title: H82_KRAS_nodox_nodrug-N1

city: Calgary

first: Marco

last: Gallo

state: AB

address: 2500 University Dr NW

department: Biochemistry and Molecular Biology

institute: University of Calgary

data_processing:
Sequencing data were aligned using bwa (0.7.17) to the hg38 assembly of the human genome
Extraneous chromosomes and low-quality reads were removed using SAMtools (v 1.10) and PCR duplicates were removed using Picard tools (Broad Institute).
Peaks were called using MACS2 using the following parameters: -g hs -q 0.05 --shift -100 --extsize 200 --nomodel -B --keep-dup all
Pileup was constructed using macs2 bdgcmp
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak of macs2 peak calls; bigwig pileup track of fold-enrichment from macs2

source_name: H82 cells treated with Dox +/- SCH, SB, A485, SB+A485

growth_protocol: All cells were cultured at 37℃ with 5% CO2 in humidified atmosphere. All cell lines except for H2107 (NCI-H2107) were cultured in RPMI 1640 medium (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% fetal bovine serum (Thermo Fisher Scientific). H2107 cells were cultured in DMEM medium (Thermo Fisher Scientific) supplemented with 5% fetal bovine serum and 1% Glutamax (Thermo Fisher Scientific)

extract_protocol:
ATAC-seq was performed using the Omni-ATAC protocol with slight modifications as below. In brief, cells were resuspended in nuclear lysis buffer (10 mM Tris-HCl pH 7.4; 10 mM NaCl; 3 mM MgCl2; 0.1% NP-40 0.1% Tween-20, 0.01% Digitonin) on ice, then spun down in a cold centrifuge at 600 x g for 10 minutes, resuspended in RSB Tween and nuclei were quantified using Trypan Blue (Invitrogen) on a Countess II (Invitrogen). An aliquot of 50,000 nuclei per sample was transferred to a fresh tube, spun down, resuspended in transposition solution and transposed for 30 minutes at room temperature as described previously74.
Libraries were prepared using standard Illumina Nextera indices. Library cleanup and dual-sided size selection was performed using SPRIselect beads (Beckman Coulter) with 0.4X and 1.2X ratios. Sequencing was performed on a NextSeq 500 (Illumina) with 150 cycles on a high-output cartridge in paired-end mode at the Center for Genomics and Health Informatics (CHGI) at the Cumming School of Medicine.

treatment_protocol: H2107-KRASG12V and H524-KRASG12V cells treated with doxycycline ± SCH772984 (1 μM) for 72 hours. H82-KRASG12V cells were treated with the following chemicals: doxycycline; doxycycline + SCH772984 (1 μM); doxycycline + SB747651A (5 μM); doxycycline + A-485 (400 nM); or doxycycline + SB747651A (5 μM) + A-485 (400 nM). After 72 hours treatment, these cells as well as corresponding non-treated control cells were collected and frozen.

tag: cell line


title: H82_KRAS_Dox_SCH-1uM-N3

status: Public on Aug 17 2021

type: SRA

country: Canada

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: treatment

value: Dox+SCH


title: C2C12 H3K27ac of H3K27ac&Pol2S2P at 100 cells replicate 3

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

description: library strategy: mtChIL-seq

data_processing:
Custom demultiplexing step of mtChIL library. (1) Extracting the index reads using bcl2fastq (version. 2.2.0) with the option: --create-fastq-for-index.  (2) Run deML (version 1.1.3): deML -if1 i1.fq.gz -if2 i2.fq.gz -f r1.fq.gz -i index.txt, where the FASTQ (fq.gz) files are i1.fq.gz (index-1), i2.fq.gz (index-2) and r1.fq.gz (read-1) respectively. The index.txt is the definition of the custom dual indices of mtChIL, which consists of the tab–delimited fields of the index-1, -2 and the sample name.
Mapping: run hisat2 (version 2.1.0)  with the option "--no-spliced-alignment" using the mouse genome index (grcm38_snp).
Signal tracks: deepTools (version 3.3.1) bamCoverage with the option "-bs 100 --smoothLength 1000 --normalizeUsing CPM --minMappingQuality 60 --ignoreDuplicates"
Count matrix: deepTools (version 3.3.1) multiBamSummary with the option "bins -bs 1000 --ignoreDuplicates --minMappingQuality 60"
Genome_build: GRCm38
Supplementary_files_format_and_content: count matrix: CSV (gzipped), signal tracks: bigWig

organism: Mus musculus

source_name: Immortal cell line

extract_protocol: Immunostaining half of the protocol includes cell dispensing, fixation, permeabilization, blocking, reaction to primary antibody and the ChIL probe. The reactive probe are integrated into a proximal genomic region to where the primary antibody is bound upon Tn5 activation. The integrated ChIL DNA is used for the linear amplification of genomic sequences and the transcribed RNAs are utilized for library preparation for deep-sequencing.

tag: antibody target

tag: primary antibody

value: mouse monoclonal anti–H3K27ac (Kimura et al., Cell Struct Funct. 2008;33(1):61-73., CMA309)

tag: number of cells


title: C2C12 H3K27ac of H3K27ac&Pol2S2P at 100 cells replicate 1

description: library strategy: mtChIL-seq


title: H82_KRAS_nodox_nodrug-N3


title: ydiP myc-tag 1

city: La Jolla

first: Ye

last: Gao

address: 9500 Gilman Dr.

country: USA

institute: UCSD

data_processing:
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from ChIP-exo were mapped onto the each reference genome using bowtie with default options to generate SAM output files
MACE program was used to define peak candidates from biological duplicates for each experimental condition with sequence depth normalization.
To reduce false-positive peaks, manual curation was performed based on the signal-to-noise(S/N) ratio value.
The calculation of S/N ratio resembles the way to calculate ChIP-chip peak intensity where IP signal was divided by Mock signal. Then, each peak was assigned to the nearest gene.
Genome_build: The reference genome  MG1655 =  NC_000913.2
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

organism: Escherichia coli K-12

source_name: bacteria cells

growth_protocol: Glycerol stocks of E. coli strains were inoculated into M9 minimal media with 0.2% (w/v) glucose. The culture was incubated at 37 oC overnight with agitation, and then was used to inoculate the fresh media (1/200 dilution). The volume of the fresh media was 150 mL for each biological replicate. The fresh culture was incubated at 37 oC with agitation to the mid-log phase (OD600 ≈ 0.5).

extract_protocol:
Lysates were clarified from sonicated uncharacterized transcripton factors-DNA complexes were isolated with myc antibody.
ChIP-exo experiment was performed following the procedures:  to identify each TF candidate binding maps in vivo, we isolated the DNA bound to each TF candidate from formaldehyde cross-linked E. coli cells by chromatin immunoprecipitation (ChIP) with the specific antibodies that specifically recognizes myc tag (9E10, Santa Cruz Biotechnology), and Dynabeads Pan Mouse IgG magnetic beads (Invitrogen) followed by stringent washings as described previously [42]. ChIP materials (chromatin-beads) were used to perform on-bead enzymatic reactions of the ChIP-exo method [11]. Briefly, the sheared DNA of chromatin-beads was repaired by the NEBNext End Repair Module (New England Biolabs) followed by the addition of a single dA overhang and ligation of the first adaptor (5’-phosphorylated) using dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs), respectively. Nick repair was performed by using PreCR Repair Mix (New England Biolabs). Lambda exonuclease- and RecJf exonuclease-treated chromatin was eluted from the beads and the protein-DNA cross-link was reversed by overnight incubation at 65oC. RNAs- and Proteins-removed DNA samples were used to perform primer extension and second adaptor ligation with following modifications. The DNA samples incubated for primer extension as described previously [12] were treated with dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs) for second adaptor ligation. The DNA sample purified by GeneRead Size Selection Kit (Qiagen) was enriched by polymerase chain reaction (PCR) using Phusion High-Fidelity DNA Polymerase (New England Biolabs). The amplified DNA samples were purified again by GeneRead Size Selection Kit (Qiagen) and quantified using Qubit dsDNA HS Assay Kit (Life Technologies). Quality of the DNA sample was checked by running Agilent High Sensitivity DNA Kit using Agilent 2100 Bioanalyzer (Agilent) before sequenced using HiSeq (Illumina) in accordance with the manufacturer’s instructions. Each modified step was also performed in accordance with the manufacturer’s instructions. ChIP-exo experiments were performed in biological duplicate.

treatment_protocol: For regulatory condition, M9 minimal media was supplemented with 1 mL trace element solution (100X) containing 1 g EDTA, 29 mg ZnSO4.7H2O, 198 mg MnCl2.4H2O, 254 mg CoCl2.6H2O, 13.4 mg CuCl2, and 147 mg CaCl2.

tag: strain

tag: myc-tagging

value: YidP myc-tagging cells

tag: chip-exo antibody

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: C2C12 CTCF at 10k cells replicate 2

description: library strategy: mtChIL-seq

value: CTCF

value: rabbit monoclonal anti–CTCF (abcam, ab188408, lot GR239192-2)


title: yidL myc-tag 2

value: YidL myc-tagging cells


title: S_15-006_16wpi [2A1]

city: Adelaide

first: Feargal

middle: J

last: Ryan

state: Adelaide

address: North Terrace

country: Australia

institute: SAHMRI

description:
Subject_006_Mild_12w.p.i [P2A1]
Subject_006 Female Mild 12w.p.i Total RNA

library_source: transcriptomic

data_processing:
Quality control with Trimmomatic version 0.38
Gene count matrix was generated with FeatureCounts version 1.5.0-p2 and Ensembl 101
Aligned to genome using HISAT2 version 2.1.0
Genome_build: GRCh38
Supplementary_files_format_and_content: FeatureCounts per gene counts

molecule: total RNA

source_name: Peripheral blood

extract_protocol:
RNA extraction and genomic DNA elimination was carried out using the PAXgene® Blood RNA kit (762164, Qiagen, Feldbachstrasse, Germany) as per the manufacturer’s instructions
Total RNA was converted to strand-specific Illumina compatible sequencing libraries using the Nugen Universal Plus Total RNA-Seq library kit from Tecan (Mannedorf, Switzerland) as per the manufacturer’s instructions (MO1523 v2) using 12 cycles of PCR amplification for the final libraries. An Anydeplete probe mix targeting both human ribosomal and adult globin transcripts (HBA1, HBA2, HBB, HBD) was used to deplete these transcripts.
Total RNA-Seq 2x150 bp paired-end reads.

tag: age

tag: Sex

value: Female

tag: disease severity

value: Mild

tag: rin

tag: sample number

tag: tissue

value: Peripheral blood

tag: timepoint


title: yjhI myc-tag 2

value: YjhI myc-tagging cells


title: C2C12 CTCF at 10k cells replicate 1

description: library strategy: mtChIL-seq


title: C2C12 H3K27ac of H3K27ac&Pol2S2P at 1k cells replicate 3

description: library strategy: mtChIL-seq


title: S_15-006_24wpi [2A2]

description:
Subject_006_Mild_20w.p.i [P2A2]
Subject_006 Female Mild 20w.p.i Total RNA


title: H82_KRAS_nodox_nodrug-N2


title: yidL myc-tag 1


title: yahB myc-tag 1

value: YahB myc-tagging cells


title: S_15-062_24wpi [1H4]

description:
Subject_062_Mild_20w.p.i [P1H4]
Subject_062 Female Mild 20w.p.i Total RNA


title: C2C12 CTCF of H3K4me3&CTCF at 10k cells replicate 3

description: library strategy: mtChIL-seq


title: C2C12 H3K27ac of H3K27ac&Pol2S2P at 100 cells replicate 2

description: library strategy: mtChIL-seq


title: ycaN myc-tag 2

value: YcaN myc-tagging cells


title: H82_KRAS_Dox_SCH-1uM-N1


title: H82_KRAS_Dox_SCH-1uM-N2


title: S_HC9_Control [1H6]

description:
HC9_Healthy_Healthy_Control [P1H6]
HC9 Male Healthy Healthy_Control Total RNA

value: Male

value: Healthy

value: Control


title: yahB myc-tag 2


title: H82_KRAS_Dox_SB-5uM-N3

value: Dox+SB


title: ycaN myc-tag 1


title: H82_KRAS_Dox_SB-5uM-N2


title: S_15-044_16wpi [1H1]

description:
Subject_044_Mild_12w.p.i [P1H1]
Subject_044 Male Mild 12w.p.i Total RNA


title: H82_KRAS_Dox_SB-A485-N3


title: C2C12 CTCF of H3K4me3&CTCF at 1k cells replicate 3

description: library strategy: mtChIL-seq


title: ybeF myc-tag 1

value: YbeF myc-tagging cells


title: ybeF myc-tag 2


title: S_HC8_Control [1G6]

description:
HC8_Healthy_Healthy_Control [P1G6]
HC8 Male Healthy Healthy_Control Total RNA


title: ybhD myc-tag 2

value: YbhD myc-tagging cells


title: S_15-044_24wpi [1H2]

description:
Subject_044_Mild_20w.p.i [P1H2]
Subject_044 Male Mild 20w.p.i Total RNA


title: C2C12 CTCF of H3K4me3&CTCF at 10k cells replicate 2

description: library strategy: mtChIL-seq


title: H82_KRAS_Dox_SB-A485-N2


title: C2C12 CTCF of H3K4me3&CTCF at 1k cells replicate 1

description: library strategy: mtChIL-seq


title: S_15-062_16wpi [1H3]

description:
Subject_062_Mild_12w.p.i [P1H3]
Subject_062 Female Mild 12w.p.i Total RNA


title: H82_KRAS_Dox_nodrug-N3

value: Dox


title: C2C12 Pol2S2P at 1k cells replicate 1

description: library strategy: mtChIL-seq

value: mouse monoclonal anti–Pol2S2P (Stasevich et al., Nature. 2014;516(7530):272-275., CMA602)


title: S_15-068_24wpi [1G4]

description:
Subject_068_Critical_20w.p.i [P1G4]
Subject_068 Male Critical 20w.p.i Total RNA

value: Critical


title: H82_KRAS_Dox_SB-5uM-N1


title: H82_KRAS_Dox_nodrug-N2


title: C2C12 CTCF of H3K4me3&CTCF at 1k cells replicate 2

description: library strategy: mtChIL-seq

value: CTCF

value: rabbit monoclonal anti–CTCF (abcam, ab188408, lot GR239192-2)


title: H82_KRAS_Dox_SB-A485-N1


title: C2C12 H3K27ac of H3K27ac&Pol2S2P at 1k cells replicate 1

description: library strategy: mtChIL-seq

value: mouse monoclonal anti–H3K27ac (Kimura et al., Cell Struct Funct. 2008;33(1):61-73., CMA309)


title: ybhD myc-tag 1

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: S_HC4_Control [1G5]

description:
HC4_Healthy_Healthy_Control [P1G5]
HC4 Female Healthy Healthy_Control Total RNA

value: Female

value: Peripheral blood


title: C2C12 H3K4me3 of H3K4me3&CTCF at 10k cells replicate 3

description: library strategy: mtChIL-seq

value: mouse monoclonal anti–H3K4me3 (Kimura et al., Cell Struct Funct. 2008;33(1):61-73., CMA304)


title: C2C12 H3K4me3 of H3K4me3&CTCF at 10k cells replicate 2

description: library strategy: mtChIL-seq


title: yehT myc-tag 2

value: YehT myc-tagging cells


title: C2C12 CTCF of H3K4me3&CTCF at 10k cells replicate 1

description: library strategy: mtChIL-seq


title: H82_KRAS_Dox_A485-400uM-N3


title: yfiE myc-tag 1

value: YfiE myc-tagging cells


title: C2C12 H3K4me3 of H3K4me3&CTCF at 1k cells replicate 2

description: library strategy: mtChIL-seq


title: S_15-011_24wpi [1G2]

description:
Subject_011_Mild_20w.p.i [P1G2]
Subject_011 Female Mild 20w.p.i Total RNA

value: Mild


title: ynfL myc-tag 2

value: YnfL myc-tagging cells


title: H82_KRAS_Dox_nodrug-N1


title: yfiE myc-tag 2


title: yehT myc-tag 1


title: S_15-036_16wpi [1F3]

description:
Subject_036_Severe_12w.p.i [P1F3]
Subject_036 Male Severe 12w.p.i Total RNA

value: Male

value: Severe


title: ynfL myc-tag 1


title: H82_KRAS_Dox_A485-400uM-N2


title: yqhC myc-tag 2

value: YqhC myc-tagging cells


title: yneJ myc-tag 2

value: YneJ myc-tagging cells


title: C2C12 H3K4me3 of H3K4me3&CTCF at 1k cells replicate 3

description: library strategy: mtChIL-seq


title: S_HC5_Control [1H5]

description:
HC5_Healthy_Healthy_Control [P1H5]
HC5 Female Healthy Healthy_Control Total RNA

value: Healthy

value: Control


title: S_HC7_Control [1F6]

description:
HC7_Healthy_Healthy_Control [P1F6]
HC7 Male Healthy Healthy_Control Total RNA


title: S_15-011_16wpi [1G1]

description:
Subject_011_Mild_12w.p.i [P1G1]
Subject_011 Female Mild 12w.p.i Total RNA


title: H524_KRAS_nodox_nodrug-N1

source_name: H524 cells treated with Dox +/- SCH


title: S_HC2_Control [1F5]

description:
HC2_Healthy_Healthy_Control [P1F5]
HC2 Male Healthy Healthy_Control Total RNA


title: S_15-007_16wpi [1F1]

description:
Subject_007_Critical_12w.p.i [P1F1]
Subject_007 Female Critical 12w.p.i Total RNA

value: Critical


title: yneJ myc-tag 1


title: H82_KRAS_Dox_A485-400uM-N1


title: C2C12 H3K4me3 of H3K4me3&CTCF at 1k cells replicate 1

description: library strategy: mtChIL-seq


title: yiaU myc-tag 1

value: YiaU myc-tagging cells


title: yiaU myc-tag 2


title: H524_KRAS_nodox_nodrug-N2


title: S_15-036_24wpi [1F4]

description:
Subject_036_Severe_20w.p.i [P1F4]
Subject_036 Male Severe 20w.p.i Total RNA


title: H524_KRAS_nodox_nodrug-N3


title: S_HC1_Control [1E5]

description:
HC1_Healthy_Healthy_Control [P1E5]
HC1 Female Healthy Healthy_Control Total RNA


title: S_15-020_24wpi [1E4]

description:
Subject_020_Mild_20w.p.i [P1E4]
Subject_020 Male Mild 20w.p.i Total RNA


title: PancOVA tumor cells after coculture with myCAF2

city: Marburg

first: Magdalena

last: Huber

country: Germany

institute: Philipps-University Marburg

description:
Processed data file: iCafvsmyCafvsqPSC.xlsx
myCaf - a5_myCaf2_R1 (GE) - Expression values

data_processing:
The paired-end reads were mapped using salmon v1.3.07 against the mouse transcriptome (Ensembl - Mus musculus - release 100) with decoys.
The quantifications from salmon were imported into R version 4.0.1 using the tximeta package (version 1.6.2)
The transcript counts were summarized to gene level. The resulting gene level quantifications served as input to DESeq2 v1.28.19.
Gene expression levels in PancOVA cells from the Tc17-iCAF, TGFb-myCAF and qPSC cocultures were compared against each other respectively, using default parameters. Gene comparisons with padj < 0.1 were considered differentially expressed. Correction for base gene expression was performed by subtracting the mean expression values of the qPSC control coculture from both Tc17-iCAF and TGFb-myCAF cocultures
All differentially expressed genes were stratified into 7 defined modules: 1. Downregulated in Tc17-iCAF & TGFb-myCAF coculture, 2. Downregulated only in Tc17-iCAF coculture, 3. Only downregulated in TGFb-myCAF coculture, 4. Downregulated in TGFb-myCAF and upregulated in Tc17-iCAF coculture, 5. Only upregulated in TGFb-myCAF coculture, 6. Upregulated in Tc17-iCAF and TGFb-myCAF coculture, 7. Differentially expressed between Tc17-iCAF and TGFb-myCAF coculture
Genome_build: Ensembl - Mus musculus - release 100
Supplementary_files_format_and_content: xlsx array table of all mapped transcripts

source_name: PancOVA cells after co-culture

growth_protocol: PancOVA cultures were grown in T75 flasks (Sarstedt) with DMEM (10% FCS) and split every 2-4 days upon reaching 70% confluence, harvested by trypsinization (1x Trypsin/EDTA, Sigma T-4174) and reseeded (5 x 105 cells / 20ml Medium  / T75 flask). Pancreatic stellate cells (mPSC45, kindly obtained from Dr. A Neese) were cultured in T75 flasks or tc-treated dishes (Sarstedt) in DMEM (10% FCS) and split every 4-7 days, upon reaching 70% confluence. They were harvested by trypsinization (1x Trypsin/EDTA, Sigma T-4174) and reseeded (2.5 x 104 cells/ml). To obtain quiescent (q)PSC, 6 x10^5 PSC were seeded in a 70µl matrigel drop (Growth Factor Reduced (GFR) Basement Membrane Matrix, Corning, 356230) mixed at a 1:1 ratio with DMEM (10 % FCS) on a 3.5 cm suspension dish (Sarstedt). The matrigel-embedded PSC were covered with 0.5 % FCS-containing DMEM and incubated for 48 h. Thereafter, the qPSC were treated with either rhTGF-1 (2 ng/ml; Peprotech, #100-21) or conditioned media (CM), followed by an incubation for 48 h.

extract_protocol:
Cocultures of primed PSCs and labelled PancOVA cells were set up by harvesting single matrigel droplets of qPSC or Tc17-iCAF or TGFb-myCAF, removing the matrigel by incubation with ice-cold DMEM and centrifugation (1000 rpm, 4°C, 5 min), removing the supernatant and adding PancOVA (3.5 × 105) cells in 70 µl of fresh matrigel. The mixture containing qPSC, Tc17-iCAF or TGFb-myCAF and labelled PancOVA cells in matrigel was re-seeded as described above. After 48 h, the matrigel droplets were harvested, dissolved by incubation with Collagenase D (5mg/ml, Roche) and DNAse 1 (10µg/ml, Roche) in HBSS at 37° for 45min. The cells washed twice with cold MACS buffer (2% FCS, 1mM EDTA in PBS), centrifuged (400g, 4°C, 5 min), resuspended in MACS buffer and stained with CD90.1 antibody (BV510, BioLegend # 202535) and sorted into eFluor670+ fractions on a FACS ARIA II. The eFluor670-CD90.1+ fibroblast population was subsequently stained and phenotype was analysed by FACS on an Attune Nxt (ThermoFisher). The eFluor670+ tumor cell fraction was resuspended in RLTplus buffer (Qiagen) and snap-frozen for RNA isolation and RNAseq.
RNA integrity was assessed on an Experion StdSens RNA Chip (Bio-Rad). RNAseq libraries were prepared using the TruSeq Stranded mRNA Library Prep kit (Illumina)
and sequenced on an Illumina platform, High Output Kit v2.5, 50 bases single-reads according to the manufacturer’s instructions

treatment_protocol: For coculture and subsequent sorting, mPSCCD90.1 were made first quiescent and then primed for either Tc17-iCAF, TGFb-myCAF or qPSC control condition as described above. PancOVA cells were harvested from adherent cell cultures, counted and stained with Cell Proliferation Dye eFluor 670 (#65-0840-90 eBioscience) according to manufacturer’s protocol.

value: PancOVA cells

value: 48h CoCulture with myCAF


title: H524_KRAS_Dox_nodrug-N3

value: Dox


title: yqhC myc-tag 1

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: PancOVA tumor cells after coculture with qPSC2

description:
Processed data file: iCafvsmyCafvsqPSC.xlsx
qPSC - a8_qPSC2_R1 (GE) - Expression values

value: 48h CoCulture with qPSC


title: S_15-020_16wpi [1E3]

description:
Subject_020_Mild_12w.p.i [P1E3]
Subject_020 Male Mild 12w.p.i Total RNA

value: Peripheral blood


title: S_15-007_24wpi [1F2]

description:
Subject_007_Critical_20w.p.i [P1F2]
Subject_007 Female Critical 20w.p.i Total RNA

value: Female


title: C2C12 H3K4me3 of H3K4me3&CTCF at 10k cells replicate 1

description: library strategy: mtChIL-seq

value: mouse monoclonal anti–H3K4me3 (Kimura et al., Cell Struct Funct. 2008;33(1):61-73., CMA304)


title: H524_KRAS_Dox_SCH-N3

value: Dox+SCH


title: PancOVA tumor cells after coculture with qPSC3

description:
Processed data file: iCafvsmyCafvsqPSC.xlsx
qPSC - a9_qPSC3_R1 (GE) - Expression values


title: S_HC6_Control [1E6]

description:
HC6_Healthy_Healthy_Control [P1E6]
HC6 Male Healthy Healthy_Control Total RNA

value: Male


title: H524_KRAS_Dox_SCH-N2


title: PancOVA tumor cells after coculture with myCAF3

description:
Processed data file: iCafvsmyCafvsqPSC.xlsx
myCaf - a6_myCaf3_R1 (GE) - Expression values


title: PancOVA tumor cells after coculture with iCAF2

description:
Processed data file: iCafvsmyCafvsqPSC.xlsx
iCaf - a2_iCaf2_R1 (GE) - Expression values

value: 48h CoCulture with iCAF


title: PancOVA tumor cells after coculture with qPSC1

description:
Processed data file: iCafvsmyCafvsqPSC.xlsx
qPSC - a7_qPSC1_R1 (GE) - Expression values


title: PancOVA tumor cells after coculture with myCAF1

description:
Processed data file: iCafvsmyCafvsqPSC.xlsx
myCaf - a4_myCaf1_R1 (GE) - Expression values


title: PancOVA tumor cells after coculture with iCAF1

description:
Processed data file: iCafvsmyCafvsqPSC.xlsx
iCaf - a1_iCaf1_R1 (GE) - Expression values


title: PancOVA tumor cells after coculture with iCAF3

description:
Processed data file: iCafvsmyCafvsqPSC.xlsx
iCaf - a3_iCaf3_R1 (GE) - Expression values


title: ydcN myc-tag 2

value: YdcN myc-tagging cells


title: H524_KRAS_Dox_nodrug-N2


title: H524_KRAS_Dox_SCH-N1


title: H524_KRAS_Dox_nodrug-N1


title: ydcN myc-tag 1


title: S_15-021_16wpi [1E1]

description:
Subject_021_Mild_12w.p.i [P1E1]
Subject_021 Female Mild 12w.p.i Total RNA

value: Mild


title: ygeR myc-tag 2

value: YgeR myc-tagging cells


title: yidZ myc-tag 2

value: YidZ myc-tagging cells


title: S_15-035_16wpi [1D5]

description:
Subject_035_Critical_12w.p.i [P1D5]
Subject_035 Female Critical 12w.p.i Total RNA

value: Critical


title: S_15-021_24wpi [1E2]

description:
Subject_021_Mild_20w.p.i [P1E2]
Subject_021 Female Mild 20w.p.i Total RNA


title: H2107_KRAS_nodox_nodrug-N3

source_name: H2107 cells treated with Dox +/- SCH


title: H2107_KRAS_nodox_nodrug-N2


title: S_15-035_24wpi [1D6]

description:
Subject_035_Critical_20w.p.i [P1D6]
Subject_035 Female Critical 20w.p.i Total RNA


title: H2107_KRAS_nodox_nodrug-N1


title: ygeR myc-tag 1


title: yihW myc-tag 1

value: YihW myc-tagging cells


title: Uterus_EZKO_rep4

city: Columbia

first: Cheryl

middle: S

last: Rosenfeld

state: MO

address: 1201 Rollins Street

department: BIOMEDICAL SCIENCES

institute: University of Missouri.edu

data_processing:
Illumina Casava1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome
The number of reads that aligned to each protein-coding gene were counted with 10X Genomics program
For spatial transcriptomics analysis, all data were aggregated and further analyze with 10X program called Loupe Browser. For this reason, there is no individual processed data, rather combined.
Genome_build: grcm38
Supplementary_files_format_and_content: aggregated loupe file, gene comparisons

extract_protocol:
One Ezh2cKO and one WT female randomly selected from four different litters. Females were ovariectomized at postnatal day (PND) 71 ± 4. Uteri were collected on PND 112±11. Uteri were embedded and frozen in Tissue-Tek optimal cutting temperature (O.C.T.) compound (Sakura Finetek USA, #25608-930). Samples were cut using a Thermo Scientific HM525 NX cryostat, and 10 µm thick sections were placed on capture areas of Visium spatial gene expression slides (10X Genomics). Immediately after sectioning, tissues were fixed and stained according to manufacturer’s recommendations. In brief, tissue sections were fixed in prechilled methanol for 30 min at -20°C, stained with Mayer hematoxylin for 7 min followed by washing in 3 changes of nuclease-free water and a 2 min incubation in bluing buffer (Dako, Agilent, Santa Clara, CA, United States). Subsequently, sections were counterstained with eosin for 1 min, then briefly washed and dried for 5 min on a slide warmer at 37ºC. Images of individual capture areas with stained sections were acquired using a Zeiss Axiovert 200M motorized microscope equipped with a 5x Plan Apochromat objective and a Leica Buffalo Grove, IL United States DFC290 camera. Image tiles were stitched with Metamorph 7.8.12 software. Pixel size of final composite images was 1.275 µm.
The cDNA library for the Illumina platform was prepared by following the 10X Genomics spatial gene expression library construction protocol. Briefly, double stranded cDNA was fragmented, end repaired, and A-tail added in a single step. The A-tailed fragments were size selected using double-sided AxyPrep Mag magnetic beads with a bead to reaction solution ratio of 0.6X and 0.8X for the for the first and second steps, respectively. Next, the adaptor was ligated and purified with 0.8X AxyPrep Mag magnetic beads. The final Illumina libraries were amplified by PCR, which added unique dual indexes to each sample. The PCR-amplified libraries were purified and size selected by using two reactions with double-sided AxyPrep Mag magnetic beads at the bead to reaction solution ratios described above. The individual library was analyzed by Fragment Analyzer (Agilent, Santa Clara, CA, United States) to determine the quality and average fragment size and quantified by Qubit (Invitrogen, Waltham, MA, United States) DNA assay. The libraries were pooled in an equimolar ratio with a total concentration of 5 nM and sequenced on the Illumina Novaseq 6000.
Spatial transcriptomics

value: mixed C57BL/6 and 129SvEv

value: Uterus

tag: genotype

value: EZ fl/fl; Prcre/+


title: yihW myc-tag 2

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: Uterus_EZKO_rep3


title: Uterus_WT_rep4

value: EZ fl/fl


title: Uterus_WT_rep3


title: S_15-012_24wpi [1D4]

description:
Subject_012_Mild_20w.p.i [P1D4]
Subject_012 Female Mild 20w.p.i Total RNA

value: Peripheral blood


title: H2107_KRAS_Dox_SCH-N2


title: H2107_KRAS_Dox_SCH-N1


title: S_15-022_24wpi [1D2]

description:
Subject_022_Critical_20w.p.i [P1D2]
Subject_022 Male Critical 20w.p.i Total RNA


title: S_15-022_16wpi [1D1]

description:
Subject_022_Critical_12w.p.i [P1D1]
Subject_022 Male Critical 12w.p.i Total RNA


title: S_15-012_16wpi [1D3]

description:
Subject_012_Mild_12w.p.i [P1D3]
Subject_012 Female Mild 12w.p.i Total RNA

value: Female


title: yidZ myc-tag 1


title: H2107_KRAS_Dox_SCH-N3


title: Uterus_WT_rep2


title: S_15-005_24wpi [1C6]

description:
Subject_005_Severe_20w.p.i [P1C6]
Subject_005 Male Severe 20w.p.i Total RNA

value: Severe


title: ycjW myc-tag 1

value: YcjW myc-tagging cells


title: H2107_KRAS_Dox_nodrug-N3

value: Dox


title: ycjW myc-tag 2


title: H2107_KRAS_Dox_nodrug-N2


title: yu6_S6_L001_R1_001

city: Madison

first: Xinyu

last: Zhao

state: Wisconsin

address: 1500 HIghland Ave, Wiasman Center North Tower T513

institute: University of Wisconsin Madison

description:
Ribosome IP sample
WT

data_processing:
Cluster generation and high-throughput sequencing were performed on a HiSeq 2500 (Illumina), using the single-end 100 bp protocol. STAR was used to align read pairs to the mm10 transcriptome and estimate gene expression levels
Genome_build: mm10
Supplementary_files_format_and_content: CSV file with raw counts

source_name: frontal cortex

growth_protocol: We generated the ribosome tagging mice (Tg(Palvalbumin-cre)::RPL22HA/WT, simplified as PV-Cre::RiboTag) by crossing transgenic driver (Tg(Palvalbumin-cre) mice (JAX Stock No:017320)with RPL22HA/WT  mice (JAX Stock No:029977). Mice were kept in 12 hours light/12 dark cycle housing.

extract_protocol:
RNA from the RiboTag IP in parvalbumin neurons in frontal cortex of Fxr1 mice was isolated using the Direct-zol™ RNA MicroPrep Kit (Zymo Research Corporation. Irvine, CA, USA).
The libraries were made using SMARTer® Stranded Total RNA-Seq Kit v2 (Takara Bio USA, Inc. Mountain View, CA) according to the user manual.

treatment_protocol: Two groups of mice: Fxr1 conditional knockout with PV-Cre and wildtype. The mice were kept in 12 hours light/12 dark cycle housing.

value: frontal cortex

tag: gender

value: male

value: wild type

tag: cell type

value: parvalbumin neurons


title: Uterus_EZKO_rep2


title: Uterus_WT_rep1


title: ydhB myc-tag 1

value: YdhB myc-tagging cells


title: yu5_S5_L001_R1_001

description:
Ribosome IP sample
cKO

value: Fxr1 conditional knockout


title: ycfQ myc-tag 2

value: YcfQ myc-tagging cells


title: S_15-005_16wpi [1C5]

description:
Subject_005_Severe_12w.p.i [P1C5]
Subject_005 Male Severe 12w.p.i Total RNA

value: Male


title: VCaP T rep3 [RNA-seq]

city: Tampere

first: Sinja

last: Taavitsainen

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

data_processing:
Sequencing reads were aligned using STAR aligner v2.5.4b (Dobin et al., 2013) and Ensembl reference genome GRCh38.
Genewise read counts were quantified using featureCounts v1.6.2 (Liao et al., 2014) and Gencode annotations release 28.
Genome_build: hg38
Supplementary_files_format_and_content: Gene count matrices in TXT format

source_name: VCaP cells

extract_protocol: RNA sequencing was performed with Illumina HiSeq 3000. 3 replicates were sequenced for each sample type.

treatment_protocol: Androgen-sensitive VCaP cells were cultured in RPMI 1640 supplemented with 10 % DCC-FBS, 1 % L-glutamine, 1 % A/A, and 10 nM testosterone (T) for seven months to establish T-dependent subclone VCaP-T. VCaP-T cells were then cultured at low testosterone (0.1 nM) for 10 months to establish VCaP-CT, an androgen-independent cell line able to grow despite low testosterone. VCaP-CT were then cultured at 10 µM enzalutamide until the cells regained ability to grow despite enzalutamide, creating enzalutamide resistant cell line VCaP-CT-ET. Another cell line was created by incubating first VCaP-CT cells with bicalutamide and subsequently with enzalutamide upon reaching bicalutamide insensitivity (VCaP-CT-BR). Ultimately these cells also gained the ability to grow despite enzalutamide, creating the multiresistant cell line VCaP-CT-BR-ER.

tag: cell line

value: VCaP

value: prostate cancer cell line

tag: androgen sensitivity

value: sensitive

tag: treatment

value: RPMI 1640 supplemented with 10 % DCC-FBS, 1 % L-glutamine, 1 % A/A, and 10 nM testosterone for seven months


title: S_15-026_24wpi [1C4]

description:
Subject_026_Mild_20w.p.i [P1C4]
Subject_026 Male Mild 20w.p.i Total RNA

value: Mild

value: Peripheral blood


title: VCaP T rep2 [RNA-seq]


title: ycfQ myc-tag 1

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: H2107_KRAS_Dox_nodrug-N1


title: VCaP T rep1 [RNA-seq]


title: S_15-008_16wpi [1C1]

description:
Subject_008_Mild_12w.p.i [P1C1]
Subject_008 Male Mild 12w.p.i Total RNA


title: yu3_S3_L001_R1_001

description:
Ribosome IP sample
cKO


title: yu4_S4_L001_R1_001

description:
Ribosome IP sample
WT


title: S_15-008_24wpi [1C2]

description:
Subject_008_Mild_20w.p.i [P1C2]
Subject_008 Male Mild 20w.p.i Total RNA


title: S_15-015_24wpi [1B6]

description:
Subject_015_Mild_20w.p.i [P1B6]
Subject_015 Female Mild 20w.p.i Total RNA

value: Female


title: yu2_S2_L001_R1_001

description:
Ribosome IP sample
WT


title: yhjC myc-tag 1

value: YhjC myc-tagging cells


title: VCaP CT rep3 [RNA-seq]

value: resistant

value: RPMI 1640 supplemented with 10 % DCC-FBS, 1 % L-glutamine, 1 % A/A, and 10 nM testosterone for seven months + 10nM testosterone for 10 months


title: Uterus_EZKO_rep1

value: mixed C57BL/6 and 129SvEv

value: Uterus

value: EZ fl/fl; Prcre/+


title: ydhB myc-tag 2

value: YdhB myc-tagging cells


title: yedW myc-tag 1

value: YedW myc-tagging cells


title: VCaP CT rep2 [RNA-seq]


title: S_15-026_16wpi [1C3]

description:
Subject_026_Mild_12w.p.i [P1C3]
Subject_026 Male Mild 12w.p.i Total RNA

value: Male


title: VCaP CT-ER rep2 [RNA-seq]

value: VCaP

value: RPMI 1640 supplemented with 10 % DCC-FBS, 1 % L-glutamine, 1 % A/A, and 10 nM testosterone for seven months + 10nM testosterone for 10 months + 10 µM enzalutamide until the cells regained ability to grow despite enzalutamide


title: yedW myc-tag 2


title: S_15-018_16wpi [1B3]

description:
Subject_018_Severe_12w.p.i [P1B3]
Subject_018 Female Severe 12w.p.i Total RNA

value: Severe


title: VCaP CT rep1 [RNA-seq]

value: prostate cancer cell line


title: S_15-015_16wpi [1B5]

description:
Subject_015_Mild_12w.p.i [P1B5]
Subject_015 Female Mild 12w.p.i Total RNA

value: Mild


title: mKO_4

city: Shanghai

first: yanhua

last: du

address: 227 South Chongqing Road, Huangpu District

department: Shanghai Institute of Immunology

country: China

institute: Shanghai Jiaotong University School of Medicine

data_processing:
Sequencing reads from each sample were mapped to the mouse reference genome (mm10 version) by using TopHat v2.1.1
Sequencing counts at the gene level were obtained using HTSeq v 0.9.1.
R (version 3.4.0) package DESeq2 was then used to normalize gene counts and identify differential expressed genes between different conditions.
Genome_build: mm10 (mouse)
Supplementary_files_format_and_content: tab-delimited text file includes normalized gene counts values for each sample

source_name: MGE

extract_protocol:
MGE cells were collected, or MGE was removed from embryo. RNA was harvested using Trizol reagent. NEBNext Ultra RNA library Prep Kit for Illumina (E7530) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the manufacturer’s protocol.

tag: cell-type/tissue

value: MGE tissue

tag: Stage

value: Embryonic day 14.5

value: Nkx2.1-cre; Ctnnb1fl/fl; Rosa26-YFP


title: yhjC myc-tag 2

tag: strain

tag: myc-tagging

value: YhjC myc-tagging cells

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: mKO_5


title: mKO_3


title: VCaP CT-ER rep3 [RNA-seq]

value: resistant


title: S_15-050_24wpi [1B2]

description:
Subject_050_Mild_20w.p.i [P1B2]
Subject_050 Male Mild 20w.p.i Total RNA

tag: age

value: Peripheral blood


title: yfeC myc-tag 2

value: YfeC myc-tagging cells

tag: chip-exo antibody


title: mKO_2


title: yfeC myc-tag 1


title: yciT myc-tag 2

value: YciT myc-tagging cells


title: yu1_S1_L001_R1_001

description:
Ribosome IP sample
cKO

value: frontal cortex

value: male

value: Fxr1 conditional knockout

value: parvalbumin neurons


title: yciT myc-tag 1


title: VCaP CT-BR rep2 [RNA-seq]

value: VCaP

value: RPMI 1640 supplemented with 10 % DCC-FBS, 1 % L-glutamine, 1 % A/A, and 10 nM testosterone for seven months + 10nM testosterone for 10 months + bicalutamide and subsequently with enzalutamide upon reaching bicalutamide insensitivity


title: VCaP CT-BR rep3 [RNA-seq]

value: prostate cancer cell line


title: S_15-050_16wpi [1B1]

description:
Subject_050_Mild_12w.p.i [P1B1]
Subject_050 Male Mild 12w.p.i Total RNA

tag: Sex

value: Male

tag: disease severity

value: Mild


title: S_15-018_24wpi [1B4]

description:
Subject_018_Severe_20w.p.i [P1B4]
Subject_018 Female Severe 20w.p.i Total RNA

value: Female

value: Severe

tag: rin

tag: sample number


title: yebK myc-tag 2

value: YebK myc-tagging cells


title: yebK myc-tag 1

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: mCtrl_4

value: MGE tissue

value: Embryonic day 14.5

value: Nkx2.1-cre; Ctnnb1fl/wt; Rosa26-YFP


title: S_15-027_16wpi [1A5]

description:
Subject_027_Critical_12w.p.i [P1A5]
Subject_027 Male Critical 12w.p.i Total RNA

value: Critical

tag: tissue

value: Peripheral blood

tag: timepoint


title: VCaP CT-ER rep1 [RNA-seq]

value: resistant

value: RPMI 1640 supplemented with 10 % DCC-FBS, 1 % L-glutamine, 1 % A/A, and 10 nM testosterone for seven months + 10nM testosterone for 10 months + 10 µM enzalutamide until the cells regained ability to grow despite enzalutamide


title: yggD myc-tag 2

value: YggD myc-tagging cells


title: S_15-048_24wpi [1A4]

description:
Subject_048_Severe_20w.p.i [P1A4]
Subject_048 Male Severe 20w.p.i Total RNA


title: yggD myc-tag 1


title: S_15-048_16wpi [1A3]

description:
Subject_048_Severe_12w.p.i [P1A3]
Subject_048 Male Severe 12w.p.i Total RNA


title: mKO_1

tag: genotype

value: Nkx2.1-cre; Ctnnb1fl/fl; Rosa26-YFP


title: mCtrl_3

value: Nkx2.1-cre; Rosa26-YFP


title: yfeD myc-tag 2

value: YfeD myc-tagging cells


title: mCtrl_1


title: VCaP CT-BR-ER rep1 [RNA-seq]

value: VCaP

tag: cell type

value: prostate cancer cell line

value: RPMI 1640 supplemented with 10 % DCC-FBS, 1 % L-glutamine, 1 % A/A, and 10 nM testosterone for seven months + 10nM testosterone for 10 months + bicalutamide until resistant +  enzalutamide until resistant


title: S_15-063_16wpi [1A1]

description:
Subject_063_Mild_12w.p.i [P1A1]
Subject_063 Male Mild 12w.p.i Total RNA

value: Male

value: Mild


title: VCaP CT-BR-ER rep3 [RNA-seq]

tag: cell line


title: S_15-027_24wpi [1A6]

description:
Subject_027_Critical_20w.p.i [P1A6]
Subject_027 Male Critical 20w.p.i Total RNA


title: yfeD myc-tag 1

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: HelaS345CKO_GFP_plus45COE_2

status: Public on Aug 16 2021

city: Copenhagen

first: Anders

middle: Henrik

last: Lund

address: Ole Maaløes Vej 5

country: Denmark

institute: University of Copenhagen,BRIC

description:
Derivative of HeLaS3_45CKO cells expressing GFP and SNORD45C
RMS_18S_28S_HelaS345CKO_GFP_plus45COE

data_processing:
Library strategy: RiboMeth-Seq
Reads per sequencing barcode de-multiplexed using a python script
Adaptor trimming using Cutadapt v. 1.2.1
Mapping to rRNA reference sequence using Bowtie2 v. 2.1.0
Counting of 5' and 3' read ends and calculation of RiboMeth-seq scores performed using RMS analysis python script
Genome_build: Human 18S and 28S rRNA sequences, based on Human ribosomal DNA complete repeating unit (gi|555853|gb|U13369.1|HSU13369 and gi|555853|gb|U13369.1|HSU13369), corrected according to high-depth sequecing coverage as defined previously in Krogh, N. and Jannson, M. et al. Profiling of 2'-O-Me in human rRNA reveals a subset of fractionally modified positions and provides evidence for ribosome heterogeneity. Nucleic acids research 44, 7884–7895 (2016).
Supplementary_files_format_and_content: Microsoft Excel files containing 5' and 3' read counts and the calculated RMS score at each nucleotide position the 18S and 28S rRNA sequences for each of three replicate RMS libraries. 2´-O-methylated rRNA psoritons (Nm), corresponding C/D box snoRNA guide RNAs (SNORD), mean RMS score and SD for each rRNA position are also given.

source_name: HeLaS3 45CKO-GFP+45C cells

growth_protocol: HeLaS3 cervical adenocarcinoma; HCT116 and HCT116p53-/- colorectal carcinoma; DLD1 colorectal carcinoma; BJhTERT immortalised fibroblasts. HeLaS3 and BJ-hTERT were the parental lines for HeLaS3-45CKO, HeLaS3-GFP, HeLaS3-45CKO-GFP, HeLaS3-45CKO-GFP+45C and BJ-MYC cells respectively. All cells were grown at 37°C, in 5% CO2, as adherent monolayer cultures on Nunclon™Δ Polystyrene dishes/plates (Nunc). Cells were maintained in DMEM (HeLaS3 and derivatives; and BJMYC) with GlutaMAX™ and Pyruvate (ThermoFisher), McCoy’s 5A (HCT116), or RPMI-1640 (DLD1). All media were supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA preparations were performed using QIAZOL (Qiagen), according to the manufacturer’s instructions.
RiboMeth-seq library construction and sequencing were performed as previously described in Krogh, N. and Jannson, M. et al. Profiling of 2'-O-Me in human rRNA reveals a subset of fractionally modified positions and provides evidence for ribosome heterogeneity. Nucleic acids research 44, 7884–7895 (2016). Briefly, triplicate libraries were produced for each cell line or condition analysed grown to ∼70–80% confluence before harvest. 4–5 µg of total RNA or purified 18S and 28S subunit rRNA (combined at 1:2.6 weight ratios to give approximate 1:1 molar ratio) were used for input. RNA was partially degraded in alkaline at denaturing temperatures. The 20–40nt fragments were purified by polyacrylamide gel electrophoresis and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2′,3′ cyclic phosphate and 5′-phosphate ends. The libraries were sequenced on the Ion Proton platform using Ion PI™ Chip Kit v3 (Life Technologies).

treatment_protocol: Specific treatment was only applied to BJ-MYC cells, where to induce MYC expression, 100ng/mL doxycycline was added to media 72 (BJ-MYC plus72) or 120h (BJ-MYC plus120) before harvest, or not added (BJ-MYC minus).

tag: genotype/variation


title: HelaS345CKO_GFP_plus45COE_3


title: VCaP CT-BR-ER rep2 [RNA-seq]

tag: androgen sensitivity

tag: treatment


title: HelaS3_45CKO_GFP_3

description:
Derivative of HeLaS3_45CKO cells expressing GFP
RMS_18S_28S_HelaS345CKO_GFP

source_name: HeLaS3 45CKO-GFP cells


title: HelaS3_45CKO_3

description:
Derivative of HeLaS3 cells where SNORD45Cis deleted
RMS_18S_28S_HelaS345CKO

source_name: HeLaS3 45CKO cells


title: S_15-063_24wpi [1A2]

description:
Subject_063_Mild_20w.p.i [P1A2]
Subject_063 Male Mild 20w.p.i Total RNA


title: HelaS3_45CKO_GFP_1


title: HelaS345CKO_GFP_plus45COE_1


title: HelaS3_45CKO_GFP_2


title: VCaP CT-BR rep1 [RNA-seq]

value: RPMI 1640 supplemented with 10 % DCC-FBS, 1 % L-glutamine, 1 % A/A, and 10 nM testosterone for seven months + 10nM testosterone for 10 months + bicalutamide and subsequently with enzalutamide upon reaching bicalutamide insensitivity


title: DLD1_3

description:
Colorectal carcinoma derived cell line
RMS_18S_28S_DLD1

source_name: DLD1 cells


title: DLD1_2


title: HCT116_p53minus_2

description:
Derivative of HCT116 colorectal carcinoma cells where TP53 is deleted
RMS_18S_28S_HCT116_p53minus

source_name: HCT116 p53-/- cells


title: mCtrl_2

tag: cell-type/tissue

value: MGE tissue

tag: Stage

value: Embryonic day 14.5


title: HelaS3_45CKO_2


title: HCT116_p53minus_3


title: HelaS3_45CKO_1


title: HCT116_p53minus_1


title: BJ_hTERT_3

description:
Foreskin fibroblast cells immortalised by hTERT expression
RMS_18S_28S_BJ_hTERT

source_name: BJ hTERT cells

value: BJ hTERT cells


title: BJ_hTERT_2


title: BJ_MYC_plus120_1

description:
BJ MYC cells, derived from BJ hTERT cells, where expression of MYC is induced for 120h
RMS_18S_28S_BJ_MYC_120h_plus

source_name: BJ MYC cells

value: BJ MYC cells


title: BJ_MYC_plus72_1

description:
BJ MYC cells, derived from BJ hTERT cells, where expression of MYC is induced for 72h
RMS_18S_28S_BJ_MYC_72h_plus


title: BJ_MYC_plus120_2


title: DLD1_1


title: BJ_MYC_minus_3

description:
BJ MYC cells, derived from BJ hTERT cells, where expression of MYC is not induced
RMS_18S_28S_BJ_MYC_minus


title: BJ_MYC_plus72_3


title: Control [1_0630]

city: Bunkyo-Ku

first: Ken

last: Tajima

state: Tokyo

address: 2-1-1 Hongo

department: Department of Respiratory Medicine

institute: Juntendo University

data_processing:
Reads were aligned using the BWA algorithm (mem mode; default settings). Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality >= 1) were used for further analysis.
Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files.
Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 1e-7, without control file, and with the –nomodel option. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Genomic “signal maps” stored in bigWig files using wigToBigWig (v4).

growth_protocol: ACC-MESO-1 cells were maintained in RPMI-1640 medium (Wako, Osaka, Japan) supplemented with 10% fetal bovine serum (FBS), penicillin (100 U/mL), and streptomycin (100 μg/mL) at 37 ℃ in 5% CO2.

extract_protocol:
Cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina).
Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter). Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems), and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina).

value: mesothelioma

tag: shRNA

value: Control


title: BJ_MYC_minus_2


title: BJ_MYC_plus72_2


title: ShLSD1 [4_0633]


title: PAC4Tmemo

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

data_processing:
RNA-seq processing:
Adapters, polyA and remaining ribosomal sequences were removed with bbduk (http://sourceforge.net/projects/bbmap/). A downsampling of reads was performed to balanced the number of reads across the samples. The resulting reads were analysed with the nextpresso(1) pipeline as follows: sequencing quality was checked with FastQC v0.11.0 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the human genome (GRCh38) with TopHat2(2) using Bowtie1(3) and Samtools(4), allowing 3 mismatches and 20 multihits. The Gencode v37 gene annotation for GRCh38 was used. Read counts were obtained with HTSeq(5). Differential expression and normalization was performed with DESeq2(6), keeping only those genes with more than 2 normalized counts in at least 30% of the samples. Finally, those genes that had an adjusted p-value below 0.05 FDR were selected. GSEAPreranked(7) was used to perform gene set enrichment analysis for the selected gene signatures on a pre-ranked gene list, setting 1000 gene set permutations. Only those gene sets with significant enrichment levels (FDR q-value < 0.25) were considered.
Genome_build: GRCh38
Supplementary_files_format_and_content: Normalized counts obtained with DESeq2

source_name: peripheral blood

growth_protocol: Peripheral blood mononuclear cells were activated and expanded for 10 days, achieving NKAE cell expansion by co-culture with irradiated Clone9.mbIL21 feeder cells in RPMI medium supplemented with 10% human AB serum plus 100 IU/mL IL-2. T cells culture CD45RA+ cells were depleted by labelling of PBMCs with CD45RA microbeads (Miltenyi Biotec) for magnetic cell separation according to the manufacturer’s instructions. Purified CD45RA− cells were primed at 2 × 106 cells/mL overnight in X-VIVO-15 (Lonza, Basel, Switzerland) supplemented with 250 IU/mL IL-2, 10 ng/mL anti-CD3 (OKT3), and 10 ng/mL anti-CD28 antibody (28.2).

extract_protocol:
Cell pellets were frozen in RLT buffer. RNA was extracted using the AllPrep DNA/RNA/protein Mini Kit (Qiagen)
Ribosomal RNA was depleted with the NEBNext rRNA Depletion Kit (E6310L) and RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760S), using indexes from NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1, E7600S). Reads were sequenced in paired-end fashion (76bp x 2) in a NextSeq 500/550 sequencer, with a High Output v2 kit. Stranded RNA-seq

treatment_protocol: NKAE cells were isolated from NKAE cultures using an NK Cell Isolation Kit (Miltenyi Biotec) and were seeded at 2×106 cells/mL. The following day, transduction was performed with a multiplicity of infection (MOI) of 5, on plates coated with RetroNectin®. Two days later, the cells were harvested for experiments. T cells were  transduced (MOI=5) on RetroNectin®-coated plates. After 10 days, the cells were harvested for experiments.

value: T cells

value: Stimulation with CD3 and CD8 antibodies and NKG2D-CAR transduction


title: PAC4NKAE

value: Natural killer cells (NK)

value: Activation and expansion with Clone9.mbIL21 cells and NKG2D-CAR transduction


title: PAC4CARTmemo


title: BJ_MYC_minus_1


title: BJ_hTERT_1


title: PAC5NKAE


title: PAC3CARNKAE


title: ShLSD1 [3_0632]


title: PAC5CARNKAE


title: BJ_MYC_plus120_3


title: PAC3NKAE


title: PAC4CARNKAE


title: Control [2_0631]


title: PAC2NKAE


title: PAC1CARTmemo


title: PAC2CARNKAE


title: PAC1Tmemo


title: PAC1CARNKAE


title: HelaS3_45CKO_RP_1

data_processing:
The sequencing data was demultiplexed using Illumina bcl2fastq (v2.20.0.422). Parameters: –barcode-mismatches 1 --create-fastq-for-index-reads --no-lane-splitting
Adaptor sequences were removed with cutadapt (v1.18) Parameters: -q 30,30 --minimum-length 20 --discard-untrimmed --trim-n -o
Reads derived from RPF and total RNA were aligned to known human rRNA and tRNA sequences with bowtie2 (v2.2.9). Mapped reads were discarded. Parameters: --local -D 20 -R 3 -N 1 -L 20 -i S,1,0.75
Cleaned reads were aligned to GRCh38.p12 (Ensembl v.97) with STAR (STAR-2.5.1a). Only reads mapping to HUGO approved genes were retained for downstream analysis. Parameters: --runMode alignReads –outFilterMultimapNmax 50 --outFilterMismatchNoverLmax 0.075 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0.95 --outSAMheaderCommentFile COfile.txt --outSAMattributes All --outSAMheaderHD @HD VN:1.4 SO:coordinate --genomeLoad NoSharedMemory --outSAMunmapped None  --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM  --limitBAMsortRAM 60000000000 --chimSegmentMin 1 --chimOutType SeparateSAMold --twopassMode Basic outWigType wiggle
RPF read alignment files were filtered with samtools (v1.10) to retain only 29 to 34nt read lengths . No read length filtering was applied to the total RNA alignment files.
The transcript coordinate alignments files were converted into genomic coordinate alignments with RSEM. Commands: rsem-prepare-reference and rsem-tbam2gbam
A single canonical transcript representing each protein-coding gene was selected from Ensembl GRCh38 gtf file. FeatureCounts (v1.5.1) was used to generate counts of reads mapping to exons of these transcripts for total RNA and RPF. Parameters: i.exon: featureCounts -R  -t exon -g transcript_id -O -M -Q 0 --largestOverlap   ii.3UTR: featureCounts -R  -t three_prime_utr -g transcript_id -O -M -Q 0 --largestOverlap --fracOverlap 0.72  iii.5UTR: featureCounts -R  -t five_prime_utr -g transcript_id -O -M -Q 0 --largestOverlap --fracOverlap 0.53
RPF and total RNA alignment files were extracted to have only exon assigned reads in FeatureCounts. All alignments were converted to CPM normalized wig files with bamCoverage functionality of deeptools (v3.3.1).  Replicates of each library were merged with WiggleTools (v1.2.3) and converted to bigwig files with wigToBigWig (v4). Paremeters: bamCoverage –binSize 1 --normalizeUsing CPM  && wiggletools write mean && wigToBigWig
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Exon spanning alignments of RPF and total RNA were converted to bigwig files with deeptools (v3.3.1). Replicates for each condition were CPM normalised individually. The Replicates from each condition were merged by calculating their mean coverage per base. For RPF bigwig files, only exon spanning 29-34nt reads were included. For total RNA bigwig files, no filtering for read length applied. Reads mapping to the canonical transcripts selected to represent each protein-coding are included in the bigwig files.

source_name: HelaS3 SNORD45C knockout cells

growth_protocol: HelaS3 (American Type Culture Collection, Manassas, VA, USA) and HelaS3-SNORD45C-KO cells (CRISPR-Cas9 knockout of SNORD45C) were propagated on Nunclon™Δ Polystyrene dishes (Nunc) in DMEM with GlutaMAX™ and Pyruvate (Thermofisher) supplemented with 10% foetal bovine serum. No antibiotics were added to the media.

extract_protocol:
Three individual replicates for each of the two cell lines were collected. A single 15cm dish corresponding to one replicate was harvested at a time. For each replicate, cell media was aspirated and cells washed with ice-cold PBS. No cycloheximide pre-treatment was was performed. After thorough removal of the PBS, the dish was fully immersed in liquid nitrogen and placed on dry ice. For cell lysis, 1ml of 1x Mammalian Lysis Buffer (Illumina) containing 100 μg/ml cycloheximide was added dropwise to the dish which was then placed on wet ice. Cells were then scraped off to the lower portion of the dish and allowed to thaw in the lysis buffer. Lysate was homogenised by pipetting and triturated ten times through a 25-gauge needle. The lysate was then transferred to a DNA LoBind 1.5ml microfuge tube (Eppendorf) and incubated on ice for 5min. The lysate was cleared by centrifugation at 20000g, 4°C for 10 minutes and the supernatant transferred to a fresh microfuge tube. Aliquots of 100 and 200µl were prepared for each replicate, flash-frozen in liquid nitrogen and stored at −80°C until further use. Thereafter, the protocol for TruSeq Ribo Profile Mammalian (Illumina) was followed to generate total RNA and ribosome protected fragment RNA-seq libraries corresponding to 3 individual replicates from each of the two cell lines.
TruSeq Ribo Profile Mammalian (Illumina), with the modifications given in "extract protocol" above

tag: molecule

value: ribosome protected fragment RNA


title: HelaS3_WT_RP_3

source_name: HelaS3 cells

value: wild type


title: HelaS3_45CKO_RP_3


title: HelaS3_45CKO_total_3

value: total RNA


title: HelaS3_45CKO_RP_2


title: HelaS3_WT_RP_1


title: HelaS3_45CKO_total_2


title: HelaS3_WT_total_2


title: HelaS3_WT_RP_2


title: HelaS3_WT_total_3


title: HelaS3_45CKO_total_1


title: Carboplatin-high Resistant SKOV3_1

city: SEONGNAM-SI

first: YOUN JUNG

last: KANG

address: 335 PANGYO-RO

department: MEDICINE

country: South Korea

institute: CHA University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

growth_protocol: SKOV3 cells were cultured in Roswell Park Memorial Institute (RPMI) 1640, HEPES Medium (GIBCO, USA) supplemented with 1% penicillin-streptomycin (GIBCO, USA) and 10% fetal bovine serum (FBS; GIBCO, USA). For the establishment of the carboplatin-resistant cell line, parental SKOV3 cells, which were not over passage 2, were continuously exposed to carboplatin (2.5uM/ml in DMSO stock solution, Selleckchem, S1215) for 3 months (passage 10; short-term resistant) and 6 months (passage 20; long term resistant)

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: parental SKOV3 ovarian cancer cells (non-R) were continuously treated with carboplatin (2.5uM) over 3 months for intermediate-resistance (Carbo-iR (over passage 10)) and over 6 months for high-resistance (Carbo-hR (over passage 20))

value: Human ovarian cancer cells


title: Carboplatin-high Resistant SKOV3_3


title: HelaS3_WT_total_1


title: Carboplatin-intermediate Resistant SKOV3_2


title: Carboplatin-high Resistant SKOV3_2


title: Non-resistance SKOV3_1


title: Carboplatin-intermediate Resistant SKOV3_3


title: PAC1NKAE


title: Non-resistance SKOV3_3


title: Non-resistance SKOV3_2


title: hTS-blast

city: Guangzhou

first: Tian

last: Zhang

state: Guangdong

address: 190 Kaiyuan Avenue,Science Park

institute: GIBH

description: hTS-blast

data_processing:
Illumina Casava1.7 software used for basecalling.
Briefly, reads were aligned to human genome (UCSC hg38) using HISAT2 (v2.0.4)
and gene expression was counted using samtools (v1.3.1) and htseq-count (v 0.6.0), filtered by a threshold of at least 20 averaged raw read counts among samples, and then normalized by GC-count and Gene-length using EDASeq (v2.12.0).
Differential expression and PCA plot were performed using DESeq (v 1.18.1) and genes with p-value < 0.05 and fold-change > 2 were considered as significant difference.
Correlation plot was performed using ggplot2 (v2.2.1) and heatmap was performed using pheatmap (v1.0.10).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: count

source_name: human trophoblast stem cells

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line/strain

value: human trophoblast stem cell line

value: human trophoblast stem cells

value: WT


title: H1-TSB

value: human embryonic stem cell H1 derived cells


title: H1-TSA


title: HN10-TSA

value: human embryonic stem cell HN10 derived cells


title: H1-ES

source_name: human embryonic stem cells

value: human embryonic stem cell H1

value: human embryonic stem cells


title: hTSC_INPUT

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were base-called and de-multiplexed using standard Illumina softwares. Bowtie2 was used to align the reads to the human genome hg38. Reads mapped to identical positions with same orientation in the genome were collapsed into one read.
The regions of H3K27me3 and H3K4me3 enrichment (peaks) were called using the SICER software package, with the input genomic DNA as a background control (parameters: W = 200; G = 600; FDR 0.01 cutoff applied).
Binding profiles and heatmaps were generated using ngsplot  and deeptools.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: bed

extract_protocol:
For  ChIP-seq, 1×10^7 cells of each sample were crosslinked in 1% formaldehyde with rotation for 10 minutes at room temperature. And then these crosslinked reactions were stopped by 0.125 M glycine with rotation for 5 minutes at room temperature. and cell sample were sonicated, and then ChIPed with H3K27me3 antibodies.
DNA libraries were prepared for sequencing using standard Illumina protocols.


title: HN10-TSB


title: Carboplatin-intermediate Resistant SKOV3_1


title: hTSC_H3K4me3

tag: chip antibody


title: hTSC-rp2

data_processing:
Illumina Casava1.7 software used for basecalling.
Adaptors were cut from reads using cutadapt (v1.13), and reads were aligned to human genome (UCSC hg38) using bowtie2 (v2.2.5).
Duplicates were removed using samtools (v1.3.1) and Picard Tools (v1.90). Signals were pileupped using MACS2 callpeak and bdgcmp, and differential open peaks were called using MACS2 bdgdiff
Signal density heatmap and profile were plotted using deeptools (v2.4.2), and motifs were found using homer.
Peaks were annotated with gene annotation using ChIPpeakAnno (v3.12.7) and gene ontology analysis was performed using clusterProfiler (v3.6.0).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: narrowPeak.gz

extract_protocol:
In brief, 5×10^4 cells of each sample were processed for ATAC-seq.
DNA libraries were prepared for sequencing using standard Illumina protocols.


title: hESC_INPUT

value: human embryonic stem cells H1


title: HN10-ES

value: human embryonic stem cell HN10


title: panel2_CX8.G1

city: Arlington

first: George

last: Locke

state: Massachusetts

department: Translational Medicine

institute: EMD Serono

description:
For transcriptome analysis of 4T1 tumors, total RNA was extracted and RNA sequencing (RNAseq) analyses were performed using a targeted mouse Immuno-Oncology panel (RMM-009Z, Qiagen) and a Qiaseq targeted RNA custom panel (Qiagen) with RT2 Profiler PCR arrays containing murine genes related to TGF-Î² signaling targets (PAMM-235Z), DNA damage signaling pathway (PAMM-029Z), DNA repair (PAMM-042Z), and fibrosis (PAMM-120Z).
10298z

data_processing:
primary analysis: Illumina Basespace
secondary analysis: QIAGEN Geneglobe (alignment, counting)
normalization: rlog (function exported by DESeq2, performed separately for each panel then rbind'ed together)
Genome_build: GRCm38
Supplementary_files_format_and_content: format: csv; content: raw counts and rlog of counts
processed data file column headers:
panel.id: panel1 is mouse Immuno-Oncology panel (RMM-009Z, Qiagen); panel2 is custom panel (Qiagen) with RT2 Profiler PCR arrays containing murine genes related to TGF-β signaling targets (PAMM-235Z), DNA damage signaling pathway (PAMM-029Z), DNA repair (PAMM-042Z), and fibrosis (PAMM-120Z).
gene.id: ensembl gene id
gene.symbol: official gene symbol
gene.strand: forward or reverse stranded probe
chrom: chromosome where this gene resides
loc.5..GRCh38: probe start position?  (note GRCh38 is Qiagen's error)
loc.3..GRCh38: probe end position?  (note GRCh38 is Qiagen's error)
control.type: the panel provides two different types of control probes: gDNA_control and reference_gene. This column is blank for "normal" gene probes.
single.exon: unknown

source_name: orthotopic tumor

value: orthotopic tumor

value: control

tag: tumor model

tag: mouse strain

value: BALB/c

tag: age

value: 6-12 weeks

tag: Sex

value: Female


title: panel2_CX6.G1

extract_protocol: total RNA was extracted and RNA sequencing (RNAseq) analyses were performed using a targeted mouse Immuno-Oncology panel (RMM-009Z, Qiagen)

tag: tissue


title: hESC_H3K27me3

tag: genotype

value: H3K27me3 (Millipore Cat.7-622, lot a1824d)


title: panel2_CX7.G1


title: hESC_H3K4me3

tag: cell type


title: hESC-rp2


title: hTSC-rp1


title: panel2_CX9.G1


title: panel2_CX5.G1


title: panel2_CX44.G5


title: panel2_CX43.G5


title: panel2_CX42.G5


title: panel2_CX41.G5


title: panel2_CX45.G5


title: panel2_CX40.G5


title: panel2_CX39.G5


title: panel2_CX26.G3

value: radiation


title: panel2_CX37.G5


title: panel2_CX4.G1


title: panel2_CX3.G1


title: panel2_CX20.G3


title: panel2_CX38.G5


title: hESC-rp1


title: panel2_CX25.G3


title: hTSC_H3K27me3


title: panel2_CX17.G2


title: panel2_CX13.G2


title: panel2_CX14.G2


title: panel2_CX15.G2


title: panel2_CX2.G1


title: panel2_CX19.G3


title: panel2_CX16.G2


title: panel2_CX23.G3


title: panel2_CX21.G3


title: panel2_CX18.G2


title: panel2_CX12.G2


title: panel1_CX9.G1

description:
For transcriptome analysis of 4T1 tumors, total RNA was extracted and RNA sequencing (RNAseq) analyses were performed using a targeted mouse Immuno-Oncology panel (RMM-009Z, Qiagen) and a Qiaseq targeted RNA custom panel (Qiagen) with RT2 Profiler PCR arrays containing murine genes related to TGF-Î² signaling targets (PAMM-235Z), DNA damage signaling pathway (PAMM-029Z), DNA repair (PAMM-042Z), and fibrosis (PAMM-120Z).
10309z


title: panel1_CX8.G1


title: panel1_CX6.G1


title: panel1_CX5.G1


title: panel2_CX22.G3


title: panel2_CX24.G3


title: panel2_CX10.G2


title: panel1_CX7.G1


title: panel1_CX42.G5


title: panel1_CX44.G5


title: panel1_CX41.G5


title: panel2_CX27.G3


title: panel2_CX11.G2


title: panel1_CX4.G1


title: panel1_CX39.G5


title: panel1_CX43.G5


title: panel2_CX1.G1


title: panel1_CX45.G5


title: panel1_CX37.G5


title: panel1_CX38.G5


title: panel1_CX25.G3


title: panel1_CX40.G5


title: panel1_CX26.G3


title: panel1_CX24.G3


title: panel1_CX22.G3


title: panel1_CX3.G1


title: panel1_CX20.G3


title: panel1_CX21.G3


title: panel1_CX18.G2


title: panel1_CX19.G3


title: panel1_CX27.G3


title: panel1_CX17.G2


title: panel1_CX23.G3


title: Parp1-Ctrl rep1 [WT_1]

city: Sacramento

first: Fuzheng

last: Guo

state: CA

address: 2425 Stockton Blvd

institute: University of California Davis

data_processing:
Raw image data file from high-throughput sequencing(Illumina ) was transformed to Sequenced Reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base  Calling). Raw Data is stored in FASTQ(fq) format files, which contain reads sequence and corresponding base quality.
Paired-end clean reads were aligned to the reference genome (mouse genome mm10) using STAR version2.5 (Spliced Transcripts Alignment to a Reference).
HTseq v0.6.1 was used to count the read numbers mapped of each gene. Readcount and normalized FPKM was calculated to indicate the expression level of all genes.
Differentially expressed genes (DEGs) were analyzed using DESeq version 2.1.6.3 and adjusted p value padj < 0.05 was assigned as DEGs.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file of FPKM values for all samples and all genes
Supplementary_files_format_and_content: tab-delimited text file of readcount values for all samples and all genes

source_name: Brain

extract_protocol:
Total RNA was prepared from forebrains of Pdgfrα-CreERT2, Parp1fl/fl mice (n = 3) and controls (n = 3) using QIAGEN RNeasy for lipid tissues with on-column DNase I digestion. The quality of RNA samples was determined by the Bioanalyzer 2100 system (Agilent Technologies). The RNA integrity number (RIN) of all our RNA samples used for RNA-seq and qPCR was greater than 6.8.
mRNA from the brain was purified from total RNA using poly-T oligo-attached magnetic beads. The resulting mRNA was fragmented randomly by addition of fragmentation buffer. The cDNA library was prepared using the NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs). The first strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). The second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Double-stranded cDNA is purified using AMPure XP beads. Remaining overhangs of the purified double-stranded cDNA are converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Finally, the final library is gotten by PCR amplification and purification of PCR products by AMPure XP beads.

treatment_protocol: Neonatal Parp1 cKO and control littermate were i.p. injected with tamoxifen at P1, P2, and P3 (once a day). Brain was harvested for total RNA preparation.

tag: strain

value: Brain

value: post natal day 9 (P9)

value: non-Cre Ctrl (Parp1fl/fl)

value: tamoxifen I.P. administered at  P1, P2, and P3

value: brain cells


title: Parp1-Ctrl rep2 [WT_2]


title: Parp1-cKO rep2 [KO_2]


title: panel1_CX2.G1


title: Parp1-cKO rep3 [KO_3]


title: panel1_CX16.G2


title: panel1_CX15.G2


title: panel1_CX12.G2


title: panel1_CX13.G2


title: GTGT16

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

country: France

institute: CIML

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were preprocessed in order to remove adapter, polyA and low-quality sequences (Phred quality score below 20). After this preprocessing, reads shorter than 40 bases were discarded for further analysis. These preprocessing steps were performed using cutadapt version 1.10.
Reads were mapped onto the mm10 assembly of Mus musculus genome using STAR version 2.5.3a.
Gene expression quantification was performed from uniquely aligned reads using htseq-count version 0.6.1p1, with annotations from Ensembl version 95 and “union” mode.
Genome_build: mm10
Supplementary_files_format_and_content: a tab separated file (csv) containing genes (ENSembl IDs) and associated raw counts

molecule: polyA RNA

source_name: YUMM1.7 tumors

growth_protocol: YUMM1.7 tumors in female IkbkbF/F and IkbkbΔXcr1, grown to a volume reaching 200-350mm3.

extract_protocol:
Tumors were minced and digested in RPMI 1640, 1 mg/ml Collagenase II (Sigma-Aldrich), 50 µg/ml DNaseI (Roche), and 0.1% (wt/vol) BSA for 30 min at 37°C with 750 rpm agitation. Cell suspensions were subsequently passed through a 70-µm cell strainer (BD Biosciences) and collected by centrifugation. Purification of total RNA from sorted cells was performed by using the RNeasy Plus Micro Kit (Qiagen) and concentration was determined using the Quant-IT RiboGreen RNA assay kit (Thermo Fisher Scientific).
Full length cDNA were generated from 1000 pg of total RNA using Clontech SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq-Amp polymerase. Six hundreds pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, CA) followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoreris.

treatment_protocol: No treatment has been applied apart from YUMM1.7 cell engraftment into female IkbkbF/F and IkbkbΔXcr1 mice


title: Parp1-Ctrl rep3 [WT_3]


title: panel1_CX14.G2


title: GTGT15


title: GTGT14


title: SC_S99_Control2

city: Berkeley

first: Karthik

last: Shekhar

address: 101D Gilman Hall

institute: University of California, Berkeley

data_processing:
Samples were aligned to the transcriptome using Bowtie2 and gene expression was quantified using RSEM
Genome_build: mm10
Supplementary_files_format_and_content: Txt files including the gene expression matrix

source_name: Mouse small intestine stem cells

extract_protocol:
Lgr5+ cells were extracted from mice either fed a control diet or high fat diet using FACS
Smart-seq2 (Picelli et al., 2014)

tag: diet


title: Parp1-cKO rep1 [KO_1]


title: GTGT10


title: GTGT13


title: panel1_CX10.G2


title: GTGT12


title: SC_S98_Control2


title: panel1_CX1.G1


title: GTGT8

value: IKKbFF


title: GTGT7


title: GTGT6


title: GTGT11


title: GTGT9


title: SC_S94_Control1


title: panel1_CX11.G2


title: SC_S91_Control1


title: SC_S92_Control1


title: GTGT2


title: SC_S93_Control1


title: GTGT3


title: GTGT5


title: GTGT1


title: SC_S97_Control2


title: GTGT4


title: SC_S90_Control1


title: SC_S89_Control1


title: SC_S87_Control1


title: SC_S9_Control1


title: SC_S8_Control1


title: RTIT3 V(D)J scRNA-seq

city: Lausanne

first: Isaac

last: Crespo

state: Vaud

address: Rue de Bugnon

department: CHUV-Oncology

country: Switzerland

institute: UNIL

data_processing:
Sequencing data were demultiplexed using the bcl2fastq2 Conversion Software (version 2.20, Illumina) and primary data analysis performed with Cell Ranger (version 3.1.0) and aligning to the GRC38 genome build and genome annotation release 94 from Ensembl.
Genome_build: GRCm38
Supplementary_files_format_and_content: QC filtered cell ranger output consists of gene by barcode (cell) count matrices in sparse matrix market format (mtx) and corresponding row and column annotation in *features.tsv and *barcode.tsv files

source_name: Tumor infiltrating immune cells

extract_protocol:
mRNA was isolated using the Dynabeads mRNA DIRECT purification kit (Lifetechnologies) and was then amplified using the MessageAmp II aRNA Amplification Kit (Ambion) with the following modifications: in vitro transcription was performed at 37°C for 16h. First strand cDNA was synthesized using the Superscript III (Thermofisher) and a collection of TRAV/TRBV specific primers. TCRs were then amplified by PCR (20 cycles with the Phusion from NEB) with a single primer pair binding to the constant region and the adapter linked to the TRAV/TRBV primers added during the reverse transcription. A second round of PCR (25 cycles with the Phusion from NEB) was performed to add the Illumina adapters containing the different indexes. The TCR products were purified with AMPure XP beads (Beckman Coulter), quantified and loaded on the MiniSeq instrument (Illumina) for deep sequencing of the TCRa/TCRb chain.
A Chromium Next GEM Chip G (10X genomics) was loaded with the appropriate number of cells, and the sequencing libraries prepared with the Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 following the manufacturer’s recommendations. Briefly, an emulsion encapsulating single cells, reverse transcription reagents and cell barcoding oligonucleotides was generated. After the actual reverse transcription step, the emulsion was broken, and double stranded cDNA generated and amplified in a bulk reaction.
For 5’ gene expression library this cDNA was fragmented, ligated to a sequencing adaptor, and PCR amplified. For V(D)J library preparation, a similar approach was followed except that 2 steps of PCR based V(D)J target enrichment were performed prior to fragmentation.
Libraries were quantified by a fluorimetric method and their quality assessed on a Fragment Analyzer (Agilent Technologies). Cluster generation was performed with 140 to 165 pM of an equimolar pool from the resulting libraries using the Illumina HiSeq 3000/4000 PE Cluster Kit reagents. Sequencing was performed on the Illumina HiSeq 4000 using HiSeq 3000/4000 SBS Kit reagents according to 10X Genomics recommendations (26 cycles read1, 8 cycles i7 index read, and 91 cycles read2).

value: Tumor infiltrating immune cells were -pre-sorted to include the following populations:CD8+ CD3+ gate, and, CD4+ CD3+ gate

value: cyclophophamide + aPD1+aCTLA4+aCD40ag  + low-dose Rx (1 gray each)


title: SC_S85_Control1


title: SC_S88_Control1


title: RTIT2 V(D)J scRNA-seq


title: SC_S83_Control1


title: NTT V(D)J scRNA-seq


title: IT V(D)J scRNA-seq


title: SC_S80_Control1


title: SC_S86_Control1


title: Myeloid scRNA-seq

extract_protocol:
RNA from snap frozen tissue biopsies was extracted using the RNA easy kit (Qiagen, Hilden, Germany). RNA quality was assessed using the Fragment Analyzer (Advances Analytical Technologies Inc., Ankeny, USA). RNA-seq libraries were prepared from 250 ng of total RNA. The RNA samples were depleted for ribosomal RNAs with the Illumina TruSeq Stranded Total RNA Gold kit. Ribosomal-RNA depleted RNA was then converted in cDNA and amplified with the kit Nugen Ovation® RNA-Seq System V2. It was used to generate sequencing libraries with the Illumina TruSeq DNA Nano kit.
A Chromium Next GEM Chip G (10X genomics) was loaded with the appropriate number of cells, and the sequencing libraries prepared with the Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 following the manufacturer’s recommendations. Briefly, an emulsion encapsulating single cells, reverse transcription reagents and cell barcoding oligonucleotides was generated. After the actual reverse transcription step, the emulsion was broken, and double stranded cDNA generated and amplified in a bulk reaction.
For 5’ gene expression library this cDNA was fragmented, ligated to a sequencing adaptor, and PCR amplified. For V(D)J library preparation, a similar approach was followed except that 2 steps of PCR based V(D)J target enrichment were performed prior to fragmentation.
Libraries were quantified by a fluorimetric method and their quality assessed on a Fragment Analyzer (Agilent Technologies). Cluster generation was performed with 140 to 165 pM of an equimolar pool from the resulting libraries using the Illumina HiSeq 3000/4000 PE Cluster Kit reagents. Sequencing was performed on the Illumina HiSeq 4000 using HiSeq 3000/4000 SBS Kit reagents according to 10X Genomics recommendations (26 cycles read1, 8 cycles i7 index read, and 91 cycles read2).

value: Tumor infiltrating immune cells were pre-sorted to include the following populations:CD8+ CD3+ gate, and, CD4+ CD3+ gate Cd11b+Cd11c-, gate Cd11b+Cd11c+, and, gate Cd11b-Cd11c

value: none; cyclophophamide + aPD1+aCTLA4+aCD40ag; cyclophophamide + aPD1+aCTLA4+aCD40ag  + low-dose Rx (1 gray each)


title: Yap_deleted_RNAseq3

city: Cincinnati

first: John

middle: M.

last: Snowball

state: OH

address: 3333 Burnet Ave

department: Pulmonary Research

institute: Cincinnati Childrens Hospital

description:
counts_yap_deleted.csv
none

data_processing:
FASTQ files were trimmed using Trimgalore and then  aligned using Bowtie2 to mouse reference genome mm10.
RNAseq Normalized gene expressions were generated using Cufflinks.
RNAseq Gene counts were obtained using Bioconductor’s GenomicAlignment.
DeSeq was used to analyze the RNAseq raw gene counts and calculate differentially expressed genes
Duplicate reads, Mitochondrial reads and reads over 100bp were removed from ATAC seq bam files pre analyses.
Mac2 or Homer was used to determine differentially open peaks.
Atac seq samples were only compared to littermate control and resulting peak files were merged.
Merged peak files annotated with Homer.
Genome_build: mm10
Supplementary_files_format_and_content: text file of RNA raw counts

source_name: Epcam+ Lung cells

extract_protocol:
RNA and Chromatin was isolated from sorted EPCAM+ lung epithelial cells as follows: AT2 cells were isolated using MACs magnetic bead (Miltenyi Biotec) selection of CD45 (BIOLEGEND), CD16/32 (Fisher), Ter119 (BIOLEGEND), CD90.2 (BIOLEGEND), CD271 (Miltenyi Biotec), and CD31 (BIOLEGEND) negative cells followed by positive selection of CD326 (Miltenyi Biotec) positive cells. Samples were split with 50,000 cells being used for ATACseq library  prep, while remaining cells were used for RNA isolation via Qiagen RNAeasy minikit with on-column DNAse digestion.
RNAseq: Libraries were prepared with Illumina RNA PolyA selection, ATAC libraries were prepared using Illumina Nextera XT library kit
RNAseq: 20-30 million reads ; Illumina HiSeq 2x150 bp sequencing, ATACseq: 50 million reads ; Illumina HiSeq 2x150 bp sequencing

treatment_protocol: Yap1 was either genetically activated or deleted at PND3 in mice AT2 cells which were then collected at PND14 via Epcam+ sorting and submitted for RNA and ATAC sequencing.

value: lung

value: Yapflox/flox SftpcCreert2

tag: yap status


title: Yap_deleted_RNAseq5

description:
counts_yap_deleted.csv
none


title: Yap_deleted_RNAseq4

description:
counts_yap_deleted.csv
none


title: SC_S76_Control1

value: control


title: Lymphoid scRNA-seq

tag: treatment


title: SC_S75_Control1


title: SC_S84_Control1


title: SC_S77_Control1


title: SC_S82_Control1


title: SC_S81_Control1


title: Yap_deleted_control_RNAseq2

description:
counts_yap_deleted.csv
none

value: Yapflox/flox


title: RTIT1 V(D)J scRNA-seq


title: Yap_deleted_control_Atac1

description:
Homer_Yap_deleted_closed_chromatin.txt
none


title: SC_S73_Control1


title: Yap_deleted_RNAseq2

description:
counts_yap_deleted.csv
none


title: SC_S79_Control1


title: SC_S7_Control1


title: SC_S70_Control1


title: Yap_active_RNAseq5

description:
counts_yap_active.csv
none


title: SC_S6_Control1


title: SC_S69_Control1


title: SC_S68_Control1


title: Yap_deleted_control_RNAseq1

description:
counts_yap_deleted.csv
none


title: SC_S74_Control1


title: SC_S64_Control1


title: Yap_deleted_RNAseq1

description:
counts_yap_deleted.csv
none


title: Yap_deleted_Atac2

description:
Homer_Yap_deleted_open_chromatin.txt
none


title: SC_S78_Control1


title: Yap_active_RNAseq6

description:
counts_yap_active.csv
none


title: SC_S72_Control1


title: Yap_deleted_Atac1


title: Yap_deleted_control_RNAseq4

description:
counts_yap_deleted.csv
none


title: Yap_active_RNAseq2

description:
counts_yap_active.csv
none


title: Yap_active_control_RNAseq2

description:
counts_yap_active.csv
none


title: SC_S71_Control1


title: Yap_active_control_RNAseq3

description:
counts_yap_active.csv
none


title: Yap_deleted_control_RNAseq3

description:
counts_yap_deleted.csv
none


title: SC_S63_Control1


title: Yap_active_RNAseq3

description:
counts_yap_active.csv
none


title: Yap_active_RNAseq4

description:
counts_yap_active.csv
none


title: Yap_active_RNAseq1

description:
counts_yap_active.csv
none


title: SC_S66_Control1


title: Yap_active_control_RNAseq4

description:
counts_yap_active.csv
none


title: SC_S65_Control1


title: SC_S5_Control1


title: SC_S67_Control1


title: Yap_active_control_Atac3


title: Yap_active_control_RNAseq1

description:
counts_yap_active.csv
none


title: Yap_active_Atac2

description:
Homer_Yap_active_open_chromatin.txt
Macs_up_mst_broadR1_peaks.broadPeak


title: SC_S62_Control1


title: SC_S58_Control1


title: Yap_active_Atac3


title: SC_S55_Control1


title: SC_S60_Control1


title: SC_S54_Control1


title: RUNX1mut1HSCPs

city: Hachioji

first: Yoshihiro

last: Hayashi

address: 1432-1 Horinouchi

institute: Tokyo University of Pharmacy and Life Sciences

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
FASTQ files were processed in the AltAnalyze (version 2.1.0)
Transcript per million estimates were calculated in AltAnalyze through a built-in call to Kallisto for read pseudoalignment and transcript quantification (Ensembl 72, mm10)
Genome_build: mm10
Supplementary_files_format_and_content: raw counts with genes in rows and samples in columns

extract_protocol:
Bone marrow cells were harvested from individual mice. HSCPs were purified using EasySep Mice CD117 positive selection kit and mutant clone was FACS sorted. Ly6G+ mutant myeloid BM cells were FACS sorted. The total RNA was isorated using RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: genotype/variation

value: RUNX1 mutant

value: BM HSCPs


title: SC_S56_Control1


title: Yap_active_control_Atac2

description:
Homer_Yap_active_closed_chromatin.txt
Macs_up_wt_broadR1_peaks.broadPeak


title: Yap_active_control_Atac1


title: Yap_active_Atac1


title: CBL-RUNX1mut2HSCPs

value: CBL/RUNX1 mutant


title: SC_S57_Control1


title: CBLmut1HSCPs

source_name: CBLmutHSCPs

value: CBL mutant


title: SC_S59_Control1


title: SC_S53_Control1


title: SC_S50_Control1


title: SC_S52_Control1


title: CBLmut2HSCPs


title: SC_S4_Control1


title: CBL-RUNX1mut1HSCPs


title: SC_S61_Control1


title: WT2HSCPs

source_name: WTHSCPs

value: wild type


title: WT1HSCPs


title: 962_1G

city: Solna

first: Jan

middle: Eric

last: Grosser

address: Solnavägen 9

country: Sweden

institute: Karolinska institutet

data_processing:
FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used for quality control of the .fastq-files.
Adapter and poor quality read trimming was performed with cutadapt.
The ChIP-seq data was mapped with the aligner BowTie2. The mapped files were sorted using samtools and aligned to the yeast genome version SacCer3.
The mapped data was deduplicated using the MarkDuplicates tool from the Picard tool set.
The bamCompare command of the deepTools suite was used to generate bigWig-files from the deduplicated .bam-files by normalizing the coverage of the Pol-eta IPs to their respective input.
Genome_build: SacCer3 downloaded from UCSC genome browser.
Supplementary_files_format_and_content: 8 bigWig files with the coverage of the Pol-eta IPs was normalized to the input coverage.

organism: Saccharomyces cerevisiae

source_name: whole cells

growth_protocol: Exponentially growing yeast cells in YEP media supplemented with 2% raffinose (final) were treated with 80 μg/ml (final) benomyl for 3 hours. The 'G2' samples were collected when cells were arrested in G2/M phase.

extract_protocol:
Cells were fixed with formaldehyde (final 1 %) for 20 minutes at room temperature, followed by addition of glycine (final 125 mM, 5 minutes) prior to harvest. Myc-tag Polη was immunoprecipitated based on protocol described in Gali VK 2017, with modifications.
An equal amount of DNA for both IPs and inputs was used for library preparation via the ThruPLEX DNA-seq by Takara Bio. After library preparation, size selection was performed using AMPure XP beads for fragments between 200 and 700 bp.
Pol-eta ChIP-Seq

treatment_protocol: Galactose (final 2%) was then added to induce DSBs (PGAL-HO) for 1-hour, to collect the '1G' samples.

tag: derivative

value: W303 derivatives

tag: antibody

value: Polη-Myc IP-2

tag: phase

value: G2/M arrest + 1-hr DSB


title: SC_S46_Control1


title: SC_S48_Control1


title: SC_S51_Control1


title: SC_S44_Control1


title: 962_IN_1G

value: Polη-Myc input-2


title: RUNX1mut2HSCPs


title: SC_S43_Control1


title: 081_IN_1G

value: Polη-untagged control input-1


title: SC_S42_Control1


title: SC_S41_Control1


title: 961_IN_1G

value: Polη-Myc input-1


title: 081_1G

value: Polη-untagged control IP-1


title: 082_IN_1G

value: Polη-untagged control input-2


title: SC_S49_Control1


title: SC_S45_Control1


title: 962_IN_G2

value: G2/M arrest


title: SC_S47_Control1


title: 961_1G

value: Polη-Myc IP-1


title: SC_S3_Control1

value: control


title: 082_G2

value: Polη-untagged control IP-2


title: 082_1G


title: 081_G2


title: 961_G2


title: SC_S38_Control1


title: SC_S40_Control1


title: SC_S382_HFD2

value: HFD


title: SC_S381_HFD2


title: 081_IN_G2


title: 082_IN_G2


title: SC_S378_HFD2


title: SC_S379_HFD2


title: SC_S37_Control1


title: 962_G2


title: SC_S377_HFD2


title: SC_S39_Control1


title: SC_S376_HFD2


title: SC_S374_HFD2


title: SC_S372_HFD2


title: SC_S375_HFD2


title: SC_S371_HFD2


title: SC_S370_HFD2


title: SC_S36_Control1


title: SC_S380_HFD2


title: 961_IN_G2


title: SC_S369_HFD2


title: liver_A22_M rep 6

type: RNA

city: Saint-Pée-sur-Nivelle

first: Thérèse

last: Callet

institute: INRA

description: Gene expression after 6 months of feeding

hyb_protocol: 600ng of Cy3-cRNA was thenfragmented with specific buffer (30 minutes at 60°C) and hybridized on a sub-array. Hybridisation was performed in a microarray hybridization oven (Agilent) for 17h at 65°C.

scan_protocol: After a washing step, slides were scanned (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (3μm and 20bits). Data were then obtained with the Agilent Feature Extraction software (10.7.1.1).

data_processing: Data from microarray analysis were transformed with a logarithmic transformation, scale-normalized and analysed using the package limma from R.

organism: Oncorhynchus mykiss

label_protocol: For each sample, 150 ng of total RNA was amplified and labelled using Cy3-CTP according to the manufacturer’s instructions (Agilent). cRNA were obtained by first reverse transcribed RNA, using a polyDT T7 primer (denaturation step: 10min at 65°C, reaction step: 2hr at 40°C, inactivation step: 5min at 70°C). cRNA were then labeled with Cy3-dye (2hr at 40°C). Excess dye was removed using a RNeasy kit (Qiagen). The level of dye incorporation was evaluated using a spectrophotometer (Nanodrop ND1000, LabTech)

growth_protocol: Fish were fed since the 1st feeding with either a plant-based diet completly devoid of fish oil and fish meal (V diet) or a marine resources based diet (ad libitum: M diet or restricted: MR diet). After 6 months of feeding, liver of 6 fish per condition were sampled.

extract_protocol: Total RNA was extracted from 6 individual fry per treatment, using the TRIzol reagent method (Invitrogen, Carlsbad, CA, USA), according to the manufacturer’s recommendations.

value: liver

value: 6 months

tag: line

value: M


title: liver_AB1_MR rep 6

value: MR


title: liver_AB1_V rep 7

value: V


title: liver_A22_M rep 5


title: liver_A22_V rep 6


title: liver_A22_MR rep 6


title: SC_S368_HFD2


title: liver_R23_MR rep 6


title: SC_S366_HFD2


title: SC_S367_HFD2


title: liver_R23_V rep6


title: SC_S365_HFD2


title: liver_R23_M rep 6


title: SC_S373_HFD2


title: SC_S364_HFD2


title: SC_S363_HFD2


title: liver_A22_V rep 5


title: SC_S362_HFD2


title: SC_S361_HFD2


title: liver_AB1_V rep 6


title: liver_R23_V rep5


title: liver_AB1_M rep 6


title: liver_A22_MR rep 5


title: SC_S359_HFD2


title: SC_S360_HFD2


title: SC_S35_Control1


title: liver_AB1_MR rep 5


title: SC_S357_HFD2


title: liver_A22_MR rep 4


title: liver_R23_MR rep 5


title: SC_S356_HFD2


title: liver_AB1_M rep 5


title: liver_AB1_V rep 4


title: liver_A22_V rep 4


title: liver_A22_M rep 4


title: SC_S355_HFD2


title: liver_AB1_V rep 5


title: SC_S354_HFD2


title: SC_S353_HFD2


title: SC_S352_HFD2


title: SC_S351_HFD2


title: liver_R23_MR rep 4


title: SC_S350_HFD2


title: SC_S34_Control1


title: liver_R23_M rep 4


title: liver_AB1_MR rep 4


title: SC_S349_HFD2


title: liver_R23_M rep 5


title: SC_S345_HFD2


title: liver_A22_V rep 3


title: liver_AB1_V rep 3


title: liver_AB1_M rep 4


title: liver_R23_M rep 3


title: liver_A22_MR rep 3


title: liver_AB1_MR rep 3


title: liver_R23_V rep4


title: SC_S347_HFD2


title: liver_AB1_M rep 3


title: SC_S346_HFD2


title: liver_A22_V rep 2


title: SC_S344_HFD2


title: SC_S343_HFD2


title: SC_S341_HFD2


title: SC_S342_HFD2


title: SC_S33_Control1


title: liver_A22_MR rep 2


title: SC_S340_HFD2


title: SC_S348_HFD2


title: liver_AB1_M rep 2


title: liver_R23_MR rep 3


title: liver_A22_V rep 1


title: liver_R23_V rep2


title: SC_S338_HFD2


title: liver_R23_V rep3


title: SC_S336_HFD2


title: liver_A22_M rep 3


title: liver_A22_MR rep 1


title: SC_S337_HFD2


title: SC_S339_HFD2


title: SC_S335_HFD2


title: SC_S333_HFD2


title: SC_S334_HFD2


title: SC_S332_HFD2


title: SC_S331_HFD2


title: SC_S32_Control1


title: SC_S330_HFD2


title: SC_S358_HFD2


title: SC_S328_HFD2


title: Human B cells from tonsil donor 3

city: Philadelphia

first: Diego

middle: A

last: Espinoza

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

description:
Single cell RNA
FACS sorted and rested overnight

data_processing: Cellranger v 3.1.0

source_name: Donor 3

extract_protocol: 10X Chromium v3.1 GEX 3' recovery

value: Tonsil


title: Human B cells from tonsil donor 2

source_name: Donor 2


title: liver_R23_MR rep 2


title: Human B cells from tonsil donor 1_c

source_name: Donor 1


title: SC_S324_HFD2


title: Human B cells from tonsil donor 1_b


title: Human B cells from tonsil donor 1_a


title: liver_AB1_V rep 1


title: SC_S325_HFD2


title: SC_S329_HFD2


title: liver_AB1_V rep 2


title: liver_R23_M rep 2


title: liver_A22_M rep 1


title: liver_AB1_MR rep 2


title: osteoarthritic cartilage mesenchymal stromal cells_2

city: PROVIDENCE

first: ALEXANDER

last: Brodsky

state: Rhode Island

address: RHODE ISLAND HOSPITAL; 593 EDDY ST.,, Aldrich 618

institute: RHODE ISLAND HOSPITAL/BROWN UNIVERSITY

data_processing:
Sequenced reads were trimmed for adaptor sequence then mapped to GRCH38 using STAR aligner.
Unique exon hit counts were calculated using Feature counts from the Subread package.
Genome_build: GRCH38
Supplementary_files_format_and_content: tab-delimited text files include counts  for each Sample .

source_name: Human osteoarthritic cartilage

growth_protocol: Cells were plated in fibronectin (10 µg/mL in PBS) coated dishes for 20 minutes at 37 °C in cell incubator. After 20 min, the adherent cells were primary OA-MSC while non-adherent cells were collected as OA chondrocytes. The MSCs were cultured in MSC medium: DMEM with 10% FBS, 1% penicillin-streptomycin, 100 mM HEPES, 1% GlutaMax, 0.1 mM ascorbic acid, 0.1 mM sodium pyruvate, and 2.7 µM L-glucose. The OAC were cultured in OAC medium: DMEM with 10% FBS, 1% penicillin-streptomycin, 100 mM HEPES.

extract_protocol:
Total RNA was purified from cultured cells using Qiagen RNAeasy kit.
Libraries with Poly(A) selection were prepared according to Illumina's instructions accompanying the VAHTS mRNA-seq V3 Library Prep Kit for Illumina(#NR611)

treatment_protocol: untreated

value: Cartilage

value: senescent mesenchymal stromal cells

tag: disease state

value: osteoarthritis

tag: sampel type

value: cell line

tag: cell line


title: osteoarthritic cartilage mesenchymal stromal cells_3


title: liver_R23_MR rep 1

tag: age


title: liver_AB1_M rep 1

tag: tissue


title: liver_A22_M rep 2


title: liver_R23_V rep1


title: liver_AB1_MR rep 1


title: liver_R23_M rep 1


title: osteoarthritic cartilage mesenchymal stromal cells_1


title: SC_S322_HFD2


title: SC_S327_HFD2


title: SC_S323_HFD2


title: normal cartilage stromal cell_3

source_name: Human normal cartilage

value: mesenchymal stromal cells

value: normal

value: nCSC


title: normal cartilage stromal cell_2


title: SC_S321_HFD2


title: SC_S326_HFD2


title: osteoarthritic chondrocytes_3

value: chondrocytes

value: primary cells


title: osteoarthritic chondrocytes_2


title: SC_S31_Control1

value: control


title: osteoarthritic chondrocytes_1


title: SC_S320_HFD2

value: HFD


title: SC_S318_HFD2


title: normal cartilage stromal cell_1


title: SC_S317_HFD2


title: SC_S316_HFD2


title: SC_S314_HFD2


title: VCaP ENZ 48hrs [scRNA-seq]

city: London

first: Paolo

last: Cremaschi

state: Non-US

address: 72 Huntley Street

department: Oncology

country: United Kingdom

institute: UCL Cancer Institute

data_processing:
Samples were pre-processed, aligned, and processed to gene-cell count matrices with Drop-seq tools v2.3.0 using default parameters and with the expectation that each sample contained 1000 cells (Macosko et al., 2015). We utilized the human reference genome version GRCh38, along with Gencode annotations version 33.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell.

source_name: VCaP cells

growth_protocol: LNCaP cells were cultured in RPMI 1640 (Sigma R0883) supplemented with 10% FBS (Sigma F7524), 2 mM Alanyl-glutamine (Sigma G8541), 1 mM sodium pyruvate (Merck TMS-005-C), 2.5 g/L glucose (Sigma G8769), and 1x Antibiotic-Antimycotic (Gibco, 15240062) in a humidified 37°C incubator with 5% CO2. VCaP cells were cultured in DMEM (Gibco) supplemented with 10% FBS in a humidified 37°C incubator with 5% CO2.

extract_protocol:
Cells were trypsinized with TrypLETM Express Enzyme (ThermoFisher Scientific, #12604021), spun down (5 min at 300xg) and washed with 0.1% BSA-PBS. After pelleting, the cells were resuspended in plain PBS and passed through a 40-micron filter. The number of viable cells was estimated with the use of trypan blue staining and Fuchs-Rosenthal hemocytometer chamber. The concentration of cells was brought down to 3x105 cells/mL in 0.1% BSA-PBS. For single-cell encapsulation, single-cell suspension, beads in lysis buffer and oil were connected with the loops and tubing to the Mitos P pumps and run through the glass microfluidic chip at the following flow rates: 100μL/min (Oil channel), 20μL/min (Bead channel); 350 mbar (Cell channel). Droplets were separated by centrifugation and beads counted with the use of Fuchs-Rosenthal hemocytometer chamber and up to 90000 beads were collected into one tube for Reverse Transcription reaction, exonuclease treatment, and amplification of cDNA library according to the original protocol (Macosko et al., 2015). Tagmentation of cDNA was performed with the Nextera XT DNA Library Preparation Kit (Illumina, #FC-131-1024). The PCR product was cleaned-up with AMPure XP beads and eluted in 10μL H2O.
Samples were prepared with Drop-seq (Macosko et al., 2015) using the Dolomite cell encapsulation system (Dolomite Bio).

treatment_protocol: Cells were seeded into 5 cm culture plate dishes and allowed to settle before exposure to 10 µM enzalutamide or DMSO vehicle control (0.1%) for 48 h or 168 h.

value: VCaP

value: prostate cancer cell line

tag: enzalutamide sensitivity

value: sensitive

value: 10µM enzalutamide for 48 hours


title: VCaP DMSO [scRNA-seq]

tag: cell type

value: 0.1% DMSO for 48 hours