title: TFi4.B11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 12.1_Preterm_H1N1

status: Public on Dec 01 2019

type: RNA

city: Maastricht

first: Christof

last: Seiler

address: Bouillonstraat 8-10

department: Department of Data Science and Knowledge Engineering

country: Netherlands

institute: Maastricht University

description: Nicholas Bayless_12.1 +_(HTA-2_0)

hyb_protocol: Samples were hybridized to microarrays in a hybridization over, with rotation at 60 rpm for 16 hr at 45°C. Following hybridization, arrays were washed according to GeneChip WT Pico Reagent Kit instructions.

scan_protocol: Samples were scanned using a GeneChip Scanner 3000 7G, with GeneChip Command Console software.

data_processing:
Normalize raw expressions using the Robust Multichip Average (RMA) algorithm (R package oligo, version 1.40.2). Remove background probes and probes that cannot be mapped to known gene symbols (R package affycoretools, version 1.48.0)
The .csv files (linked as supplementary files on the Series record) report RMA-normalized signals.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood mononuclear cells

label_protocol: Extracts were labeled using the GeneChip Whole Transcript Pico Reagent Kit, according to kit instructions. Briefly, RNA was reverse transcribed, amplified, and terminally labeled with biotin.

growth_protocol: Human PMBC samples were thawed, washed twice with RPMI culture medium and maintained in RPMI for ~7 hours at 37C.

extract_protocol: After incubation, RNA was extracted from PBMC samples using the Qiagen RNeasy Mini kit, according to manufacturer's instructions. RNA quality was evaluated by Nanodrop and Bioanalyzer.

treatment_protocol: PMBC samples (10^5/well) were either left unstimulated (US samples), or stimulated with H1N1 influenza virus (MOI = 1) for 4 hours at 37C. See methods section for further details.

tag: condition

value: Preterm

tag: treatment

tag: rin

tag: viability

tag: ptidno

tag: cell type

value: peripheral blood mononuclear cells (PBMCs)


title: TFi4.B10

type: SRA

city: Yokoham

first: Joachim

middle: Felix

last: Luginbühl

state: Kanagawa

address: 1-7-22 Suehiro-cho

country: Japan

institute: RIKEN

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.7
Single-cell RNAseq reads were aligned to the human transcriptome build hg19 using Kallisto v0.42.4 with the default parameter settings for paired-end reads.
We excluded chambers containing no cells, multiple cells or cells exhibiting morphological features of cell death based on visual inspection using the IN Cell Analyzer 6000 (GE Healthcare).
Additionally, cells not expressing either of the two housekeeping genes ACTB and GAPDH (encoding β-actin and glyceraldehyde-3-phosphate dehydrogenase, respectively), or expressing them at less than three standard deviations below the mean, were scored as unhealthy and removed.
Genome_build: hg19
Supplementary_files_format_and_content: comma-separated values files contain counts and TPM/CPM values for each sample after quality control

source_name: Transcription factor induced fibroblasts

growth_protocol: Human dermal fibroblasts were purchased from Lonza (passages 4-8) and cultured in DMEM containing 10% FBS/L-glutamine/10% Penicilin&Streptomycin at 37°C 5% CO2 until virus infection. For TFi generation, a total of 6 MOI (~0.3 MOI per virus) were pooled into culture medium containing 8 mg*ml-1 Polybrene (SIGMA) to increase infection efficiency. The virus pool was infected and incubated overnight at 37°C 5% CO2. On the following day, virus-containing medium was removed and cells were incubated for an additional day in fresh culture medium at 37°C 5% CO2. For iN generation, infected cells were split onto Poly-d-lysine (100μg*ml-1) / Laminin (50μg*ml-1) (SIGMA)-coated culture plates and incubated overnight in culture medium at 37°C 5% CO2. On the following day, medium was changed to neuronal induction medium containing DMEM/F12 and Neurobasal-A (Thermo Fisher Scientific) mixed at a 1:1 ratio, 2% (vol/vol) B27 supplement and 0.5% N2 Supplement (GIBCO), 1x nonessential amino acids (Thermo Fisher Scientific), 1% GlutaMAX supplement, 10ng*ml-1 BDNF (GIBCO), 10ng*ml-1 NT3 (R&D Systems), 10ng*ml-1 GDNF (Thermo Fisher Scientific), VPA (0.5mM, WAKO), L-Ascorbic acid (200nM, SIGMA), Y-27632 (10μM, WAKO), dcAMP (0.5mM, SIGMA), 10% FBS and 10% Penicilin&Streptomycin (WAKO). The concentrations of small molecules used were as follows: CHIR99021 (2μM, Abcam), SB-431542 (10μM, SIGMA), LDN-193189 (0.5μM, Stemgent), Noggin (100ng*ml-1, SIGMA). Neuronal induction medium was changed every third day, during which the concentration of FBS was gradually reduced from 10% to 1%. After 2 weeks, neuronal induction medium was replaced with neuronal maturation medium without small molecules and 1% FBS and the medium was changed every third day until further analysis.

extract_protocol: Single cell RNA-seq analysis was performed using the Fluidigm C1 platform following the manufacturer’s protocol (P100-7168L1, Fluidigm). Briefly, cell number and cell viability were assessed using the Countess II Automated Cell Counter (ThermoFisher). After priming medium size C1 Single-cell Open App IFCs, 250 cells/μL were loaded and capture efficiency and cell morphology was assessed using the IN Cell Analyzer 6000 (GE Healthcare). To exclude chambers loaded with no cells, more than one cell (cell doublets) or dead cells for downstream analysis, we took 11 z-stacking images per chamber. Next, cells were lysed with 20,000-fold diluted ERCC RNA Spike-In Mix1 (L/N 00329960 Life Technologies) and reverse transcription (RT) and cDNA amplification were performed using the SMARTer Ultra Low RNA Kit for the Fluidigm C1TM System (Clontech). The amplified cDNAs were harvested into 96 well plates and quantified with Quant-iT TM  PicoGreen dsDNA Assay kit. Library preparation was performed with the Nextera XT DNA Library Preparation kit (Illumina), Nextera XT Index Kit v2 (Illumina) and AMpure XP beads (Beckman Coulter). Libraries were quantified by High Sensitivity DNA Reagents (Agilent Technologies) and KAPA Library Quantification kit (KAPA BIOSYSTEMS).

tag: time

value: 21 days after induction

tag: passages

value: Ectopic expression of transcription factors

tag: batch


title: PBMCs, 11.2_Preterm_H1N1

description: Nicholas Bayless_11.2 +_(HTA-2_0)


title: PBMCs, 11.3_Term_Mock

description: Nicholas Bayless_11.3 -_(HTA-2_0)

value: Term

value: Mock


title: TFi4.C10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Transcription factor induced fibroblasts


title: TFi4.B09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 11.2_Preterm_Mock

description: Nicholas Bayless_11.2 -_(HTA-2_0)


title: PBMCs, 11.1_Term_H1N1

description: Nicholas Bayless_11.1 +_(HTA-2_0)


title: PBMCs, 13.1_Term_Mock

description: Nicholas Bayless_US 13.1_(HTA-2_0)


title: TFi4.B07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 11.1_Term_Mock

description: Nicholas Bayless_11.1 -_(HTA-2_0)


title: PBMCs, 10.3_Term_H1N1

description: Nicholas Bayless_10.3 +_(HTA-2_0)


title: PBMCs, 10.3_Term_Mock

description: Nicholas Bayless_10.3 -_(HTA-2_0)


title: TFi4.B05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 10.1_Preterm_H1N1

description: Nicholas Bayless_10.1 +_(HTA-2_0)


title: TFi4.B08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 10.2_Term_Mock

description: Nicholas Bayless_10.2 -_(HTA-2_0)


title: TFi4.B03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.B02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.B01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 9.3_Term_H1N1

description: Nicholas Bayless_9.3 +_(HTA-2_0)


title: PBMCs, 10.1_Preterm_Mock

description: Nicholas Bayless_10.1 -_(HTA-2_0)


title: PBMCs, 9.3_Term_Mock

description: Nicholas Bayless_9.3 -_(HTA-2_0)


title: TFi4.A12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 9.2_Preterm_H1N1

description: Nicholas Bayless_9.2 +_(HTA-2_0)


title: TFi4.A10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 9.2_Preterm_Mock

description: Nicholas Bayless_9.2 -_(HTA-2_0)


title: TFi4.A09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.A11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.A08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 9.1_Term_Mock

description: Nicholas Bayless_9.1 -_(HTA-2_0)


title: PBMCs, 9.1_Term_H1N1

description: Nicholas Bayless_9.1 +_(HTA-2_0)


title: PBMCs, 8.3_Preterm_H1N1

description: Nicholas Bayless_8.3 +_(HTA-2_0)


title: TFi4.B06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.A07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.A05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.A06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 10.2_Term_H1N1

description: Nicholas Bayless_10.2 +_(HTA-2_0)


title: TFi4.B04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.A04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 8.3_Preterm_Mock

description: Nicholas Bayless_8.3 -_(HTA-2_0)


title: PBMCs, 8.2_Term_H1N1

description: Nicholas Bayless_8.2 +_(HTA-2_0)


title: TFi4.A03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 8.2_Term_Mock

description: Nicholas Bayless_8.2 -_(HTA-2_0)


title: PBMCs, 8.1_Term_Mock

description: Nicholas Bayless_8.1 -_(HTA-2_0)


title: PBMCs, 8.1_Term_H1N1

description: Nicholas Bayless_8.1 +_(HTA-2_0)


title: PBMCs, 7.3_Term_H1N1

description: Nicholas Bayless_7.3 +_(HTA-2_0)


title: PBMCs, 7.3_Term_Mock

description: Nicholas Bayless_7.3 -_(HTA-2_0)


title: PBMCs, 7.2_Preterm_Mock

description: Nicholas Bayless_7.2 -_(HTA-2_0)


title: TFi3.H10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.A01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 7.2_Preterm_H1N1

description: Nicholas Bayless_7.2 +_(HTA-2_0)


title: TFi3.H11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi4.A02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.H08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 7.1_Term_H1N1

description: Nicholas Bayless_7.1 +_(HTA-2_0)


title: TFi3.H12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 7.1_Term_Mock

description: Nicholas Bayless_7.1 -_(HTA-2_0)


title: TFi3.H09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.H07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 6.3_Term_Mock

description: Nicholas Bayless_US 6.3_(HTA-2_0)


title: PBMCs, 6.3_Term_H1N1

description: Nicholas Bayless_H1N1 6.3_(HTA-2_0)


title: TFi3.H06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.H05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 6.2_Term_Mock

description: Nicholas Bayless_US 6.2_(HTA-2_0)


title: PBMCs, 6.2_Term_H1N1

description: Nicholas Bayless_H1N1 6.2_(HTA-2_0)


title: TFi3.H03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.H04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 6.1_Preterm_Mock

description: Nicholas Bayless_US 6.1_(HTA-2_0)


title: TFi3.H01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.H02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 6.1_Preterm_H1N1

description: Nicholas Bayless_H1N1 6.1_(HTA-2_0)


title: TFi3.G12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.G11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 5.3_Preterm_H1N1

description: Nicholas Bayless_H1N1 5.3_(HTA-2_0)


title: PBMCs, 4.3_Term_Mock

description: Nicholas Bayless_US 4.3_(HTA-2_0)


title: PBMCs, 4.3_Term_H1N1

description: Nicholas Bayless_H1N1 4.3_(HTA-2_0)


title: PBMCs, 5.1_Term_H1N1

description: Nicholas Bayless_H1N1 5.1_(HTA-2_0)


title: TFi3.G08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.G07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.G09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.G06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.G05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 3.3_Preterm_H1N1

description: Nicholas Bayless_H1N1 3.3_(HTA-2_0)


title: TFi3.G10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 3.3_Preterm_Mock

description: Nicholas Bayless_US 3.3_(HTA-2_0)


title: TFi3.G04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 2.3_Term_Mock

description: Nicholas Bayless_US 2.3_(HTA-2_0)


title: PBMCs, 3.2_Term_H1N1

description: Nicholas Bayless_H1N1 3.2_(HTA-2_0)


title: PBMCs, 2.3_Term_H1N1

description: Nicholas Bayless_H1N1 2.3_(HTA-2_0)


title: TFi3.G02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.F12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.G01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 3.2_Term_Mock

description: Nicholas Bayless_US 3.2_(HTA-2_0)


title: TFi3.F11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.F10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 5.3_Preterm_Mock

description: Nicholas Bayless_US 5.3_(HTA-2_0)


title: PBMCs, 2.1_Preterm_H1N1

description: Nicholas Bayless_H1N1 2.1_(HTA-2_0)


title: PBMCs, 2.1_Preterm_Mock

description: Nicholas Bayless_US 2.1_(HTA-2_0)


title: PBMCs, 5.1_Term_Mock

description: Nicholas Bayless_US 5.1_(HTA-2_0)


title: TFi3.F09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 1.3_Term_Mock

description: Nicholas Bayless_US 1.3_(HTA-2_0)


title: PBMCs, 1.3_Term_H1N1

description: Nicholas Bayless_H1N1 1.3_(HTA-2_0)


title: TFi3.F08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.F06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 1.2_Preterm_Mock

description: Nicholas Bayless_US 1.2_(HTA-2_0)


title: TFi3.F07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.F04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.F05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.G03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 1.1_Term_Mock

description: Nicholas Bayless_US 1.1_(HTA-2_0)


title: PBMCs, 2.2_Term_Mock

description: Nicholas Bayless_US 2.2_(HTA-2_0)


title: PBMCs, 1.1_Term_H1N1

description: Nicholas Bayless_H1N1 1.1_(HTA-2_0)


title: TFi3.F01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.F02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: PBMCs, 2.2_Term_H1N1

description: Nicholas Bayless_H1N1 2.2_(HTA-2_0)


title: Heatin_7d_hightemp_2_M_TOPHAT.norm.txt

city: Utrecht

first: Martijn

last: van Zanten

address: Padualaan 8

department: Institute of Environmental Biology

institute: Utrecht University

data_processing:
Quality Control (QC) was performed in house on the raw sequencing reads prior to analysis using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc).
Subsequently the raw reads were aligned to the Arabidopsis genome (TAIR10) using TopHat v2.0.131 with the parameter settings: ‘bowtie’, ‘no-novel-juncs’, ‘p 6’, ‘G’, ‘min-intron-length 40’, ‘max-intron-length 2000’.
Aligned reads were summarized over annotated gene models using HTSeq-count v0.6.12 with settings: ‘-stranded no’, ‘-i gene_id’. From the TAIR10 GTF file all ORFs of which the annotation starts with ‘CPuORF’ were manually removed prior summarization to avoid not counting all double annotated genes.
Sample counts were depth-adjusted and differential expression was determined using the DESeq package with default settings
Genome_build: TAIR 10
Supplementary_files_format_and_content: Tab-delimited text with normalized counts

organism: Arabidopsis thaliana

source_name: 7 day-old whole mount seedling

growth_protocol: Seeds were stratified on 1% MS-Agar plates at 4oC in the dark. Thereafter, plates were moved to a growth cabinet at the indicated temperature at 22oC or 27oC, in short day photoperiod (8h light/16h dark) at app. 100 umol m-2 s-1 PAR light intensity

extract_protocol:
Two day-old or 7d day-old seedlings were harvested at the moment of dawn (lights on), and snap frozen in liquid Nitrogen. RNA was isolated using the Sigma Spectrum Plant Total RNA isolation kit and gDNA was removed by on-column DNAse treatment (Sigma-Aldrich). RNA integrity and concentration was checked using RNA 6000 Nano Chips on a Bioanalyzer (Agilent-2100). For RNA-seq library preparation in total 3 samples were prepared for each genotype, treatment and time-point, by combining isolated RNA of 3 individually harvested batches per sample.
Illumina TruSeq RNA Library preparation and Illumina HiSeq2500 (high-throughput) single-end 50 bp sequencing was outsourced to Macrogen, Korea.

treatment_protocol: Control and high temperature conditions (22oC vs 27oC) with compound Heatin disolved in the medium (8.5 micromolar in 0.1% DMSO) or 0.1% DMSO solvent mock control

tag: ecotype

tag: genotype

value: wild type

tag: age

value: 7 day-old

value: high temperature 27oC + compound Heatin

tag: tissue

value: seedling


title: Heatin_7d_hightemp_3_M_TOPHAT.norm.txt


title: TFi3.E12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Heatin_7d_hightemp_1.norm.txt


title: Heatin_7d_Control_3_M_TOPHAT.norm.txt

value: control temperature 22oC + compound Heatin


title: TFi4.B12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.E10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.E11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Heatin_7d_Control_2_M_TOPHAT.norm.txt

value: control temperature 22oC +compound Heatin


title: Heatin_7d_Control_1_M_TOPHAT.norm.txt


title: PBMCs, 1.2_Preterm_H1N1

description: Nicholas Bayless_H1N1 1.2_(HTA-2_0)


title: TFi3.E08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.F03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.E06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.E05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.E04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Heatin_2d_Control_3_M_TOPHAT.norm.txt

source_name: 2 day-old whole mount seedling

value: 2 day-old


title: TFi3.E03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Heatin_2d_hightemp_1_M_TOPHAT.norm.txt


title: Heatin_2d_Control_1_M_TOPHAT.norm.txt


title: Heatin_2d_hightemp_2_M_TOPHAT.norm.txt


title: Heatin_2d_Control_2_M_TOPHAT.norm.txt


title: TFi3.E02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.E01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.D11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.E09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.D12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Col_7d_hightemp_3_M_TOPHAT.norm.txt

value: high temperature 27oC + DMSO solvent mock


title: Col_7d_Control_3_M_TOPHAT.norm.txt

value: control temperature 22oC + DMSO solvent mock


title: Col_7d_Control_2_M_TOPHAT.norm.txt


title: TFi3.D08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.D09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Col_2d_hightemp_3_M_TOPHAT.norm.txt


title: Col_7d_Control_1_M_TOPHAT.norm.txt


title: TFi3.D10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.D07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Heatin_2d_hightemp_3_M_TOPHAT.norm.txt

value: high temperature 27oC + ompount Heatin


title: Col_2d_hightemp_2_M_TOPHAT.norm.txt


title: Col_7d_hightemp_1_M_TOPHAT.norm.txt


title: TFi3.E07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Col_2d_hightemp_1_M_TOPHAT.norm.txt


title: Col_2d_Control_3_M_TOPHAT.norm.txt


title: TFi3.D05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Col_2d_Control_1_M_TOPHAT.norm.txt


title: Col_7d_hightemp_2_M_TOPHAT.norm.txt


title: TFi3.D04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.D02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.D03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Col_2d_Control_2_M_TOPHAT.norm.txt


title: BCP20_3

city: Louisville

first: Christopher

last: Frost

state: KY

address: 139 LSB

department: Biology

country: USA

institute: University of Louisville

description:
FPKM_geneMatrix_NORMALIZED.txt
CF-11-UFH001-20uMCARYOPHYLLENE-H-3_S11

data_processing:
A total of four single-end raw .fastq files for each replicate from two different runs were concatenated into one single-end .fastq file using the unix cat command, generating six files representing three biological replicates of two conditions.
Quality control (QC) of the raw sequence data was performed using FastQC (version 0.10.1)
The concatenated sequences were directly aligned to the Homo sapiens hg38 reference genome assembly (hg38.fa) using tophat2 (version 2.0.13)
Differentially expressed genes between Control, 20uM BCP, and 200 uM BCP samples were determined using cufflinks-cuffdiff2 (version 2.2.1)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file that includes normalized FPKM values for each sample

source_name: UFH-001 Triple Negative Breast Cancer Cells_20uM BCP

growth_protocol: UFH-001 cells were plated in 10 cm dishes at a density of 10,000 cells/mL and maintained in DMEM supplemented with 10% FBS. All cell lines were maintained at 37 °C in humidified air with 5% CO2. Experiments were conducted when cells achieved ~70% confluency

extract_protocol:
RNA was isolated from the UFH-001 cells using the Qiagen RNAeasy kit per manufacturer's protocols
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All cells were exposed to hypoxia at the same time that cells were exposed (or not) to β-caryophyllene.  Specifically, cells were provided fresh medium an hour before hypoxic treatment, along with the appropriate concentration β-caryophyllene (20μM, 200μM or vehicle control [DMSO]).  Cells were were placed in humidified Billups Rothenberg Metabolic Chambers and exposed to 1% O2, 5% CO2 and balanced N2 for 16h at 37°C..

tag: cell line

value: Triple Negative Breast Cancer Cells


title: Control_3

description:
FPKM_geneMatrix_NORMALIZED.txt
identical to GSM3514420
CF-10-UFH001-DMSO-H-3_S10

source_name: UFH-001 Triple Negative Breast Cancer Cells_control (hypoxia)


title: TFi3.C12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.D01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.C11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: BCP20_2

description:
FPKM_geneMatrix_NORMALIZED.txt
CF-07-UFH001-20uMCARYOPHYLLENE-H-2_S7


title: BCP200_2

description:
FPKM_geneMatrix_NORMALIZED.txt
CF-08-UFH001-200uMCARYOPHYLLENE-H-2_S8

source_name: UFH-001 Triple Negative Breast Cancer Cells_200uM BCP


title: TFi3.C06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.C05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Normoxia_3

description:
sample name in processed data file:
CF-09-UFH001-DMSO-N-3_S9

data_processing:
A total of four single-end raw .fastq files for each replicate from two different runs were concatenated into one single-end .fastq file using the unix cat command, generating six files representing three biological replicates of two conditions.
Quality control (QC) of the raw sequence data was performed using FastQC (version 0.10.1)
The concatenated sequences were directly aligned to the Homo sapiens hg38 reference genome assembly (hg38.fa) using tophat2 (version 2.0.13)
Differentially expressed genes between Hypoxic vs. Normoxic samples were determined using cufflinks-cuffdiff2 (version 2.2.1)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file that includes normalized FPKM values for each sample

source_name: UFH-001 Triple Negative Breast Cancer Cells

growth_protocol: UFH-001 cells were plated in 10 cm dishes at a density of 10,000 cells/mL and maintained in DMEM supplemented with 10% FBS. All cell lines were maintained at 37 °C in humidified air  (21% Oxygen) with 5% CO2. Experiments were conducted when cells achieved ~70% confluency

treatment_protocol: For hypoxia treatment, cells were placed in humidified Billups Rothenberg Metabolic Chambers and exposed to 1% O2, 5% CO2 and balanced N2 for 16 hours. For normoxia samples, cells are maintained at 21% Oxygen (normal air).


title: TFi3.C04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.C03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Hypoxia_3

description:
sample name in processed data file:
CF-10-UFH001-DMSO-H-3_S10

growth_protocol: UFH-001 cells were plated in 10 cm dishes at a density of 10,000 cells/mL and maintained in DMEM supplemented with 10% FBS. All cell lines were maintained at 37 °C in humidified air (21% Oxygen) with 5% CO2. Experiments were conducted when cells achieved ~70% confluency

value: UFH-001 Triple Negative Breast Cancer Cells


title: BCP20_1

description:
FPKM_geneMatrix_NORMALIZED.txt
CF-03-UFH001-20uMCARYOPHYLLENE-H-1_S3


title: Hypoxia_2

description:
sample name in processed data file:
CF-06-UFH001-DMSO-H-2_S6


title: TFi3.C08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: 21 days after induction


title: TFi3.C07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Ectopic expression of transcription factors


title: TFi3.C09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.C10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: BCP200_1

description:
FPKM_geneMatrix_NORMALIZED.txt
CF-04-UFH001-200uMCARYOPHYLLENE-H-1_S4


title: Control_1

description:
FPKM_geneMatrix_NORMALIZED.txt
identical to GSM3514416
CF-02-UFH001-DMSO-H-1_S2


title: Normoxia_2

description:
sample name in processed data file:
CF-05-UFH001-DMSO-N-2_S5


title: TFi3.B12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Hypoxia_1

description:
sample name in processed data file:
CF-02-UFH001-DMSO-H-1_S2


title: TFi3.C01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.C02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Normoxia_1

description:
sample name in processed data file:
CF-01-UFH001-DMSO-N-1_S1


title: BCP200_3

description:
FPKM_geneMatrix_NORMALIZED.txt
CF-12-UFH001-200uMCARYOPHYLLENE-H-3_S12


title: TFi3.D06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.B11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.B09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ag4

city: Singapore

first: Jingxian

last: Zhang

state: Singpaore

address: 61 Biopolis Drive Proteos

department: IMCB

country: Singapore

institute: Institute of Molecular and Cell Biology (IMCB), A-Star, Singapore

data_processing:
The sequenced reads were mapped tomm9 build of the human genome using STAR 2.5.1a with default parameters
FPKMs were calculated by Cufflink (2.2.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: peripheral blood-derived mast cells

growth_protocol: Peripheral blood-derived CD34+ cells were cultured with 5 ng/ml hIL-3, 100 ng/ml hSCF and 50 ng/ml hIL-6 for 3 weeks. Subsequently,100 ng/ml hSCF and 50 ng/ml hIL-6 were used for additional 7 weeks

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Human myeloma IgE (0.5  μg/ml) treatment for 18 h, anti-IgE (1 μg/ml) treatment for 2h after IgE treatment

value: Myeloma IgE and anti-IgE treated

tag: source

value: CD34+ derived

value: peripheral blood-derived mast cells

value: >98% FcεRI+ CD117+, 10 weeks

value: WT


title: Control_2

description:
FPKM_geneMatrix_NORMALIZED.txt
identical to GSM3514418
CF-06-UFH001-DMSO-H-2_S6


title: Ag3


title: TFi3.B10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Transcription factor induced fibroblasts


title: Ag1


title: IgE3

value: Myeloma IgE-treated


title: IgE4


title: TFi3.B06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.B05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.B07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: IgE2


title: TFi3.B03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.B08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.B01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.B02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: UT3

value: Untreated


title: UT2


title: TFi3.B04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: UT1


title: TFi3.A11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: ChIP-Seq of H3K4M3 in untreated cell

library_source: genomic

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie2 version 2.2.6 with the following configurations : -v 2 -m 1 -k 1  --best
Peak calling was done by MACS 2.0.10 with default settings
Genome_build: hg19
Supplementary_files_format_and_content: broadpeak files were generated by MACS 2.0.10

molecule: genomic DNA

extract_protocol:
CHIP-seq libraries were prepared with NEB NEXT Ultra kit using 10 ng starting material
Single read - Illumina nextseq 500

tag: chip antibody

value: H3K4me3 (Millipore 07-473)


title: TFi3.A12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: UT4


title: TFi3.A07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.A09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: ChIP-Seq of H3K27ac in untreated replicate 1


title: ChIP-Seq of H3K27ac in IgE-treated replicate 2


title: TFi3.A06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.A08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: ChIP-Seq of H3K27ac in untreated replicate 2


title: Ag2


title: IgE1


title: ChIP-Seq of H3K4M3 in IgE and anti-IgE treated cell


title: ChIP-Seq of H3K27ac in IgE-treated replicate 1


title: TFi3.A05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: ChIP-Seq of H3K27ac in IgE and anti-IgE treated replicate 2


title: ChIP-Seq of H3K27ac in IgE and anti-IgE treated replicate 1


title: TFi3.A04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.A02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.A03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi3.A01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: ChIP-Seq input for H3K4me3, H3K27Ac replicate 1


title: ChIP-Seq input for H3K27Ac replicate 2


title: TFi3.A10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: ChIP-Seq of H3K4M3 in IgE-treated


title: TFi2.H11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: 9 days after induction


title: TFi2.H12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: CapC_B105_B33_D4_rep3

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

description: Capture-C

data_processing:
Library strategy: Capture-C
5C sequencing reads were processed using 5C-Pro pipeline, available at https://github.com/bioinfo-pf-curie/5C-Pro. Single-end sequencing reads are trimmed and aligned using bowtie2. Quality controls were performed using the HiTC BioConductor package.
Capture-C sequencing reads were trimmed using the Trim Galore! pipeline (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), and then processed using the HiC-Pro pipeline 72 (v2.8.0).
RNA sequencing reads were aligned on the mouse genome using the STAR mapper. Raw counts have been generated from the STAR mapper using the GENCODE annotation database vM1.
ATAC-seq paired-end reads were trimmed of the adaptor sequences and aligned to the NCBIm37 genome using STAR v2.4.2a.  Duplicate fragments were removed using PICARD tools v1.90, only unique mapped fragments between 38bp and 1500bp in length were retained.  ATAC-seq peaks were called on the 1bp transposase cut-sites using MACS2 (with shift size 100 and extension size 200). Only the peaks considered reproducible by IDR (version 2), with an IDR threshold of 0.05, were kept.
Genome_build: mm9 / NCBIm37

organism: Mus musculus

source_name: mouse ESC (Pgk12.1)

growth_protocol: Feeder-independent male mouse ESC (E14) were grown on gelatin-coated flasks in Glasgow medium supplemented with 2 mM L-Glutamine, 0.1 mM NEAA and 1 mM sodium pyruvate (GIBCO) with 15% FBS (GIBCO), 10M b-mercaptoethanol (Sigma), 1000 U/ml of leukemia inhibitory factor (LIF, Chemicon). Feeder-independent female mouse ESC (Pgk12.1) were grown on gelatin-coated flasks in DMEM supplemented with 15% FBS (GIBCO), 10M b-mercaptoethanol (Sigma) and 1000 U/ml of leukemia inhibitory factor (LIF, Chemicon). Cells were cultivated in 8% CO2, and passaged when needed. Medium was changed daily. Cells were checked for mycoplasma infection every 3-4 months and tested negative.

extract_protocol:
For Chromosome Conformation Capture (5C and Capture-C) cells were fixed in culture plates or flasks and scraped off. For RNA-seq cells were washed once with PBS and lysed in Trizol in the culture plate. For ATAC-seq, cells were washed once with PBS and directly incubated in the transposition reaction.
5C libraries were generated based on a custom Illumina-compatible protocol (Nora et al 2017); Capture-C libraries were generated using KAPA Hyper Prep Kit (KK8500, Kapa Biosystems); RNA-seq libraries were generated using the TruSeq Stranded Total RNA kit (Illumina); ATAC-seq libraries were generated based on a Nextseq-compatible protocol (Buenrostro et al 2013).

value: mouse ESC (Pgk12.1)

tag: strain

value: XX, 129/Ola-Hsd x (C3H/He-Pgk-1a/Ws x 129/Ola-Hsd)F1

value: wild type

tag: differentiation stage

value: day 4

tag: capture-c viewpoint

value: LinxP


title: TFi2.H07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

tag: treatment


title: TFi2.H09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: CapC_B104_B35_D0_rep3

description: Capture-C

value: day 0 (undifferentiated)


title: TFi2.H08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Ectopic expression of transcription factors


title: CapC_B77_B35_D4_rep1

description: Capture-C


title: CapC_B77_B35_D2_rep1

description: Capture-C

value: day 2


title: CapC_B79_B34_D4_rep2

description: Capture-C


title: TFi2.H05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: CapC_B79_B33_D0_rep2

description: Capture-C


title: TFi2.H06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: CapC_B77_B35_D0_rep1

description: Capture-C


title: TFi2.H04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.H01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.H10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.H02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.G12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: CapC_B77_D4_rep4

value: Xist


title: CapC_B77_D1_rep3

value: day 1


title: CapC_B79_B34_D2_rep2

description: Capture-C


title: TFi2.G11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: CapC_B79_34-D4_rep2


title: CapC_B79_D1_rep2


title: CapC_B79_D0_rep2


title: CapC_B79_34-D2_rep2


title: TFi2.G08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: CapC_E117_D4_rep1


title: TFi2.G10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.G07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.G05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.G06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.G03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.G04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: CapC_B77_D2_rep3


title: CapC_B79_D4_rep3


title: 5C_B20_E14-2_wt1

description:
Xic3_MAIN_primer_pool_mm9_my5C_FOR.bed
Xic3_MAIN_primer_pool_mm9_my5C_REV.bed

data_processing:
Library strategy: 5C
5C sequencing reads were processed using 5C-Pro pipeline, available at https://github.com/bioinfo-pf-curie/5C-Pro. Single-end sequencing reads are trimmed and aligned using bowtie2. Quality controls were performed using the HiTC BioConductor package.
Capture-C sequencing reads were trimmed using the Trim Galore! pipeline (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), and then processed using the HiC-Pro pipeline 72 (v2.8.0).
RNA sequencing reads were aligned on the mouse genome using the STAR mapper. Raw counts have been generated from the STAR mapper using the GENCODE annotation database vM1.
ATAC-seq paired-end reads were trimmed of the adaptor sequences and aligned to the NCBIm37 genome using STAR v2.4.2a.  Duplicate fragments were removed using PICARD tools v1.90, only unique mapped fragments between 38bp and 1500bp in length were retained.  ATAC-seq peaks were called on the 1bp transposase cut-sites using MACS2 (with shift size 100 and extension size 200). Only the peaks considered reproducible by IDR (version 2), with an IDR threshold of 0.05, were kept.
Genome_build: mm9 / NCBIm37

source_name: mouse ESC (E14)

value: mouse ESC (E14)

value: XY, 129/Ola


title: TFi2.G02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Transcription factor induced fibroblasts


title: TFi2.H03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.G01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.G09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.F12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.F11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.F09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.F08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: CapC_E117_D0_rep1


title: CapC_E117_D1_rep1


title: TFi2.F07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: CapC_E117_D2_rep1


title: TFi2.F06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.F05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.F04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.F03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.F02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.F01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.F10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.E12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: keratinocytes_GP19S_rep2

city: Ichikai, Haga

first: Yasutaka

last: Kuroda

state: Tochigi

address: Akabane 2606

institute: Kao Corporation

description:
GP-2
GP19S 3 mg/mL, 3h

hyb_protocol: The cDNAs were hybridized with the GeneChip Hybridization, Wash and Stain Kit (Affymetrix, Santa Clara, CA, USA) to the GeneChip Human Gene 2.0 ST Array (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s instructions.

scan_protocol: The scanned fluorescent images were analyzed with Affymetrix GeneChip Command Console Software to generate a CEL file.

data_processing: The data were analyzed using GeneSpring GX 14.5 (Agilent Technologies, Santa Clara, CA, USA) with RMA16 as normalization method and a baseline transformation to the medians of all samples were used.

source_name: human primary keratinocytes, GP19S, replicate2

label_protocol: The cRNA synthesis and the subsequent single-strand cDNA synthesis were performed with the GeneChip WT Plus Reagent Kit (Affymetrix, Santa Clara, CA, USA) and 100 ng total RNA. The single-strand cDNAs was fragmented and labeled with the GeneChip WT Terminal labeling kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Primary human neonatal keratinocytes (Thermo Fisher Scientific/Life Technologies, Waltham, MA, USA) were cultured in HuMedia KG2 (Kurabo, Osaka, Japan) and seeded at 4.5 × 10e4 cells/well in flat-bottomed, 24-well culture plates.

extract_protocol: The total RNA was extracted from the lysed cells using the RNeasy Micro Kit in combination with QIAshredder (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: The cells placed in 400 μL culture medium were treated with 100 μL of the prepared sample for 3 hr. After removing the medium/test sample, the remaining adherent cells were processed by the direct addition of 350 μL of RLT buffer (Qiagen, Hilden, Germany) bearing 3.5 μL of 2-mercapto-ethanol (Thermo Fisher Scientific) to each well.

value: Primary neonatal keratinocytes


title: keratinocytes_GP19S_rep3

description:
GP-3
GP19S 3 mg/mL, 3h

source_name: human primary keratinocytes, GP19S, replicate3


title: keratinocytes_HSA_rep1

description:
HU-1
HSA 66 mg/mL, 3h

source_name: human primary keratinocytes, HSA, replicate1

value: HSA


title: TFi2.E11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: keratinocytes_buffer1_rep2

description:
Buffer1-2
PBS 1/5, 3h

source_name: human primary keratinocytes, PBS, replicate2

value: PBS


title: TFi2.E09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: 9 days after induction


title: TFi2.E10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: keratinocytes_buffer2_rep2

description:
Buffer2-2
Tris-HCL 5%, 3h

source_name: human primary keratinocytes, Tris-HCL, replicate2

value: Tris-HCL


title: keratinocytes_buffer2_rep3

description:
Buffer2-3
Tris-HCL 5%, 3h

source_name: human primary keratinocytes, Tris-HCL, replicate3


title: keratinocytes_buffer1_rep1

description:
Buffer1-1
PBS 1/5, 3h

source_name: human primary keratinocytes, PBS, replicate1


title: keratinocytes_HSA_rep2

description:
HU-2
HSA 66 mg/mL, 3h

source_name: human primary keratinocytes, HSA, replicate2


title: TFi2.E08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

source_name: Transcription factor induced fibroblasts


title: keratinocytes_buffer2_rep1

description:
Buffer2-1
Tris-HCL 5%, 3h

source_name: human primary keratinocytes, Tris-HCL, replicate1


title: keratinocytes_GP19S_rep1

description:
GP-1
GP19S 3 mg/mL, 3h

source_name: human primary keratinocytes, GP19S, replicate1


title: keratinocytes_buffer1_rep3

description:
Buffer1-3
PBS 1/5, 3h

source_name: human primary keratinocytes, PBS, replicate3


title: TFi2.E07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: keratinocytes_HSA_rep3

description:
HU-3
HSA 66 mg/mL, 3h

source_name: human primary keratinocytes, HSA, replicate3


title: mouse_p53null-mammary-tumor_BALB/c wt_DIR-irradiated host_replicate 18

city: San Francisco

first: Jade

last: Moore

state: California

address: 2340 Sutter St, S371

institute: University of California San Francisco

description: Total RNA of p53null mammary tumor, BALB/c-Irradiated host

hyb_protocol: 12.5 micrograms of fragmented cRNA was hybridized for 16 hr to the Affymetrix MG 430 2.0 arrays using GeneChip Hybridization Oven 640 and Genechip® fluidics station FS 450, following standard Affymetrix protocols.

scan_protocol: Affymetrix GeneChip scanner 7G

data_processing: Feature intensity was extracted by Affymetrix GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using Agilent GeneSpring GX10 program. No further adjustments were made to the data in the table.

label: incorporated biotinylated UTP

source_name: 30 cGy Si - 42

label_protocol: 100 ng of total RNA were used to prepare cRNA following the Affymetrix 3’IVT Express Kit labeling protocol. cRNA converted from total RNA by reverse transcription and in vitro transcription of the intermediate cDNA product

growth_protocol: Mammary epithelium of inguinal glands was surgically removed from 3-week-old wild type balb/c mice and were aged to 10 months old.

extract_protocol: Total RNA was extracted using Trizol Reaget (Invitrogen), according to manufacturer's instructions.

treatment_protocol: Mice received whole body irradiation with 10, 50, or 100 cGy sparsely ionizing γ-rays or 49 cGy for Ar or 30 cGy for Si densely ionizing rays.

value: mammary tumor

tag: tissue preparation

value: From frozen mammary tumors


title: TFi2.E06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: mouse_p53null-mammary-tumor_BALB/c wt_DIR-irradiated host_replicate 19

source_name: 30 cGy Si - 43


title: mouse_p53null-mammary-tumor_BALB/c wt_DIR-irradiated host_replicate 17

source_name: 30 cGy Si - 41


title: mouse_p53null-mammary-tumor_BALB/c wt_DIR-irradiated host_replicate 15

source_name: 30 cGy Si - 39


title: TFi2.E05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: mouse_p53null-mammary-tumor_BALB/cc wt_sham-irradiated host_replicate 9

source_name: Sham IR host 38


title: mouse_p53null-mammary-tumor_BALB/c wt_DIR-irradiated host_replicate 16

source_name: 30 cGy Si - 40


title: TFi2.E04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: mouse_p53null-mammary-tumor_BALB/c wt_sham-irradiated host_replicate 8

source_name: Sham IR host 37


title: TFi2.E03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: mouse_p53null-mammary-tumor_BALB/c wt_sham-irradiated host_replicate 6

source_name: Sham IR host 35


title: TFi2.D12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.D08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.D09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.D10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.E01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.D11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.D07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: mouse_p53null-mammary-tumor_BALB/c wt_sham-irradiated host_replicate 5

source_name: Sham IR host 34


title: TFi2.D05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.D06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.E02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.D03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: mouse_p53null-mammary-tumor_BALB/c wt_sham-irradiated host_replicate 3

source_name: Sham IR host 32


title: mouse_p53null-mammary-tumor_BALB/c wt_sham-irradiated host_replicate 7

source_name: Sham IR host 36


title: mouse_p53null-mammary-tumor_BALB/c wt_DIR-irradiated host_replicate 10

source_name: 49 cGy Ar -  25


title: mouse_p53null-mammary-tumor_BALB/c wt_sham-irradiated host_replicate 4

source_name: Sham IR host 33


title: mouse_p53null-mammary-tumor_BALB/c wt_DIR-irradiated host_replicate 12

source_name: 49 cGy Ar -  27


title: mouse_p53null-mammary-tumor_BALB/c wt_sham-irradiated host_replicate 1

source_name: Sham_IR host 30


title: mouse_p53null-mammary-tumor_BALB/c wt_DIR-irradiated host_replicate 5

source_name: 49 cGy Ar -  20


title: mouse_p53null-mammary-tumor_BALB/c wt_DIR-irradiated host_replicate 13

source_name: 49 cGy Ar -  28


title: mouse_p53null-mammary-tumor_BALB/c wt_DIR-irradiated host_replicate 8

source_name: 49 cGy Ar -  23


title: mouse_p53null-mammary-tumor_BALB/c wt_sham-irradiated host_replicate 2

source_name: Sham IR host 31


title: TFi2.D01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

source_name: Transcription factor induced fibroblasts


title: mouse_p53null-mammary-tumor_BALB/c wt_DIR-irradiated host_replicate 9

source_name: 49 cGy Ar -  24


title: TFi2.C12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: mouse_p53null-mammary-tumor_BALB/c wt_DIR-irradiated host_replicate 14

source_name: 49 cGy Ar -  29


title: mouse_p53null-mammary-tumor_BALB/c wt_DIR-irradiated host_replicate 6

source_name: 49 cGy Ar -  21


title: TFi2.C11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.D02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: mouse_p53null-mammary-tumor_BALB/c wt_DIR-irradiated host_replicate 4

source_name: 49 cGy Ar -  19


title: mouse_p53null-mammary-tumor_BALB/c wt_DIR-irradiated host_replicate 11

source_name: 49 cGy Ar - 26


title: mouse_p53null-mammary-tumor_BALB/c wt_DIR-irradiated host_replicate 7

source_name: 49 cGy Ar -  22


title: TFi2.D04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.C10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.C09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: mouse_p53null-mammary-tumor_BALB/c wt_DIR-irradiated host_replicate 1

source_name: 49 cGy Ar -  16


title: TFi2.C08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: mouse_p53null-mammary-tumor_BALB/c wt_DIR-irradiated host_replicate 2

source_name: 49 cGy Ar - 17


title: mouse_p53null-mammary-tumor_BALB/c wt_DIR-irradiated host_replicate 3

source_name: 49 cGy Ar - 18


title: TFi2.C07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.C06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.C05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: mouse_p53null-mammary-tumor_BALB/c wt_SIR-irradiated host_replicate 15


title: mouse_p53null-mammary-tumor_BALB/c wt_SIR-irradiated host_replicate 13


title: TFi2.C04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: mouse_p53null-mammary-tumor_BALB/c wt_SIR-irradiated host_replicate 12


title: mouse_p53null-mammary-tumor_BALB/c wt_SIR-irradiated host_replicate 14


title: TFi2.C01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.C03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: mouse_p53null-mammary-tumor_BALB/c wt_SIR-irradiated host_replicate 9

source_name: 50 cGy γ - 9


title: mouse_p53null-mammary-tumor_BALB/c wt_SIR-irradiated host_replicate 10


title: TFi2.C02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.B11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: mouse_p53null-mammary-tumor_BALB/c wt_SIR-irradiated host_replicate 7

source_name: 10 cGy γ - 7


title: mouse_p53null-mammary-tumor_BALB/c wt_SIR-irradiated host_replicate 11


title: mouse_p53null-mammary-tumor_BALB/c wt_SIR-irradiated host_replicate 8

source_name: 50 cGy γ - 8


title: TFi2.B10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Lipoic acid 72

city: Cagliari

first: Gabriella

last: Simbula

state: CA

address: Porcel 4

country: Italy

institute: THE UNIVERSITY OF CAGLIARI

description: Hepatoma cell FaO

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina BeadStudio 3.0.19.0 software (Illumina Inc) and BRB Array Tools (Version 4.2.0)

organism: Rattus norvegicus

source_name: Hepatoma cell

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Hepatoma cells FaO were grown in DMEM Plus Glutamax I (Invitrogen, Life Technologies) supplemented with Pen Strep and 10% heat-inactivated FCS (Life Technologies) in a humidified atmosphere of 5% CO2/95% air, at 37°C

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Fao cells were treated in the presence of 2% FCS and treated with a single dose of 0.1µM Thapsigargin and daily with 500 µM α-Lipoic acid. RNA was extracted after  treatment with TG  for 6 and 18 hrs and after treatment with α-Lipoic acid for 6, 18, 24, 30, 42, 48 and72 hrs. Three wells for each sample were pooled

value: FaO

value: hepatocyte


title: mouse_p53null-mammary-tumor_BALB/c wt_SIR-irradiated host_replicate 6

source_name: 10 cGy γ - 6


title: Thapsigargin 24

description: Hepatoma cell FaO


title: Lipoic acid 42

description: Hepatoma cell FaO


title: Lipoic acid 30

description: Hepatoma cell FaO


title: Lipoic acid 24

description: Hepatoma cell FaO


title: Thapsigargin 18

description: Hepatoma cell FaO


title: Control_3

description: Hepatoma cell FaO


title: mouse_p53null-mammary-tumor_BALB/c wt_SIR-irradiated host_replicate 4

source_name: 10 cGy γ - 4


title: Lipoic acid 48

description: Hepatoma cell FaO


title: Lipoic acid 6

description: Hepatoma cell FaO


title: mouse_p53null-mammary-tumor_BALB/c wt_SIR-irradiated host_replicate 5

source_name: 10 cGy γ - 5


title: TFi2.B08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

source_name: Transcription factor induced fibroblasts


title: mouse_p53null-mammary-tumor_BALB/c wt_SIR-irradiated host_replicate 2

source_name: 10 cGy γ - 2


title: Control_1

description: Hepatoma cell FaO


title: Uterine Implantation Site, WT with GFPBMT_79 (scRNA-seq)

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

data_processing:
The data from sequencer was processed using bcl2fastq progam provided by the vendor (10X genomics).  This program demultiplexes the data.
The resulting output was procssed using cellranger program provided by the vendor (10X genomics).  This program aligns, the reads, and uses the barcode information to generate diigital gene expression matrix data.
The data was filtered, normalized (SCTransform), and clustered in Seurat (version 3) within R.
After principal component analysis, first 30 principal components were used for clustering.  The data was further visualized using Seurat 3 and R.
Genome_build: mm10 with added sequences for GFP
Supplementary_files_format_and_content: The 3 file output from CellRanger 3 and average gene expression excel for average gene expression per cluster.

source_name: Uterine Implantation Site

extract_protocol:
The uterine implantation tissues were finely minced, and subsequently digested with a solution of Hanks' balanced salt solution containing HEPES (25mM), collagenase B (1mg/mL) and deoxyribonuclease I (0.1 mg/mL) for 30min at 37°C. Thereafter, the cell suspension was filtered sequentially through a 70 μm filter then through a 40 μm filter, and centrifuged at 2000 rpm for 8 min at 4°C. The cell pellet was washed with PBS by centrifugation and cell viability (>70% cells alive) and concentration were assessed by the Countess II Cell Counter.
10 X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit v2.1

treatment_protocol: Wildtype animals were given a bone marrow transplant from UBC-GFP transgenic animals. After mating, implantation sites were removed on ED 9.5 for scRNA-seq analysis.

tag: host strain

tag: host genotype

value: Wild-type

tag: donor strain

tag: donor genotype

value: GFP transgene


title: Lipoic acid 18

description: Hepatoma cell FaO

tag: cell type


title: Control_2

description: Hepatoma cell FaO


title: TFi2.B07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

tag: time

tag: passages

value: Ectopic expression of transcription factors

tag: batch


title: TFi2.B09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: SNB19 ZBTB18 shCTBP2 R3

city: Freiburg

first: Maria Stella

last: Carro

address: Breisacherstraße 64

country: Germany

institute: Freiburg University Medical Center

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: SNB19  cells transduced with ZBTB18 and shCTBP2

growth_protocol: SNB19 cells were grown in DMEM +10% FBS

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: SNB19 cells were transduced with lentiviral particles expressing specific proteins or shRNA (EV, ZBTB18, shCTBP2 or ZBTB18+shCTBP2)

tag: tissue

value: SNB19 cells


title: SNB19 ZBTB18 shCTBP2 R1


title: mouse_p53null-mammary-tumor_BALB/c wt_SIR-irradiated host_replicate 1

source_name: 10 cGy γ - 1


title: SNB19 ZBTB18 shCTBP2 R2


title: A1402_1OL - SHAM23

description: cRNA converted from total RNA by reverse transcription and in vitro transcription of the intermediate cDNA product

data_processing:
Read mapping was performed using Tophat 2.0.9
BAM alignment files were processed using the HTSeq 0.6.1 python framework and respective mm10 GTF gene annotation, obtained from the University of California, Santa Cruz (UCSC) database
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample entitled DESeq2 Count

source_name: Total RNA of p53null mammary tumor, BALB/c-Irradiated host

growth_protocol: Mammary epithelium of inguinal glands was surgically removed from 3-week-old wild type balb/c mice and were aged to 10 weeks old.

extract_protocol:
Total RNA was extracted using Trizol Reaget (Invitrogen), according to manufacturer's instructions.
Express RNA sequencing was performed from tumors derived from CAPE and control treated irradiated hosts using TruSeq RNA Sample Preparation Guide Protocol by Illumina® (#15008136 A).

treatment_protocol: Irradiated hosts with 100 cGy γ-rays or sham-irradiated at NYUSOM. Sham or irradiated mice were then randomly assigned to receive either control diet (7012 meal) with 1% sucrose or diets containing 10 nmol/moue/day CAPE 4 weeks after transplant until 14 weeks, increased to 500 nmol at 26 weeks and to 1000 nmol at 38 weeks which was maintained for the duration of the experiment.

value: BALB/c

tag: gender

value: female

value: frozen p53null mammary tumors

value: Mammary Gland


title: mouse_p53null-mammary-tumor_BALB/c wt_SIR-irradiated host_replicate 3

source_name: 10 cGy γ - 3


title: TFi2.B06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Transcription factor induced fibroblasts


title: TFi2.B05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: A1402_1JR - SHAM22


title: SNB19 ZBTB18 shCtr R2

source_name: SNB19  cells transduced with shCTBP2 and EV


title: SNB19 ZBTB18 shCtr R1


title: TFi2.B04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: A1402_1FR - SHAM21


title: A1402_1DL - SHAM20


title: TFi2.B03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: A1402_1CR - SHAM19


title: TFi2.B02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: SNB19 EV shCtr R3

source_name: SNB19 cells transduced with control vectors (EV and shCtr)


title: TFi2.B01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: SNB19 EV shCtr R1


title: SNB19 EV shCTBP2 R2

source_name: SNB19  cells transduced with ZBTB18 and shCtr


title: SNB19 EV shCTBP2 R1


title: SNB19 EV shCTBP2 R3


title: SNB19 EV shCtr R2


title: A1402_2OL - CAPE18


title: SNB19 ZBTB18 shCtr R3


title: A1402_2IR - CAPE16


title: A1402_2JR - CAPE17


title: TFi2.A12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.A11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: HUVEC_K1801/10strain_rep3

city: Münster

first: Dzmitry

last: Sinitski

address: Vesaliusweg 2-4

department: Anatomy and Vascular Biology

institute: University of Münster

description: replicate 3

hyb_protocol: Standard Illumina direct hybridization assay protocol

scan_protocol: Standard Illumina scanning protocol, BeadScan software, Illumina BeadArray Reader hardware

data_processing: The data were normalised using quantile normalisation with Genome Studio

source_name: Human umbilical cord

label_protocol: Biotinylated cRNA were prepared with the TargetAmp™-Nano Labeling Kit for Illumina arrays

growth_protocol: HUVEC were seeded in 6-well plates (30.000 cells/cm²) and were grown till confluence.

extract_protocol: Total RNA was extracted with QIAGEN RNeasy mini kit, followed by clean-up and DNase I treatment with QIAGEN RNase-Free DNase Set in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: HUVEC culture were infected with respective strain of Staphylococcus aureus (MOI=50) for 3 hours. Extracellular bacteria were washed with lysostaphin (20µg/ml) for 30 minutes. Cells were further incubated till 7 hours postinfection. Negative control - Mock infection. Positive control - 3,5 hours of TNF-alpha stimulation (100 ng/ml).

tag: donor

value: Endothelium


title: HUVEC_K2900/10strain_3

description: replicate 3


title: TFi2.A10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: HUVEC_6850_rep3

description: replicate 3


title: HUVEC_9657/04strain_rep3

description: replicate 3


title: HUVEC_TNF-α_rep3

description: replicate 3

value: TNF-alpha treated


title: HUVEC_K70058396strain_rep3

description: replicate 3


title: HUVEC_9657/04strain_rep2

description: replicate 2


title: HUVEC_K1801/10strain_rep2

description: replicate 2


title: A1402_3KR - GAMMA13


title: A1402_2GR - CAPE15


title: HUVEC_mock_rep3

description: replicate 3

value: Mock treated


title: HUVEC_6850_rep2

description: replicate 2


title: HUVEC_K2900/10strain_2

description: replicate 2


title: HUVEC_8325-4strain_rep2

description: replicate 2


title: HUVEC_K70058396strain_rep2

description: replicate 2


title: TFi2.A08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: 9 days after induction


title: TFi2.A07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: A1402_2CL - CAPE14


title: A1402_3DL - GAMMA11


title: TFi2.A06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.A05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi2.A09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: A1402_3AL - GAMMA10


title: HUVEC_mock_rep2

description: replicate 2


title: HUVEC_8325-4strain_rep3

description: replicate 3


title: A1402_4OL - CAPEg9


title: HUVEC_K2900/10strain_1

description: replicate 1


title: HUVEC_K70058396strain_rep1

description: replicate 1


title: TFi2.A04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: HUVEC_6850_rep1

description: replicate 1


title: A1402_4NR - CAPEg8


title: TFi2.A03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: HUVEC_TNF-α_rep2

description: replicate 2


title: A1402_4PR- CAPEg7


title: VECTOR F NCC 1

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

description:
JGL_Neuroblastoma_model_Count_Matrix.csv
processed data header: SJMMNORM046476_C1-VECTOR-F-NCCs

data_processing:
Illumina base calling
STAR mapping (v2.7.1a)
STAR counting using -"quantMode GeneCounts" option
Genome_build: GRCm38.p6  with a GTF from ensembl genebuild v97
Supplementary_files_format_and_content: transcript level raw read count

source_name: mouse neural crest cells

growth_protocol: This study was performed in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institute of Health. All animal experiments were approved by the Institutional Animal Care and Use Committee (IACUC) at St. Jude Children’s Research Hospital. For subcutaneous tumor experiments, cells were injected into the hind flank of 6–8 week old C57Bl/6 mice (Charles River Laboratories). Genetically engineered NCCs were injected at 1.5x106 cells per mouse in 100µl total volume. Cells were injected in a 1:1 mix of cells and Matrigel (BD Biosciences) and tumor growth was monitored by measuring the size by digital caliper. Tumor volume was calculated using the formula by ½ x (length x width2). Mice were sacrificed and tumors isolated when they were at least 1500mm3 or earlier if ulcerated. We used ten mice per treatment group for NCCs control, 1p36-del NCCs, 1p36/Mycn NCCs and Mycn-alone NCCs. Mice were housed with 4 to 5 mice per cage with corn cob bedding in normal light-dark cycling at room temperature (~23°C). Food and water were provided ad libitum. Mice were sacrificed using CO2 asphyxiation followed by cervical dislocation.  Mouse NCCs samples were growth in CDM (Fukuta et al., 2014), which contains Iscove's modified Dulbecco's medium/Ham's F-12 1∶1, 1X chemically defined lipid concentrate (GIBCO), 1X µg/ml Insulin-transferrin-selenium (Thermo Fisher Scientific), 450 µM monothioglycerol (Sigma), 5 mg/ml purified BSA (Sigma), 7 µg/ml Insulin (Thermo Fisher Scientific), and penicillin/streptomycin (Invitrogen). Culture dishes were coated with fibronectin (Corning). The medium was supplemented with EGF (R&D) and FGF2 (R&D) to modulate growth factor signals and SB431542 (SB) (Sigma) as a TGF-beta signaling pathway suppressor. For differentiation assays the regular CDM medium was replaced with DMEM/F12 supplemented with 1 x N2 supplement, we removed the EGF and FGF growth factors and added 10 ng/ml BDNF, GDNF, NT-3 and NGF (R&D). The medium was changed every 48h.

extract_protocol:
Total RNA was extracted using an RNeasy Plus Mini Kit (Qiagen)
total stranded RNA protocol

value: normal cell line

tag: genotype

value: Vector F


title: VECTOR F NCC 3

description:
JGL_Neuroblastoma_model_Count_Matrix.csv
processed data header: SJMMNORM046476_C3-VECTOR-F-NCCs


title: HUVEC_8325-4strain_rep1

description: replicate 1


title: HUVEC_9657/04strain_rep1

description: replicate 1


title: HUVEC_K1801/10strain_rep1

description: replicate 1


title: VECTOR F NCC 2

description:
JGL_Neuroblastoma_model_Count_Matrix.csv
processed data header: SJMMNORM046476_C2-VECTOR-F-NCCs


title: NMYC NCC 2

description:
JGL_Neuroblastoma_model_Count_Matrix.csv
processed data header: SJMMNORM046475_C2-NMYC-NCCs

value: NMYC


title: HUVEC_TNF-α_rep1

description: replicate 1


title: NMYC NCC 3

description:
JGL_Neuroblastoma_model_Count_Matrix.csv
processed data header: SJMMNORM046475_C3-NMYC-NCCs


title: A1402_4JR - CAPEg6

tag: strain


title: TFi2.A02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NMYC NCC 1

description:
JGL_Neuroblastoma_model_Count_Matrix.csv
processed data header: SJMMNORM046475_C1-NMYC-NCCs


title: TFi2.B12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: WT NCC 3

description:
JGL_Neuroblastoma_model_Count_Matrix.csv
processed data header: SJMMNORM046474_C3-WT-NCCs

value: WT


title: A1402_4HL - CAPEg5


title: WT NCC 1

description:
JGL_Neuroblastoma_model_Count_Matrix.csv
processed data header: SJMMNORM046474_C1-WT-NCCs


title: A1402_4GL - CAPEg4


title: NMYC tumor 5

description:
JGL_Neuroblastoma_model_Count_Matrix.csv
processed data header: SJMMNBL046479_D2-NMYC-tumor


title: TFi1.H12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NMYC tumor 4

description:
JGL_Neuroblastoma_model_Count_Matrix.csv
processed data header: SJMMNBL046479_D1-NMYC-tumor

source_name: mouse tumor

value: tumor


title: A1402_4DL - CAPEg3


title: Vector F tumor 6

description:
JGL_Neuroblastoma_model_Count_Matrix.csv
processed data header: SJMMNBL046478_D6-Vector-F-tumor


title: TFi2.A01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi1.H10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Vector F tumor 5

description:
JGL_Neuroblastoma_model_Count_Matrix.csv
processed data header: SJMMNBL046478_D5-Vector-F-tumor


title: Vector F tumor 4

description:
JGL_Neuroblastoma_model_Count_Matrix.csv
processed data header: SJMMNBL046478_D4-Vector-F-tumor


title: A1402_4BR - CAPEg2


title: A1402_4BL - CAPEg1


title: Vector F tumor 2

description:
JGL_Neuroblastoma_model_Count_Matrix.csv
processed data header: SJMMNBL046478_D2-Vector-F-tumor


title: TFi1.H09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: WT NCC 2

description:
JGL_Neuroblastoma_model_Count_Matrix.csv
processed data header: SJMMNORM046474_C2-WT-NCCs


title: Vector F tumor 3

description:
JGL_Neuroblastoma_model_Count_Matrix.csv
processed data header: SJMMNBL046478_D3-Vector-F-tumor


title: dTGS.1079

city: Seattle

first: Guo-Liang

last: Chew

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences and Public Health Sciences

institute: Fred Hutchinson Cancer Research Center

description: severe pathology

data_processing:
Merge gene annotations from UCSC knownGene, Ensembl 71, MISO v2.0
RSEM v1.2.4 used to call Bowtie with option '-v 2' to align to merged annotation
Remaining reads mapped to genome with TopHat v2.0.8b
Genome_build: mm10

molecule: polyA RNA

source_name: gastrocnemius muscle

extract_protocol:
Total RNA (5µg) was isolated from gastrocnemious muscles of 3 mice per group (ACTA1-MCM, FLExD, ACTA1-MCM; FLExD moderate TMX, and ACTA1-MCM; FLExD severe TMX). Total RNA was extracted from dissected mouse muscles homogenized in 10 volumes of TRIzol (ThermoFisher) using the TissueLyser LT (Qiagen), as per manufacturer’s instructions followed by on-column DNaseI treatment and clean-up using the RNeasy mini kit (Qiagen).
mRNAs were purified using poly(A) selection and then fragmented. First strand cDNA synthesis used random priming followed by second strand synthesis. The resulting double strand cDNA was end repaired, phosphorylated, and A-tailed. Adapters were ligated and PCR amplification was performed. The library was sequenced using the Illumina HiSeq2500 platform in a 1x50 base pair single-read configuration in Rapid Run mode, with a total of at least 120 million reads per lane.

treatment_protocol: Tamoxifen (TMX) was administered to mice by intraperitoneal (IP) injection at a final concentration of 5 or 10mg/kg.  For the mild model, ACTA1-MCM; FLExD bi-transgenic animals were injected once with 5mg/kg TMX.  For the severe model, ACTA1-MCM; FLExD bi-transgenic mice were injected on two consecutive days with 10mg/kg TMX.

value: muscle

value: two 10 mg/kg IP injections of tamoxifen on consecutive days

tag: mouse id


title: NMYC tumor 3

description:
JGL_Neuroblastoma_model_Count_Matrix.csv
processed data header: SJMMNBL046477_D3-NMYC-tumor


title: NMYC tumor 2

description:
JGL_Neuroblastoma_model_Count_Matrix.csv
processed data header: SJMMNBL046477_D2-NMYC-tumor


title: TFi1.H07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

data_processing:
Basecalls performed using CASAVA version 1.7
Single-cell RNAseq reads were aligned to the human transcriptome build hg19 using Kallisto v0.42.4 with the default parameter settings for paired-end reads.
We excluded chambers containing no cells, multiple cells or cells exhibiting morphological features of cell death based on visual inspection using the IN Cell Analyzer 6000 (GE Healthcare).
Additionally, cells not expressing either of the two housekeeping genes ACTB and GAPDH (encoding β-actin and glyceraldehyde-3-phosphate dehydrogenase, respectively), or expressing them at less than three standard deviations below the mean, were scored as unhealthy and removed.
Genome_build: hg19
Supplementary_files_format_and_content: comma-separated values files contain counts and TPM/CPM values for each sample after quality control

value: Ectopic expression of transcription factors


title: Vector F tumor 1

description:
JGL_Neuroblastoma_model_Count_Matrix.csv
processed data header: SJMMNBL046478_D1-Vector-F-tumor


title: NMYC tumor 1

description:
JGL_Neuroblastoma_model_Count_Matrix.csv
processed data header: SJMMNBL046477_D1-NMYC-tumor


title: TFi1.H08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: dTGS.1047

description: severe pathology


title: dTGS.1066

description: severe pathology


title: A1402_3EL - GAMMA12

description: cRNA converted from total RNA by reverse transcription and in vitro transcription of the intermediate cDNA product

value: BALB/c


title: BERKO left M1 cortex 4

city: Huddinge

first: Ivan

last: Nalvarte

address: Hälsovägen 7C, NEO

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

description:
BERKO4_BLC4
STRT-Seq
processed data file: readsCortex.txt
processed data file: nreadsCortex.txt
processed data file: annotationsCortex.txt

data_processing:
Data processing of the sequenced RNA libraries was performed using the STRTprep pipeline (https://github.com/shka/STRTprep).
The reads from the 3 lanes were de-multiplexed into individual samples using the sample-specific barcodes, then mapped to the mouse genome assembly MGSCv37 (mm9) with RefSeq annotations using Bowtie1 and assembled into transcript regions using Tophat v.2.0.12.
For quality control, samples with low read counts (< 200,000 reads/sample), high redundancy (>10), shallow spike-in counts (< 700 reads/sample), low spike-in map rate (< 90%), and low map rate to 5’-end of genes (< 70%) were excluded from subsequent analyses. The read counts were normalized to relative amounts compared to total spike-in counts. Differential expression analysis was performed using SAMstrt. Reads within the 5′‐UTR or up to 500 bp upstream of the protein‐coding genes were analyzed in the differential expression analysis. Variation caused by technical noise was estimated from technical replicates using a generalized linear model with a gamma distribution. Samples from 1 BERKO mouse was removed as its transcription profile was completely different from the other BERKO profiles. As the technical variations were determined to be smaller than biological variations, the sum of read counts from technical replicates of each sample were used for the final differential expression analysis.
The raw files contain demultiplexed sample reads in compressed fastq format. The processed files contain demultiplexed reads of samples with unaligned reads filtered out.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: readsCortex.txt file contains raw counts of reads aligned to TFEs (transcript start site mapping of reads clusters).
Supplementary_files_format_and_content: nreadsCortex.txt file contains normalized counts of the TFEs (relative to total counts of spike-in RNAs).
Supplementary_files_format_and_content: annotationsCortex.txt file contains annotation of the TFEs in terms of their locations in genes (upstream of gene, 5-UTR, coding regions CDS, introns, 3-UTR, etc.)

source_name: mouse cortex tissue

growth_protocol: Age matched and genotyped 16 – 20 week old C57BL/6 WT or BERKO male mice were housed in a room of standard temperature (22 ± 1 °C) with a regular 12 h light, 12 h dark cycle and given free access to water and standard rodent chow.

extract_protocol:
Mice were anesthetized with sodium pentobarbital (50mg/kg, intramuscularly) and either transcardially perfused with 1x PBS, followed by 4% paraformaldehyde (in 0.1 M PBS, pH 7.4) or sacrificed through cervical dislocation (for RNA extraction) and the brain was thereafter dissected out. Left and right primary motor cortex was biopsied either by needle puncture (for RNA-sequencing) or using small dissection forceps (approx. 1.0 x 1.0 mm pieces for other biochemical analyses) and put individually in tubes containing RNAlater solution (Invitrogen). The tubes were stored at -80°C before RNA extraction. Total RNA was isolated using the RNeasy Plus Micro kit and the RNeasy kit respectively (both from Qiagen, Hilden, Germany) according to manufacturer’s recommendations.
10 ng of RNA from left and right primary motor cortex biopsies from 6 WT and 6 BERKO mice were processed using the Single-cell Tagged Reverse Transcription (STRT) RNA sequencing protocol. Briefly, RNA samples were placed in a 48-well plate in which a universal primer, template-switching helper oligos, and a well-specific 6 bp barcode sequence (for sample identification) were added to each well. Reverse transcription reagents and ERCC RNA Spike-In Mix I (both from Thermo Fischer Scientific) were added to generate first-strand cDNA. The synthesized cDNAs from the samples were then pooled into one library and amplified by single-primer PCR with the universal primer sequence. The resulting amplified library was then sequenced in 3 lanes using Illumina HiSeq 2000 instrument.

tag: strain/background

tag: genotype/variation

value: ERb-/-

tag: Sex

value: Male

value: M1 cortex

tag: cortex side

value: Left

tag: mouse


title: BERKO left M1 cortex 6

description:
BERKO6_BLC6
STRT-Seq
processed data file: readsCortex.txt
processed data file: nreadsCortex.txt
processed data file: annotationsCortex.txt


title: BERKO left M1 cortex 5

description:
BERKO5_BLC5
STRT-Seq
processed data file: readsCortex.txt
processed data file: nreadsCortex.txt
processed data file: annotationsCortex.txt


title: TFi1.H11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Transcription factor induced fibroblasts

tag: treatment


title: dTGM.1331

description: moderate pathology

value: one 5 mg/kg IP injection of tamoxifen


title: dTGM.1308

description: moderate pathology


title: BERKO left M1 cortex 3

description:
BERKO3_BLC3
STRT-Seq
processed data file: readsCortex.txt
processed data file: nreadsCortex.txt
processed data file: annotationsCortex.txt


title: dTGM.1236

description: moderate pathology


title: BERKO right M1 cortex 6

description:
BERKO6_BRC6
STRT-Seq
processed data file: readsCortex.txt
processed data file: nreadsCortex.txt
processed data file: annotationsCortex.txt

value: Right


title: FLExD.1378

description: mild pathology

value: no tamoxifen


title: BERKO left M1 cortex 2

description:
BERKO2_BLC2
STRT-Seq
processed data file: readsCortex.txt
processed data file: nreadsCortex.txt
processed data file: annotationsCortex.txt


title: TFi1.H05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: 9 days after induction


title: TFi1.H06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi1.H03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: WT left M1 cortex 6

description:
WT6_BLC6
STRT-Seq
processed data file: readsCortex.txt
processed data file: nreadsCortex.txt
processed data file: annotationsCortex.txt


title: BERKO right M1 cortex 4

description:
BERKO4_BRC4
STRT-Seq
processed data file: readsCortex.txt
processed data file: nreadsCortex.txt
processed data file: annotationsCortex.txt


title: BERKO right M1 cortex 5

description:
BERKO5_BRC5
STRT-Seq
processed data file: readsCortex.txt
processed data file: nreadsCortex.txt
processed data file: annotationsCortex.txt


title: TFi1.H01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: WT left M1 cortex 5

description:
WT5_BLC5
STRT-Seq
processed data file: readsCortex.txt
processed data file: nreadsCortex.txt
processed data file: annotationsCortex.txt


title: BERKO right M1 cortex 2

description:
BERKO2_BRC2
STRT-Seq
processed data file: readsCortex.txt
processed data file: nreadsCortex.txt
processed data file: annotationsCortex.txt


title: BERKO right M1 cortex 3

description:
BERKO3_BRC3
STRT-Seq
processed data file: readsCortex.txt
processed data file: nreadsCortex.txt
processed data file: annotationsCortex.txt


title: TFi1.H04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi1.G12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: FLExD.1367

description: mild pathology


title: FLExD.1358

description: mild pathology


title: MCM.1349

description: control


title: TFi1.G11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: MCM.1246

description: control


title: WT left M1 cortex 4

description:
WT4_BLC4
STRT-Seq
processed data file: readsCortex.txt
processed data file: nreadsCortex.txt
processed data file: annotationsCortex.txt


title: WT left M1 cortex 3

description:
WT3_BLC3
STRT-Seq
processed data file: readsCortex.txt
processed data file: nreadsCortex.txt
processed data file: annotationsCortex.txt


title: WT left M1 cortex 1

description:
WT1_BLC1
STRT-Seq
processed data file: readsCortex.txt
processed data file: nreadsCortex.txt
processed data file: annotationsCortex.txt


title: MCM.1127

description: control


title: WT right M1 cortex 5

description:
WT5_BRC5
STRT-Seq
processed data file: readsCortex.txt
processed data file: nreadsCortex.txt
processed data file: annotationsCortex.txt


title: WT left M1 cortex 2

description:
WT2_BLC2
STRT-Seq
processed data file: readsCortex.txt
processed data file: nreadsCortex.txt
processed data file: annotationsCortex.txt


title: WT right M1 cortex 6

description:
WT6_BRC6
STRT-Seq
processed data file: readsCortex.txt
processed data file: nreadsCortex.txt
processed data file: annotationsCortex.txt


title: TFi1.G09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi1.G07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: MC3T3 cells, D6_50ng_per_ml_BMP2_+_5microM_GSK126

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 2.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

source_name: Calvarial osteoblasts

extract_protocol:
Direct-zol™ RNA kit (Zymo Research) and TRIzol reagent (Invitrogen)
mRNA version 2 library prep kit (Illumina)

tag: cell line

value: osteoblast precursor cell line MC3T3

tag: passage

value: day 6


title: MC3T3 cells, D6_5microM_GSK126

tag: time


title: TFi1.G10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

extract_protocol: Single cell RNA-seq analysis was performed using the Fluidigm C1 platform following the manufacturer’s protocol (P100-7168L1, Fluidigm). Briefly, cell number and cell viability were assessed using the Countess II Automated Cell Counter (ThermoFisher). After priming medium size C1 Single-cell Open App IFCs, 250 cells/μL were loaded and capture efficiency and cell morphology was assessed using the IN Cell Analyzer 6000 (GE Healthcare). To exclude chambers loaded with no cells, more than one cell (cell doublets) or dead cells for downstream analysis, we took 11 z-stacking images per chamber. Next, cells were lysed with 20,000-fold diluted ERCC RNA Spike-In Mix1 (L/N 00329960 Life Technologies) and reverse transcription (RT) and cDNA amplification were performed using the SMARTer Ultra Low RNA Kit for the Fluidigm C1TM System (Clontech). The amplified cDNAs were harvested into 96 well plates and quantified with Quant-iT TM  PicoGreen dsDNA Assay kit. Library preparation was performed with the Nextera XT DNA Library Preparation kit (Illumina), Nextera XT Index Kit v2 (Illumina) and AMpure XP beads (Beckman Coulter). Libraries were quantified by High Sensitivity DNA Reagents (Agilent Technologies) and KAPA Library Quantification kit (KAPA BIOSYSTEMS).

tag: cell type

tag: passages


title: MC3T3 cells, D6_50ng_per_ml_BMP2


title: AF9 E531R Rep 1

city: Charlottesville

first: John

last: Bushweller

state: Virginia

address: 1340 Jefferson Park Avenue

department: Molecular Physiology and Biological Physics

institute: University of Virginia

data_processing:
Verification with FastQC
Adapters acquired with bbmerge
Adapters removed and reads trimmed based on quality with cutadapt
Reads aligned using Hisat2
Aligned reads sorted with Samtools
Reads counted with featureCounts
Differential Expression analyzed with DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: CSV of Differential Expression results, generated using DESeq2.

source_name: Femur bone marrow

growth_protocol: c-Kit positive cells were selected from femur bone marrow .

extract_protocol: none provided by the submitter

treatment_protocol: Infected with MSCVneo-MLL-AF9 WT or E531R, and selected on G418 and serial passage in methylcellulose with cytokines.

tag: tissue

value: bone marrow


title: MC3T3 cells, D6_10ng_per_ml_BMP2_+_5microM_GSK126


title: AF9 E531R Rep 3


title: TFi1.G08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

source_name: Transcription factor induced fibroblasts

tag: batch


title: TFi1.G06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: MC3T3 cells, D6_10ng_per_ml_BMP2


title: TFi1.G05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi1.H02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: AF9 WT Rep 3


title: MC3T3 cells, D6_Vehicle

value: Vehicle


title: WT right M1 cortex 4

description:
WT4_BRC4
STRT-Seq
processed data file: readsCortex.txt
processed data file: nreadsCortex.txt
processed data file: annotationsCortex.txt

value: WT


title: WT right M1 cortex 2

description:
WT2_BRC2
STRT-Seq
processed data file: readsCortex.txt
processed data file: nreadsCortex.txt
processed data file: annotationsCortex.txt


title: WT right M1 cortex 1

description:
WT1_BRC1
STRT-Seq
processed data file: readsCortex.txt
processed data file: nreadsCortex.txt
processed data file: annotationsCortex.txt


title: MC3T3 cells, D1_50ng_per_ml_BMP2_+_5microM_GSK126

value: day 1


title: MC3T3 cells, D1_10ng_per_ml_BMP2_+_5microM_GSK126


title: MC3T3 cells, D1_5microM_GSK126


title: AF9 E531R Rep 2


title: WT right M1 cortex 3

description:
WT3_BRC3
STRT-Seq
processed data file: readsCortex.txt
processed data file: nreadsCortex.txt
processed data file: annotationsCortex.txt


title: MC3T3 cells, D1_50ng_per_ml_BMP2


title: MC3T3 cells, D1_10ng_per_ml_BMP2


title: 5C_B39-2_Pgk-D4_rep2

description:
Xic3_MAIN_primer_pool_mm9_my5C_FOR.bed
Xic3_MAIN_primer_pool_mm9_my5C_REV.bed

source_name: mouse ESC (Pgk12.1)

value: mouse ESC (Pgk12.1)

value: XX, 129/Ola-Hsd x (C3H/He-Pgk-1a/Ws x 129/Ola-Hsd)F1

value: wild type

tag: differentiation stage

value: day 4

tag: capture-c viewpoint


title: MC3T3 cells, D1_Vehicle

tag: strain


title: TFi1.G01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Ectopic expression of transcription factors


title: TFi1.F11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi1.F12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: 5C_B39-1_Pgk-D2_rep1

tag: genotype

value: day 2


title: 5C_B39-2_Pgk-D2_rep2


title: TFi1.G04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Transcription factor induced fibroblasts


title: 5C_B39-1_Pgk-D1_rep1


title: Hoxa11+/- KO BMT 272

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The first 6 nucleotides and the last nucleotides at the point where the Phred score of an examined base fell below 20 were trimmed using in-house scripts.  If, after trimming, the read was shorter than 45-bp, the whole read was discarded.
Trimmed reads were mapped to the mouse reference genome (mm10) with a known transcriptome index (UCSC Known Gene annotation) with Tophat v2.1.1 using the very-sensitive preset, first strand library type, and providing the corresponding gene model annotation. Only the reads that mapped to a single unique location within the genome, with a maximum of two mismatches in the anchor region of the spliced alignment, were reported in these results.
Tophat alignments were then processed by Cuffdiff to obtain differential gene expression using first strand library type, providing gene model annotation and the genome sequence file for detection and correction of sequence-specific bias that random hexamer can cause during library preparation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKMs, fold changes, and p-values for each condition. Cuffdiff output format.

extract_protocol:
Total RNA was extracted using the TRIZOL-chloroform extraction method. RNA was cleaned using the QIAGEN Rneasy Cleanup kit.
Poly-A, strand-specific RNA library construction was performed by the Yale Center for Genomic Analysis utilizing the TruSeq Library Prep Kit 2.0 per the manufacturers specifications. . Following first-strand synthesis with random primers, second strand synthesis was performed with dUTP for generating strand-specific sequencing libraries.

treatment_protocol: B6.129-Hoxa11tm1Dmwe/J heterozygote and wildtype animals were given a bone marrow transplant from either wild type or knockout animals. After mating, implantation/decidualization sites were removed on ED 5.5 for RNA-seq analysis.

tag: host hoxa11 genotype

tag: donor hoxa11 genotype

tag: mouse strain


title: Hoxa11+/- WT BMT 582


title: Hoxa11+/- WT BMT 98


title: AF9 WT Rep2


title: TFi1.G03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi1.F10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: 5C_B39-2_Pgk-D0_rep2

value: day 0 (undifferentiated)


title: TFi1.F09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Hoxa11+/- WT BMT 589


title: Hoxa11+/- KO BMT 86


title: TFi1.G02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi1.F08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: AF9 WT Rep 1


title: 5C_B39-1_Pgk-D0_rep1


title: 5C_B51_59.30_LinxP-del_mut2_rep2

source_name: mouse ESC (E14)

value: mouse ESC (E14)

value: XY, 129/Ola

value: LinxP deletion


title: 5C_B51_A18_LinxP-del_mut1_rep2


title: Hoxa11+/+ WT BMT 376


title: 5C_B29_59.30_LinxP-del_mut2_rep1


title: Hoxa11+/- KO BMT 271


title: 5C_B39-2_Pgk-D1_rep2


title: TFi1.F07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: 9 days after induction


title: 5C_B62_D13_LinxE-del_mut2

value: LinxE deletion


title: 5C_B29_A18_LinxP-del_mut1_rep1


title: Hoxa11+/+ WT BMT 218


title: 5C_B39-1_Pgk-D4_rep1


title: Hoxa11+/+ WT BMT 76


title: 5C_B38_LPi1_LinxP-inv_mut1

value: LinxP inversion


title: 5C_B38_LPi4_LinxP-inv_mut2


title: TFi1.F05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TFi1.F06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: 5C_B29_62.25_Linx-int1-del_mut1

value: Linx-int1 deletion


title: TFi1.F04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: 5C_B101_E14_wt4


title: TFi1.F03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: 21_p7f_YFP_pos

city: Davis

first: Mark

middle: O.

last: Huising

address: One Shields Avenue

department: Neurobiology, Physiology and Behavior

institute: University of California, Davis

description: This sample was previously accessioned in GEO as GSM2133077

data_processing:
reads were mapped to GenCode M8 (GRCm38.p4) using STAR v2.5
FeatureCounts was used to create count tables of the sorted bam files using reads aligning to RefSeq defined exons.
EdgeR v3.14.0 was used for statistical comparison.
Genome_build: GenCode M8 (GRCm38.p4)
Supplementary_files_format_and_content: RPKM Expression values for all replicates generated using Gencode defined exons and EdgeR v3.14.0.

source_name: FACS-purified delta cells

growth_protocol: Isolated were isolated by collagenase injection through the common bile duct per common protocols. Isolated islets were cultured overnight in RPMI supplemented with 5.5 mM glucose and 10% FBS and pen/strep and dissociated the following morning by trypsin (0.25%) EDTA and gentle titturation for FACS purification.

extract_protocol:
Cells were collected in Trizol post FACS purification and isolated by a chloroform extraction, assisted by phase lock tubes. RNA was precipitated by isopropanol and cleaned up over an RNEasy microcolumn per the Qiagen's taking great care to avoid carry over of ethanol following the column washes. Elution volume was 30 microliter.
Indexed sequencing libraries were constructed using the TruSeq RNA sample prep Kit v2 per Illumina instructions.

value: FACS-purified delta cells

tag: Stage

value: adult

tag: gender

value: female


title: 5C_B29_E14R_wt2


title: 17_p7m_YFP_pos

description: This sample was previously accessioned in GEO as GSM2133075

value: male


title: TFi1.F02

city: Yokoham

first: Joachim

last: Luginbühl

institute: RIKEN

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

growth_protocol: Human dermal fibroblasts were purchased from Lonza (passages 4-8) and cultured in DMEM containing 10% FBS/L-glutamine/10% Penicilin&Streptomycin at 37°C 5% CO2 until virus infection. For TFi generation, a total of 6 MOI (~0.3 MOI per virus) were pooled into culture medium containing 8 mg*ml-1 Polybrene (SIGMA) to increase infection efficiency. The virus pool was infected and incubated overnight at 37°C 5% CO2. On the following day, virus-containing medium was removed and cells were incubated for an additional day in fresh culture medium at 37°C 5% CO2. For iN generation, infected cells were split onto Poly-d-lysine (100μg*ml-1) / Laminin (50μg*ml-1) (SIGMA)-coated culture plates and incubated overnight in culture medium at 37°C 5% CO2. On the following day, medium was changed to neuronal induction medium containing DMEM/F12 and Neurobasal-A (Thermo Fisher Scientific) mixed at a 1:1 ratio, 2% (vol/vol) B27 supplement and 0.5% N2 Supplement (GIBCO), 1x nonessential amino acids (Thermo Fisher Scientific), 1% GlutaMAX supplement, 10ng*ml-1 BDNF (GIBCO), 10ng*ml-1 NT3 (R&D Systems), 10ng*ml-1 GDNF (Thermo Fisher Scientific), VPA (0.5mM, WAKO), L-Ascorbic acid (200nM, SIGMA), Y-27632 (10μM, WAKO), dcAMP (0.5mM, SIGMA), 10% FBS and 10% Penicilin&Streptomycin (WAKO). The concentrations of small molecules used were as follows: CHIR99021 (2μM, Abcam), SB-431542 (10μM, SIGMA), LDN-193189 (0.5μM, Stemgent), Noggin (100ng*ml-1, SIGMA). Neuronal induction medium was changed every third day, during which the concentration of FBS was gradually reduced from 10% to 1%. After 2 weeks, neuronal induction medium was replaced with neuronal maturation medium without small molecules and 1% FBS and the medium was changed every third day until further analysis.

tag: treatment


title: 20_p6f_Chy_pos

description: This sample was previously accessioned in GEO as GSM2133080

source_name: FACS-purified beta cells

value: FACS-purified beta cells


title: 5C_B100_E14_wt3

value: wild type


title: TFi1.F01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Ectopic expression of transcription factors


title: TFi1.E12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: 5C_B60_20_LinxE-del_mut1


title: 16_p6m_Chy_pos

description: This sample was previously accessioned in GEO as GSM2133078


title: 22_p8f_DP

source_name: FACS-purified delta transdifferentiated cells


title: 5C_B60_62_Linx-int1-del_mut2


title: Thyroid tumor, TC-125_S14_R1_001 (RNA-seq)

city: Moscow

first: Daniil

last: Nikitin

address: Miklucho-Maklaya

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

data_processing:
RNA sequencing FASTQ files were processed with STAR aligner in ‘GeneCounts’ mode with the Ensembl human transcriptome annotation (Build version GRCh38 and transcript annotation GRCh38.89).
Genome_build: GRCh38
Supplementary_files_format_and_content: Read counts table generated by merging of STAR output. Ensembl gene IDs were converted to HGNC gene symbols using Complete HGNC dataset

source_name: Thyroid gland, primary tumor

extract_protocol:
Tissue specimens were formalin fixed and embedded in paraffin.
RNA was extracted from the FFPE samples using RecoverAll™ Total Nucleic Acid Isolation  Kit. KAPA  RNA Hyper with RiboErase (KAPA Biosystem) Kit was used for further depletion of ribosomal  RNA and library preparation. Different adaptors were used for multiplexing samples in one  sequencing run.
Illumina Library prep kit

tag: subtype

value: thyroid cancer

value: Primary


title: Thyroid tumor, TC-126_S15_R1_001 (RNA-seq)


title: Thyroid tumor, TC-127_S12_R1_001 (RNA-seq)


title: Thyroid tumor, TC-128_S16_R1_001 (RNA-seq)


title: TFi1.E10

address: 1-7-22 Suehiro-cho

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Transcription factor induced fibroblasts


title: 18_p8m_DP

value: FACS-purified delta transdifferentiated cells


title: Thyroid tumor, TC-124_S13_R1_001 (RNA-seq)


title: TFi1.E09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: cG13-treat_Subtel_10p+18p_OICR

city: Haifa

first: Shir

last: Toubiana

address: 1 Efron st.

country: Israel

institute: Technion

data_processing:
BISMARK (v0.17.0): Adaptors and low quality bases were trimmed out. Reads were then aligned to the customized reference human genome GRCh38 by using the Bismark aligner.
Methylation scores were performed using Bismark methylation extractor script.
For 10qMultiple and 10q_2q+4q files the different subtelomeres were told apart based on single nucleotide differences compared to subtelomere 10q. We used a Perl homemade script.
Genome_build: hg38

source_name: iPSCs

growth_protocol: IPSCs were cultured on plates coated with Cultrex® Reduced Growth Factor Basement Membrane Matrix (343300501, Trevigen, MD, USA), and grown in either mTeSR-1 media (85850, StemCell Technologies, Vancouver, Canada) or PepRoGrow™ hESC Media (hESC-100, PepRoTech, NJ, USA). Cells were passaged every 4–6 days. Cell were dissociated from plates with 0.5 mM EDTA and following each passage, 2mM Thiazovivin (14245, Cayman CHEMICAL, MI, USA was added to the media. FLs derived from iPSCs  were grown in fibroblast media (DMEM media supplemented with 20% fetal bovine serum, 2 mM glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin) at standard conditions.

extract_protocol:
Genomic DNA was extracted according to standard procedures and was bisulfite-converted with the Methylamp DNA Modification kit (EPIGENTEK, NY, USA)
PCR products were purified by QIAquick PCR purification kit (28104, QIAGEN, MD, USA). Further amplicon processing, sequencing, and analysis were performed as described (Sagie, Toubiana, et al. 2017).

treatment_protocol: For drug treatment, iPSCs were treated with 1 μM of OICR-9429 (SML1209, MERCK) or 0.1% DMSO for 72 hours, replacing the medium every 24 hours.

tag: passage (p), population doubling (pd)

value: ICF1 cells with corrected DNMT3B (DNMT3B p. wt/ p.S780L)


title: Thyroid tumor, TC123_S19_R1_001 (RNA-seq)


title: TFi1.E08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

tag: time


title: Thyroid tumor, TC121_S18_R1_001 (RNA-seq)