10 min. Samples were centrifuged, resuspended in 1 mL LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1x Compete protease inhibitor), and incubated rotating at 4°C for 10 min. Finally, samples were centrifuged, resuspended in 1 mL LB3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na deoxycholate, 0.5% N-lauroylsarcosine, 1% Triton X-100, 1x Complete protease inhibitor), and homogenized by passing two times through a 27-gauge needle. Chromatin extracts were sonicated for 8 min (anti-HA ChIP) or 12 min (anti-histone PTM ChIP) using a Covaris E220 focused ultra-sonicator at peak power 140, duty factor 5, and cycles/burst 200. For histone PTM ChIP-Rx, after centrifugation soluble chromatin was spiked-in with soluble chromatin from Drosophila S2 cells that was similarly prepared and equivalent to 5-10% of the mouse/human cell chromatin. The lysates were incubated with 100 μl Pierce anti-HA beads (Themo Scientific, 88836) or with anti-H3K4me1 (Abcam, ab8895), anti-H3K9me3 (Abcam, ab8898), anti-H3K27ac (Active Motif, 39133), anti-H3K27me3 (Cell Signaling Tech, 9733), anti-H3K36me2 (Cell Signaling, 2901) or anti-H3K36me3 (Active Motif, 61101) antibody bound to 75 μl protein A or protein G Dnya1 magnetic beads (Invitrogen) and incubated overnight at 4°C with 5% kept as input DNA. Magnetic beads were washed with low salt buffer (150 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl), high salt buffer (500 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl), LiCl buffer (150 mM LiCl; 0.5% Na deoxycholate; 0.1% SDS; 1% Nonidet P-40; 1 mM EDTA; 50 mM Tris-HCl) and TE buffer (1 mM EDTA; 10 mM Tris-HCl). For ChIP-seq, beads were resuspended in elution buffer (1% SDS, 50 mM Tris-HCl pH 8.0, 10mM EDTA, 200 mM NaCl) and incubated for 30 min at 65°C. After centrifugation the eluate was reverse cross-linked overnight at 65°C. The eluate was then treated with RNaseA for 1 hr at 37°C and with Proteinase K (Roche) for 1 hr at 55°C and DNA was recovered using Qiagen PCR purification kit.
KAPA Hyper Prep Kit

tag: chip antibody

value: H3K27ac (Active Motif #39133)

tag: cell line

value: ESC line V6.5 1A

value: C57BL/6 x 129S4/SvJae F1 embryo-derived embryonic stem cells


title: miR28_1

value: overexpression miR-28-3p


title: MMP13KO rep2 (S2)

description: MMP13KO rep2 (S2)

tag: strain

value: dental pulp


title: H3K27me1_ChIP-seq_mESC_sgNSD1

description: According to manufacturer's protocol

value: H3K27me1 (Active Motif #61015)


title: BALBc_p53null_PLK2null_1963

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

data_processing:
BAM files were sorted and indexed using Samtools and quality control was performed using Picard
QC: Picard 2.22.4 CollectRnaSeqMetrics
Resulting fastq files were aligned to the mouse mm10 reference genome using the STAR aligner (STAR 2.7.6a)
Transcript read counts were quantified with Salmon 1.4.0 to quantify gene expression
Gene level quantification was performed by summing transcript counts
Genome_build: Mm10
Supplementary_files_format_and_content: Matrix of salmon quantified normalized gene expressions

source_name: mammary tumor

growth_protocol: Tumors were orthotopically injected in sygeneic hosts and allowed to grow without treatment

extract_protocol:
RNA was extracted using Qiagen Rneasy kits. mRNA quality was assessed using the Agilent Bioanalyzer.
Libraries for mRNA-seq made using total RNA and the Illumina TruSeq mRNA sample preparation kit
Paired end (2x50bp) sequencing was performed on the Illumina HiSeq 2000/2500 sequencer at the UNC High Throughput Sequencing Facility

treatment_protocol: No Treatment

value: balb/c; p53-null; PLK2-null

value: mammary tumor


title: PMBC_FastRebound_week0_A12

description:
200999740198_R03C01_Red.idat
200999740198_R03C01_Grn.idat
BCN02 clinical trial
Sample_34

value: PBMC

value: Fast

tag: Sex

value: male

tag: age


title: BALBc_p53null_PLK2null_1965


title: PMBC_LateRebound_week1_A05

description:
200999740198_R02C02_Red.idat
200999740198_R02C02_Grn.idat
BCN02 clinical trial
Sample_19

value: Late


title: Molar WT rep4 (S4)

description: Molar WT rep4 (S4)

value: WT


title: KO_12h_1

description: treated with ricin

value: lung

value: female


title: WT MB 2

description: replicate 2

value: myoblasts


title: siZC3H4-HEK293-total RNA-seq-rep1

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

description: Strand-specific RNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Paired-end reads were aligned to GRCh37/hg19 reference using STAR aligner.
Gene counts were calculated using FeatureCounts
Expression QC was performed using RSeQC.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes counts and RPKM values for each Sample

source_name: HEK293 cells

extract_protocol:
Strand-specific RNA-seq: Total RNA was isolated using Trizol reagent. The RNA-Seq libraries were generated from 200 ng of total RNA using TruSeq Stranded Total RNA Library Prep kit (Illumina) according to the manufacturer's protocol.
Strand-specific RNA-seq: The libraries were generated using TruSeq Stranded Total RNA Library Prep kit (Illumina) according to the manufacturer's protocol.

tag: sirna

value: siRNA ZC3H4


title: KO_12h_3

description: treated with ricin

value: treated with ricin


title: WT_4h_2

description: treated with ricin

value: wild type


title: WT MB 1

description: replicate 1

source_name: Proliferating myoblasts


title: H3K27me1_ChIP-seq_mESC_Parental

description: According to manufacturer's protocol

value: ESC line V6.5 1A

value: C57BL/6 x 129S4/SvJae F1 embryo-derived embryonic stem cells

value: wild-type


title: KO_72h_1

description: treated with ricin


title: PMBC_LateRebound_week0_B03

description:
200999740198_R05C01_Red.idat
200999740198_R05C01_Grn.idat
BCN02 clinical trial
Sample_66


title: DU145_TAZ

value: Prostate

tag: knockdown

value: TAZ

value: merged


title: BALBc_p53null_PLK2null_733

value: balb/c; p53-null; PLK2-null

value: mammary tumor


title: WT_12h_2

description: treated with ricin


title: BALBc_p53null_PLK2null_1964


title: BALBc_p53null_PLK2null_7747


title: WT_4h_1

description: treated with ricin