title: Capan-1_CD44v6 Kd

city: Heidelberg

first: Jan

last: Provaznik

state: Baden-Wuerttemberg

address: Meyerhofstr. 1

department: Genomics Core Facility

institute: EMBL Heidelberg

description:
miRNA
HC_08

hyb_protocol: Hybridization was done as described in miRNA Microarray System protocol v 1.7 from Agilent Technologies

scan_protocol: Scanning was done on Agilent Microarray Scanner G2565BA, Agilent Scan Control Software,

data_processing:
IPA was used for miRNA analysis and for correlating miRNA with protein expression after predicted targets were selected by miRNA databases (http://www.microrna.org, http://www.targetscan.org). For pathway analysis PANTHER (http://pantherdb.org), KEGG (http://www.kegg.jp), Reactome (https://reactome.org), and STRING (http://string-db.org) databases were used
after normalization, data were compared between identical non-transfected versus transfected cells and exosomes, respectively. In most instances, 2-fold differences were considered significant. In exosome preparations, 1.5-fold differences were occassionally included. For processed data, the programm suggestions were followed.

source_name: total cell preparation

label_protocol: Labeling was done as described in miRNA Microarray System protocol v 1.7 from Agilent Technologies

growth_protocol:
The human pancreatic adenocarcinoma lines  lines A818.4 and Capan-1 are maintained in RPMI1640/10%FCS/pyruvate/L-glutamine/antibiotics. Confluent cells are trypsinized and split.
A818.4-Tspan8kd, A818.4-CD151kd, A818.4-CD44v6kd, Capan-1-CD44v6kd  cells were derived from transfection with shRNA (Qiagen, Hilden, Germany) and maintained in RPMI1640/10%FCS/pyruvate/L-glutamine/antibiotics containing 0.5µg/ml G418. Single cell kd clones were derived by 2 rounds of single cell cloning.
The human colorectal cancer lines HT29 and SW948 are maintained in RPMI1640/10%FCS/L-glutamine/antibiotics. Confluent cells are trypsinized and split.
Ht29-cld7 kd lines were derived from transfection with shRNA (Qiagen, Hilden, Germany) and maintained in RPMI1640/10%FCS/pyruvate/L-glutamine/antibiotics containing 0.5µg/ml G418. Single cell kd clones were derived by 2 rounds of single cell cloning.

extract_protocol: Cell and exosome mRNA/microRNA was extracted using the miRNeasyMinikit following the supplier's suggestion (Qiagen, Hildesheim, Germany). Exosomes were pretreated with RNAse to avoid contamination by attached free mRNA.

treatment_protocol: Cells have not undergone any special treatment. All exosome preparation were derived from culture supernatant after cells have been cultured in serum-free medium for 48h-72h. Culture supernatant was collected and cleared (2x10min, 500g, 1x20min, 2000g, 1x30min, 10000g), filter sterizied (0.2µm) and were centrifuged (120min, 100000g). The pellet was washed (PBS, 120min, 100000g), resuspended in 40% sucrose overlaid by a discontinuous sucrose gradient (30%-5%) and centrifuged (16h, 100000g). Exosomes were collected from the 10%-5% sucrose interface (light density fractions, d: 1.15-1.56g/ml).

tag: genotype

value: CD44v6 Kd


title: A818.4_CD44v6 Kd

status: Public on Aug 25 2018

type: RNA

country: Germany

description:
miRNA
HC_07

molecule: total RNA

organism: Homo sapiens

tag: cell line


title: HT-29_Cld7 Kd

description:
miRNA
HC_06

value: Cld7 Kd


title: 4_3D14_17_Active Fx 100mJ +ANS d3

city: Aachen

first: Sebastian

last: Huth

address: Pauwelsstr. 30

institute: Uniklinik RWTH Aachen

hyb_protocol: Hybridization cocktails containing 5.5 Ig of fragmented, end-labelled cDNA were prepared and applied to GeneChip Human Gene 2.0 ST arrays. Hybridization was performed in 45°C hybridization oven at 60 rpm for 16 hours. Using the GeneChip® Fluidics Station 450 the hybridized GeneChip® Human Gene 2.0 ST Arrays were washed and stained (Fluidics Protocol FS450_0001).

scan_protocol: Arrays were scanned using Affymetrix GeneChip® Scanner 3000 7G controlled by GeneChip®Operating Software (GCOS) version 1.4 to produce CEL intensity files.

data_processing:
Data analysis from the exon arrays were processed using GeneSpring GX 14.9 software (Agilent Technologies).
HuGene-2_0-st
Affymetrix.ExonExprChip.HuGene-2_0-st_na35_hg19_2015-04-15

label: biotin

source_name: fibroblasts and keratinocytes

label_protocol: 300µg total RNA from each model were processed using the WT Expression Kit (Ambion)  to generate amplified sense-strand cDNA. Fragmentation and labeling was done using the Affymetrix® GeneChip® WT Terminal Labeling Kit Assay (Affymetrix, Inc., Santa Clara, CA, USA).

growth_protocol: Normal primary human keratinocytes and fibroblasts were isolated from biopsies of adult non-keratinized oral mucosa. Single cell suspension of NHOK was grown in serum free KGM (Lonza). Isolated fibroblasts were grown in DMEM Medium high glucose and L-Glutamin (Invitrogen), containing 10% FCS (Biochrom, Berlin, Germany). To construct the lamina propria equivalent, collagen gels were prepared by mixing 8 volumes of ice-cold bovine collagen I solution (Vitrogen; Cohesion Technologies, Palo Alto, CA, USA) with 1 volume of 10x Hank’s balanced salt solution (Gibco/Invitrogen). After neutralization with 1 M NaOH, 1 volume of NHOF suspended in FCS was added. The final concentration of NHOF in this gel solution was 5 x 105 cells/ml. Three milliliters of this gel solution were poured into each polycarbonate membrane insert (3,0 µm pore size; Thermo Fisher Scientific, Langenselbold, Germany) on 1 ml acellular collagen gel and placed in 6-well plates. Following complete polymerization, gels were covered with DMEM containing 10% FCS, 50µg/ml ascorbic acid, 100 U/ml penicillin and 100 mg/ml streptomycin and incubated in a humidified atmosphere at 37 ° C and 5% CO2. After 2 days, 2 x 106 NHOK were seeded on each lamina propria equivalent. The originated models were cultured in equal volumes of DMEM and keratinocyte growth medium containing 5% FCS, 100 U/ml penicillin, 100 mg/ml streptomycin, 50 µg/ml ascorbic acid and 10ng/ml KGF.  After 2 days of submerged culture, the mucous membrane equivalents were lifted to the air-liquid interface. Cultivation of the models was continued and medium change was done every other day.

extract_protocol: Total RNA was isolated using the Nucleo Spin II RNA Mini Kit, (Macherey-Nagel, Düren, Germany) according to the manufacturer’s instructions, including on-column digestion of DNA with RNase-free DNase I.

treatment_protocol: Irradiation induced lesions were performed on complete stratified and organized 3D mucous membrane models. Models were irradiated with the non‐sequential ultrapulsed fractional carbon dioxid (CO2) laser (Encore®, Lumenis, Dreieich, Germany; CPG handpiece, energy 100 mJ, 100 Hz, density 1, 1 pass). During laser irradiation, culture medium was removed and models were placed on a cooling plate to compensate and reduce thermal effects of laser Radiation intensity was kept under equal conditions by fixing the laser head on a tripod.  After treatment, models were cultivated with fresh culture medium and harvested on day 0, 3 and 5 in OCT compound for cryosectioning. An untreated model was maintained as a negative control at given times.  Lesional 3D skin equivalents were subsequently treated topically with 5% dexpanthenol-containing verum (eye and nose ointment®;Bayer, Leverkusen, Germany), or without 5% dexpanthenol-containing placebo (Bayer) on a daily basis.

tag: tissue

value: oral mucosa


title: HT-29_wt

description:
miRNA
HC_05

value: wt


title: miR-25 A 24h

city: Herston

first: Berit

last: Genz

state: Queensland

address: 300 Herston Road

department: Cell and Molecular Biology

country: Australia

institute: QIMR Berghofer Medical Research Institute

description: Replicate 1

hyb_protocol: standard nanoString nCounter protocol

scan_protocol: standard nanoString nCounter protocol

data_processing: The raw counts were corrected using background probes, and scaling was performed using positive probes as per nSolver standard analysis by the manufacturer. Corrected RNA counts for genes in each array were normalised to the average counts in each sample (i.e. normalized counts = N/average of all counts). The ratio of expression of genes after miRNA transfection was calculated against control transfection for each replicate (n=3 per time point). In order to correct for transfection efficiency, we defined unchanged genes as those with average ratio (across the triplicates) of miR 25/control between 0.98 and 1.02. Genes with miR-25/control ratios < 0.98 were defined as downregulated and the ratios were corrected by multiplication with transfection efficiency. Genes with miR-25/control ratios > 1.02 were defined as upregulated and the ratios were corrected by dividing by transfection efficiency.

label: Reporter probes

source_name: LX-2 cell line

label_protocol: 50 ng of RNA was hybridised to the Reporter and Capture probes at 65°C for 16 h.

growth_protocol: LX-2 cells were cultured in DMEM, 2% FCS, 1% Glutamin, 1% penicillin/streptomycin at 37°C, 5% CO2.

extract_protocol: RNA from miR-25 and control miRNA transfected LX-2 cells was extracted using the RNeasy Kit (Qiagen).

treatment_protocol: Cells were cultured in 6-well plates until 80% confluency and transfected with 10 pmol/ml miR-25 mimics (MISSION microRNA mimics, Sigma Aldrich, St. Louis, MO, USA) using Lipofectamine LTX (Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions. A non-specific miRNA mimic based upon a Caenorhabditis elegans sequence (MISSION microRNA mimics negative control 2; Sigma) served as control. In parallel one well of each plate was transfected with a fluorescein-labelled control miRNA (Bioneer Corporation, Daejeon, South Korea) and transfection efficiency was set as percentage of fluorescein-positive cells from all cells.

tag: sample type

tag: transfection efficiency

tag: rel. mir-25 expression


title: 1_3D13_16_Active Fx 100mJ Placebo-2 d3


title: Control B 24h

description: Replicate 2

value: control


title: 3_3D14_17_Active Fx 100mJ +Placebo d3


title: WBCs (panCK-/CD45+ cells)

type: genomic

city: Taipei

first: Ching-Fei

last: Li

address: No.155, Sec.2, Linong Street

country: Taiwan

institute: YM University

description: WBCs from a HNSCC patient

hyb_protocol: The yield DNA was hybridized to a microarray chip at 67 °C for 16 h.

scan_protocol: The image on a chip was acquired with an Agilent scanner (G2505C, Agilent Technologies, CA, USA).

data_processing:
The data were analyzed with Agilent Genomic Workbench software (Agilent Technologies).
Aberrations were detected by using default setting with an algorithm of ADM-2 conjugated with a filter of a minimum of 5 Mb aberrations.

molecule: genomic DNA

source_name: WBCs

label_protocol: Approximately 1 μg of amplified DNA was fluorescently labeled with Cy5 d-CTP or Cy5-dCTP using SureTag DNA Labeling Kit (Agilent Technologies, CA, USA) and then cleaned up by Microcon YM-30 centrifugal filter unit (Millipore, MA, USA).

extract_protocol: Whole genome amplification (WGA) was performed using REPLI-g Single Cell Kit (Qiagen, Hilden, Germany) and following the manufacturer’s instructions. Briefly, we added the lysis solution to cells at 65°C 10 min then stopped the reaction by adding the neutralizing buffer. Next, Amplification Master Mix containing Repli-G sc DNA polymerase were added to the reaction to amplify the library at 31°C for 85 min. Finally, REPLI-g sc DNA Polymerase was heat inactivated at 65°C for 10 min. Amplified DNA were examined by Qubit fluorometer (Thermo Fisher Scientific, Delaware, USA).

tag: cell

value: White blood cells

tag: gender

value: Male

source_name: Normal control

tag: provider

value: Promega Corporation


title: A818.4_Tspan8 Kd

description:
miRNA
HC_02

value: Tspan8 Kd


title: Capan-1_wt

description:
miRNA
HC_04


title: 3D13_16_Active Fx 100mJ Placebo-1 d3


title: wild type rpoS Rep1

type: SRA

city: Bangalore

first: Savita

last: Chib

state: Karnataka

address: Bellary Road

country: India

institute: National Centre For Biological Sciences

description:
W3110 ΔlacU169 tna -2 wt rpoS
processed data file: rpoS819_vs_wtrpoS.csv
processed data file: rpoS92_vs_wtrpoS.csv

library_source: transcriptomic

data_processing:
Read quality was checked by fastQC.
Reads were aligned to W3110 reference genome NC_007779.1 using bwa with parameter q =20.
Read counts for each gene were obtained from SAM files using a perl script.
For differential gene-expression, read count files (without any normalization) were then fed into DESeq pipeline.
Genome_build: NC_007779.1
Supplementary_files_format_and_content: *csv: Comma-separated text files are generated from DESeq output.

organism: Escherichia coli

source_name: wild type rpoS

growth_protocol: Bacterial strains were grown in Lysogeny broth at 37 degree Celsius and 200 rpm.

extract_protocol:
Bacterial sample was flash frozen and total RNA was extracted using Trizol method followed by DNase treatment. Before library preparation, mRNA was enriched by depleting ribosomal RNA using Ambion's microbe express kit.
Libraries were prepared by standard Illumina protocol for TruSeq RNA library prep kit v2.

treatment_protocol: Samples were collected at 16 hours of growth.

tag: strain/background

tag: genotype/variation

value: W3110 <delta>lacU169 tna -2 wt rpoS

tag: growth media

value: LB Broth

tag: growth phase

value: Stationary (16 hours)


title: A818.4_CD151 Kd

description:
miRNA
HC_03

value: CD151 Kd


title: CTCs (panCK+/CD45- cells)

description: CTCs from a HNSCC patient

source_name: CTCs

value: Circulating tumor cells


title: Control A 24h

description: Replicate 1


title: 2_3D13_16_Active Fx 100mJ +ANS-1 d3


title: Control C 24h

description: Replicate 3


title: Msx2 WT

status: Public on Aug 24 2018

city: Shenyang

first: ziyan

last: yu

state: Liaoning

address: 11 Xinhua Road

country: China

institute: China  Medical University

description: msx

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated.
Index of the reference genome was built using STAR and paired-end  clean reads were aligned to the reference genome using STAR (v2.5.1b). STAR used  the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping  result for junction reads.
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then  FPKM of each gene was calculated based on the length of the gene and reads count  mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript  sequence per Millions base pairs sequenced, considers the effect of sequencing depth  and gene length for the reads count at the same time, and is currently the most  commonly used method for estimating gene expression levels.
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the  DESeq2 R package (1.10.1). DESeq2 provide statistical routines for determining  differential expression in digital gene expression data using a model based on the  negative binomial distribution. The resulting P-values were adjusted using the  Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes  with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially  expressed.
Genome_build: ftp://ftp.ensembl.org/pub/release-83/fasta/mus_musculus/dna/
Supplementary_files_format_and_content: tab-delimited text files include FPKM  values for each Sample

organism: Mus musculus

source_name: Lens

extract_protocol:
Lens were removed, sample name were labeled and sended them to Beijing Novogene Biotech Company for RNA extraction. After the samples were qualified, mRNA sequencing.were performed.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: lens

tag: age

value: post natal day 60

value: Msx2 WT


title: A818.4_wt

description:
miRNA
HC_01


title: 3D13_16_Active Fx 100mJ+ANS-2 d3


title: SAS-shSNAI1_24hr_2.5D

description: Gene expression after 24hr in 2.5D cultured system

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE v2 8x60K Microarray for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: SAS-shSNAI1 cells, 24hr, 2.5D cultured condition

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick-Amp Labeling kit v6.5 (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: SAS cells were kept in DMEM medium supplemented with 10% heat-inactivated fetal bovine serum.

extract_protocol: RNA was prepared using the TRIzol® Reagent (Thermo Fisher Scientific Inc., Waltham, MT) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: SAS cells were cultured on thick collagen (1.7mg/mL) for 24 h following by harvesting total RNA.

tag: cell type

value: Head and neck squamous cell carcimoma

value: SAS

value: Snail-depleted


title: Msx2 CKO

description: lecremsx

value: Msx2 CKO


title: SAS-pLKO_24hr_2.5D

source_name: SAS-pLKO cells, 24hr, 2.5D cultured condition

value: control


title: MuRF1+/+ (strain-matched/sibling to MuRF1-/-)_2 weeks hypoxia_rep1

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

country: USA

institute: NIEHS

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5 and v12.0), using the 1-color defaults for all parameters.

source_name: Right ventricular tissue_Wildtype (MuRF1+/+)_Post-Hypoxia

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: Cardaic tissue was flash frozen at the end of the experimental period and stored at -80C until RNA extraction.

extract_protocol: Total RNA was isolated using Trizol (Life Technologies Corp., Catalog # 4331348, Grand Island, NY) according to the manufacturer’s protocols.

treatment_protocol: As Descrbied in PMID: 24811453: Following a week-long quarantine, mice were moved to a control chamber or normobaric hypoxia chamber, but maintained in standard shoebox cages with food and water available ad libitum throughout. The hypoxia chamber was set at 10.0% oxygen (partial pressure of oxygen roughly 65 mmHg in Albuquerque) and monitored both by the digital feedback control system (Biospherix, Colorado) as well as by a secondary O2/CO2 monitor (O2Cap, OxiGraf, Inc.; Mountain View, CA). The hypoxia exposure lasted 3 weeks with twice-weekly cage changes and standard 12 h light:dark cycle. Procedures were conducted under full isoflurane anesthesia to minimize or eliminate risk of pain and discomfort. All procedures were conducted with full approval by the University of New Mexico Institutional Animal Care and Use Committee and carried out in compliance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals.

tag: strain background

value: mixed B6/129S

value: Wildtype (MuRF1+/+)

value: 8-12 weeks

value: heart; right ventricular tissue


title: MuRF1-/-_2 weeks hypoxia_rep1

value: Male


title: MuRF1-/-_2 weeks hypoxia_rep2


title: MuRF1+/+ (strain-matched/sibling to MuRF1-/-)_2 weeks hypoxia_rep3


title: Identification of miR-101-5p target genes in 786-O

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

country: Japan

institute: Chiba University

hyb_protocol: Agilent two-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution. Images were quantified using Agilent Feature Extraction software version 10.7.3.1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

source_name: mock

label_protocol: Agilent two-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: Normal cell culture medium RPMI 1640 or DMEM.

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions.

treatment_protocol: microRNA or siRNA transfection using Lipofectamine RNAiMAX (Invitrogen).

value: renal cell carcinoma

tag: transfection

value: no transfection

source_name: miR-101-5p transfected cell line


title: Wildtype (strain-matched/sibling to MuRF1 Tg+)_2 weeks hypoxia_rep3

source_name: Right ventricular tissue_Wildtype (MuRF1 Tg+ strain)_Post-Hypoxia

value: mixed B6/DBA

value: Wildtype (MuRF1 Tg+ strain)


title: Identification of si-DHRS2 target genes in TE8

tag: cell line

value: esophagus cancer

source_name: si-DHRS2 transfected cell line


title: alpha-MHC_MuRF1 Tg+_2 weeks hypoxia_rep2

source_name: Right ventricular tissue_a-MHC MuRF1 Tg+_Post-Hypoxia

value: a-MHC MuRF1 Tg+

tag: tissue


title: alpha-MHC_MuRF1 Tg+_2 weeks hypoxia_rep3


title: Identification of si-MYO1B target genes in TE8

source_name: si-MYO1B transfected cell line


title: MuRF1+/+ (strain-matched/sibling to MuRF1-/-)_2 weeks hypoxia_rep6


title: MuRF1+/+ (strain-matched/sibling to MuRF1-/-)_2 weeks hypoxia_rep5


title: Wildtype (strain-matched/sibling to MuRF1 Tg+)_2 weeks hypoxia_rep2


title: Identification of miR-184 target genes in 786-O

source_name: miR-184 transfected cell line


title: Identification of miR-101-3p target genes in 786-O

source_name: miR-101-3p transfected cell line


title: MuRF1-/-_2 weeks hypoxia_rep3


title: Identification of si-EPS8_3 target genes in PANC1

value: pancreatic cancer

source_name: si-EPS8_3 transfected cell line


title: MuRF1-/-_2 weeks hypoxia_rep4


title: MuRF1+/+ (strain-matched/sibling to MuRF1-/-)_2 weeks hypoxia_rep2


title: Wildtype (strain-matched/sibling to MuRF1 Tg+)_2 weeks hypoxia_rep1


title: MuRF1+/+ (strain-matched/sibling to MuRF1-/-)_2 weeks hypoxia_rep4


title: alpha-MHC_MuRF1 Tg+_2 weeks hypoxia_rep1


title: Identification of miR-184 target genes in A498


title: Identification of si-EPS8_2 target genes in PANC1

source_name: si-EPS8_2 transfected cell line


title: single-cell RNA-seq Zeugopod cell Z_125

city: Lausanne

first: Marion

last: LELEU

address: EPFL-SV-ISREC-UPDUB- Station 19

department: School of Life Sciences

country: Switzerland

institute: EPFL

data_processing:
Mapping and RNA-seq analyses were done through HTSstation (David et al, 2014 PLoS ONE and http://htsstation.epfl.ch/).
Reads were uniquely mapped to mm10 (GRCm38) and ERCC sequences with bowtie2 (REF: doi:10.1038/nmeth.1923) with parameters --end-to-end --sensitive
Counts per gene and ERCC were obtained with the program rnacounter (https://pypi.python.org/pypi/rnacounter) which is part of the RNA-seq module of HTSstation.
Cells and genes were filtered using the following specifications: the counts were used to filter out some low-quality cells based on the following criteria: total number of reads mapped > 250, number of genes "expressed" > 2000 ("expressed"=with count > 0), and percent of reads mapped to Spike-Ins sequences < 25%. A total of 199 cells was retained (123 zeugopods and 76 autopods cells). Genes expressed at low levels were also removed from the rest of the analysis and only genes present (raw count > 0) in at least 10% of either the 76 autopods or the 123 zeugopods cells were retained. Hox genes were manually added if they did not satisfy these criteria. A total of 10'948 genes remained. ERCC with null counts through the remaining cells were also excluded from the rest of the analysis.
Raw counts were normalized considering the spike-in counts with the R package scran (methods used computeSpikeFactors and normalize version 1.0.4) (doi:10.18129/B9.bioc.scran).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: raw counts (incl. ERCC) for all 225 cells and normalised counts for the remaining 199 cells.

molecule: polyA RNA

source_name: Zeugopod cells E12.5

growth_protocol: Pools of embryonic forelimbs obtained from eight embryos were dissociated into a single-cell suspension using collagenase from Sigma (collagenase type XI) at 37C for 15min with 10 sec trituration. Cells were then resuspended in FACS solution (10% FCS in PBS with 2mM EDTA)

extract_protocol:
Sequencing of C1-generated libraries
Chemistry: NextSeq v2
SMARTer kit v2, nextera XT

treatment_protocol: Fluorescence activated cell sorting was performed using the MoFlow ASTRIOS EQ cell sorter with a 100-μ m nozzle.

value: mixed;  C57Bl6CBAF1 in which a tau-GFP knock-in was inserted in frame with Hoxd11 coding sequence

value: Hoxd11::GFP heterozygous

tag: developmental stage

value: embryonic day 12.5 (E12.5)

value: dissociated forelimb

tag: run id


title: single-cell RNA-seq Zeugopod cell Z_126


title: single-cell RNA-seq Zeugopod cell Z_124


title: single-cell RNA-seq Zeugopod cell Z_123


title: single-cell RNA-seq Zeugopod cell Z_129


title: single-cell RNA-seq Zeugopod cell Z_128


title: single-cell RNA-seq Zeugopod cell Z_122


title: single-cell RNA-seq Zeugopod cell Z_127


title: WT 3

city: La Jolla

first: Ruth

middle: T

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

description: Gene expression data from mouse BM cells

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scan protocol

data_processing: RNA from murine cells were processed with Affymetrix Mouse 430 2.0 Array Hybridization. Raw expression data (CEL files) were processed using the MAS5.0 signals to obtain the intensities for each probe set.  Prior to identification of differentially expressed genes, raw data were normalized based on the Cross-Correlation method1. Significant changes in gene expression were identified based on the average fold change cutoff of 1.5, and the cutoff of the FDR-corrected p-value cross all replicates at 0.05

source_name: WT, BM cells

label_protocol: Standard Affymetrix labeling protocol

growth_protocol: BM cells from either WT or Cry DKO mice were cultured in Iscove's Modified Dulbecco's Media (Invitrogen, CA) with 20% fetal bovine serum (FBS) plus 10 ng/ml IL-7 (Peprotech).

extract_protocol: Total RNA from cultured cells was extracted using RNeasy Mini Kit (Qiagen).

treatment_protocol: not applicable

value: BM cells

value: wild-type


title: Chd7-het 4

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

institute: German Cancer Research Center DKFZ

description: Gene expression data from mouse tumor sample

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: For normalization of the expression data we used the MAS5.0 algorithm (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 = 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).

source_name: Mouse tumor tissue

label_protocol: Affymetrix protocol

extract_protocol: Total RNA from samples was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using the TRIzol reagent (Invitrogen, Carlsbad, USA), and subsequently passed over a RNeasy Mini Spin Column (Qiagen, Hilden, Germany) for the removal of small fragments. Integrity control and sample quantitation of total extracted RNA was performed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).

value: cerebellar tumor

value: mixed CD1xC57BL/6


title: single-cell RNA-seq Zeugopod cell Z_118


title: WT 2


title: MuRF1-/-_2 weeks hypoxia_rep5

value: mixed B6/129S

value: 8-12 weeks

value: heart; right ventricular tissue


title: CD45.1 from LMP1+CD45.1 rep1

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: CD45.1 from LMP1+CD45.1 rep1

hyb_protocol: Before hybridization, 600 ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 5µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: The array was scanned using Agilent G2505C DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Data were analyzed using the bioinformatics software GeneSpring 13.0 (Agilent)

source_name: spleen

label_protocol: 100 ng of total RNAs were independently reverse-transcribed using oligo-dT primers containing the T7 RNA polymerase promoter sequence to generate cDNAs and AffinityScript, RTase, which were then subjected to in vitro transcription using T7 RNA polymerase to label the cRNAs with Cy3-CTP (Amersham Pharmacia Biotech, Piscataway, NJ) using a Low input Quick-Amp Labeling Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from cells using an miRNeasy Mini kit according to the manufacturer’s instructions (Qiagen). The quality of the RNAs was estimated by using the RNA 6000 Nano LabChip Kit on the Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: CD45.1 positive cells were isolated by cell sorting from the spleen of leukemic mice.

tag: disease state

value: leukemic

value: spleen

value: CD45.1 from LMP1+CD45.1


title: CD45.1 from LMP1+CD45.1 rep2

description: CD45.1 from LMP1+CD45.1 rep2


title: DKO 2

source_name: DKO, BM cells

value: Cry 1/2 double KO


title: DKO 3


title: LMP1 from LMP1+CD45.1 rep1

description: LMP1 from LMP1+CD45.1 rep1

value: LMP1 from LMP1+CD45.1


title: DKO 1


title: CD45.1 from GFP+CD45.1 rep1

description: CD45.1 from GFP+CD45.1 rep1

value: CD45.1 from GFP+CD45.1


title: WT 1


title: Chd7-het 1


title: Chd7-het 2


title: single-cell RNA-seq Zeugopod cell Z_121

value: mixed;  C57Bl6CBAF1 in which a tau-GFP knock-in was inserted in frame with Hoxd11 coding sequence


title: Chd7-het 5


title: single-cell RNA-seq Zeugopod cell Z_119

value: Hoxd11::GFP heterozygous


title: single-cell RNA-seq Zeugopod cell Z_117

value: embryonic day 12.5 (E12.5)


title: single-cell RNA-seq Zeugopod cell Z_120

value: dissociated forelimb


title: CD45.1 from GFP+CD45.1 rep2

description: CD45.1 from GFP+CD45.1 rep2


title: single-cell RNA-seq Zeugopod cell Z_116


title: LMP1 from LMP1+CD45.1 rep2

description: LMP1 from LMP1+CD45.1 rep2


title: single-cell RNA-seq Zeugopod cell Z_115


title: single-cell RNA-seq Zeugopod cell Z_114


title: single-cell RNA-seq Zeugopod cell Z_108


title: single-cell RNA-seq Zeugopod cell Z_105


title: single-cell RNA-seq Zeugopod cell Z_106


title: single-cell RNA-seq Zeugopod cell Z_107


title: single-cell RNA-seq Zeugopod cell Z_110


title: single-cell RNA-seq Zeugopod cell Z_109


title: single-cell RNA-seq Zeugopod cell Z_111


title: single-cell RNA-seq Zeugopod cell Z_104


title: single-cell RNA-seq Zeugopod cell Z_103


title: single-cell RNA-seq Zeugopod cell Z_102


title: single-cell RNA-seq Zeugopod cell Z_100


title: single-cell RNA-seq Zeugopod cell Z_99


title: single-cell RNA-seq Zeugopod cell Z_98


title: single-cell RNA-seq Zeugopod cell Z_97


title: single-cell RNA-seq Zeugopod cell Z_112


title: single-cell RNA-seq Zeugopod cell Z_113


title: single-cell RNA-seq Zeugopod cell Z_96


title: single-cell RNA-seq Zeugopod cell Z_95


title: single-cell RNA-seq Zeugopod cell Z_94


title: single-cell RNA-seq Zeugopod cell Z_92


title: single-cell RNA-seq Zeugopod cell Z_91


title: single-cell RNA-seq Zeugopod cell Z_88


title: single-cell RNA-seq Zeugopod cell Z_89


title: single-cell RNA-seq Zeugopod cell Z_86


title: single-cell RNA-seq Zeugopod cell Z_87


title: single-cell RNA-seq Zeugopod cell Z_85


title: single-cell RNA-seq Zeugopod cell Z_84


title: single-cell RNA-seq Zeugopod cell Z_83


title: single-cell RNA-seq Zeugopod cell Z_82


title: single-cell RNA-seq Zeugopod cell Z_81


title: single-cell RNA-seq Zeugopod cell Z_80


title: single-cell RNA-seq Zeugopod cell Z_78


title: single-cell RNA-seq Zeugopod cell Z_101


title: single-cell RNA-seq Zeugopod cell Z_75


title: single-cell RNA-seq Zeugopod cell Z_76


title: single-cell RNA-seq Zeugopod cell Z_74


title: single-cell RNA-seq Zeugopod cell Z_73


title: single-cell RNA-seq Zeugopod cell Z_71


title: single-cell RNA-seq Zeugopod cell Z_69


title: single-cell RNA-seq Zeugopod cell Z_90


title: single-cell RNA-seq Zeugopod cell Z_72


title: single-cell RNA-seq Zeugopod cell Z_68


title: single-cell RNA-seq Zeugopod cell Z_66


title: single-cell RNA-seq Zeugopod cell Z_65


title: single-cell RNA-seq Zeugopod cell Z_64


title: single-cell RNA-seq Zeugopod cell Z_79


title: single-cell RNA-seq Zeugopod cell Z_63


title: single-cell RNA-seq Zeugopod cell Z_57


title: single-cell RNA-seq Zeugopod cell Z_58


title: single-cell RNA-seq Zeugopod cell Z_61


title: single-cell RNA-seq Zeugopod cell Z_59


title: single-cell RNA-seq Zeugopod cell Z_93


title: single-cell RNA-seq Zeugopod cell Z_67


title: single-cell RNA-seq Zeugopod cell Z_62


title: single-cell RNA-seq Zeugopod cell Z_54


title: single-cell RNA-seq Zeugopod cell Z_52


title: single-cell RNA-seq Zeugopod cell Z_55


title: single-cell RNA-seq Zeugopod cell Z_53


title: single-cell RNA-seq Zeugopod cell Z_51


title: single-cell RNA-seq Zeugopod cell Z_77


title: single-cell RNA-seq Zeugopod cell Z_70


title: single-cell RNA-seq Zeugopod cell Z_50


title: single-cell RNA-seq Zeugopod cell Z_48


title: single-cell RNA-seq Zeugopod cell Z_47


title: single-cell RNA-seq Zeugopod cell Z_46


title: single-cell RNA-seq Zeugopod cell Z_44


title: single-cell RNA-seq Zeugopod cell Z_45


title: single-cell RNA-seq Zeugopod cell Z_60


title: single-cell RNA-seq Zeugopod cell Z_43


title: single-cell RNA-seq Zeugopod cell Z_35


title: single-cell RNA-seq Zeugopod cell Z_33


title: single-cell RNA-seq Zeugopod cell Z_32


title: single-cell RNA-seq Zeugopod cell Z_28


title: single-cell RNA-seq Zeugopod cell Z_42


title: single-cell RNA-seq Zeugopod cell Z_25


title: single-cell RNA-seq Zeugopod cell Z_39


title: single-cell RNA-seq Zeugopod cell Z_41


title: single-cell RNA-seq Zeugopod cell Z_22


title: single-cell RNA-seq Zeugopod cell Z_37


title: single-cell RNA-seq Zeugopod cell Z_34


title: single-cell RNA-seq Zeugopod cell Z_24


title: single-cell RNA-seq Zeugopod cell Z_23


title: single-cell RNA-seq Zeugopod cell Z_21


title: single-cell RNA-seq Zeugopod cell Z_20


title: single-cell RNA-seq Zeugopod cell Z_17


title: single-cell RNA-seq Zeugopod cell Z_36


title: single-cell RNA-seq Zeugopod cell Z_31


title: single-cell RNA-seq Zeugopod cell Z_56


title: single-cell RNA-seq Zeugopod cell Z_38


title: single-cell RNA-seq Zeugopod cell Z_49


title: single-cell RNA-seq Zeugopod cell Z_40


title: single-cell RNA-seq Zeugopod cell Z_18


title: single-cell RNA-seq Zeugopod cell Z_27


title: single-cell RNA-seq Zeugopod cell Z_30


title: single-cell RNA-seq Zeugopod cell Z_26


title: single-cell RNA-seq Zeugopod cell Z_29


title: single-cell RNA-seq Zeugopod cell Z_15


title: single-cell RNA-seq Zeugopod cell Z_16


title: single-cell RNA-seq Zeugopod cell Z_14


title: single-cell RNA-seq Zeugopod cell Z_11


title: single-cell RNA-seq Zeugopod cell Z_13


title: single-cell RNA-seq Zeugopod cell Z_12


title: single-cell RNA-seq Zeugopod cell Z_9


title: single-cell RNA-seq Zeugopod cell Z_10


title: single-cell RNA-seq Zeugopod cell Z_8


title: single-cell RNA-seq Zeugopod cell Z_4


title: single-cell RNA-seq Zeugopod cell Z_6


title: single-cell RNA-seq Zeugopod cell Z_3


title: single-cell RNA-seq Zeugopod cell Z_1


title: single-cell RNA-seq Zeugopod cell Z_7


title: single-cell RNA-seq Autopod cell A_96

source_name: Autopod cells E12.5


title: single-cell RNA-seq Autopod cell A_95


title: single-cell RNA-seq Zeugopod cell Z_19


title: single-cell RNA-seq Zeugopod cell Z_5


title: single-cell RNA-seq Zeugopod cell Z_2


title: single-cell RNA-seq Autopod cell A_91


title: single-cell RNA-seq Autopod cell A_94


title: single-cell RNA-seq Autopod cell A_93


title: single-cell RNA-seq Autopod cell A_89


title: single-cell RNA-seq Autopod cell A_92


title: single-cell RNA-seq Autopod cell A_90


title: single-cell RNA-seq Autopod cell A_87


title: single-cell RNA-seq Autopod cell A_86


title: single-cell RNA-seq Autopod cell A_88


title: single-cell RNA-seq Autopod cell A_85


title: single-cell RNA-seq Autopod cell A_84


title: single-cell RNA-seq Autopod cell A_82


title: single-cell RNA-seq Autopod cell A_83


title: single-cell RNA-seq Autopod cell A_79


title: single-cell RNA-seq Autopod cell A_76


title: single-cell RNA-seq Autopod cell A_78


title: single-cell RNA-seq Autopod cell A_80


title: single-cell RNA-seq Autopod cell A_77


title: single-cell RNA-seq Autopod cell A_81


title: single-cell RNA-seq Autopod cell A_74


title: single-cell RNA-seq Autopod cell A_71


title: single-cell RNA-seq Autopod cell A_68


title: single-cell RNA-seq Autopod cell A_73


title: single-cell RNA-seq Autopod cell A_70


title: single-cell RNA-seq Autopod cell A_67


title: single-cell RNA-seq Autopod cell A_69


title: single-cell RNA-seq Autopod cell A_72


title: single-cell RNA-seq Autopod cell A_65


title: single-cell RNA-seq Autopod cell A_63


title: single-cell RNA-seq Autopod cell A_62


title: single-cell RNA-seq Autopod cell A_66


title: single-cell RNA-seq Autopod cell A_61


title: single-cell RNA-seq Autopod cell A_64


title: single-cell RNA-seq Autopod cell A_60


title: single-cell RNA-seq Autopod cell A_58


title: single-cell RNA-seq Autopod cell A_57


title: single-cell RNA-seq Autopod cell A_55


title: single-cell RNA-seq Autopod cell A_56


title: single-cell RNA-seq Autopod cell A_59


title: single-cell RNA-seq Autopod cell A_52


title: single-cell RNA-seq Autopod cell A_54


title: single-cell RNA-seq Autopod cell A_50


title: single-cell RNA-seq Autopod cell A_53


title: single-cell RNA-seq Autopod cell A_49


title: single-cell RNA-seq Autopod cell A_51


title: single-cell RNA-seq Autopod cell A_48


title: single-cell RNA-seq Autopod cell A_75


title: single-cell RNA-seq Autopod cell A_46


title: single-cell RNA-seq Autopod cell A_43


title: single-cell RNA-seq Autopod cell A_44


title: single-cell RNA-seq Autopod cell A_42


title: single-cell RNA-seq Autopod cell A_47


title: single-cell RNA-seq Autopod cell A_40


title: single-cell RNA-seq Autopod cell A_45


title: single-cell RNA-seq Autopod cell A_39


title: single-cell RNA-seq Autopod cell A_37


title: single-cell RNA-seq Autopod cell A_36


title: single-cell RNA-seq Autopod cell A_35


title: single-cell RNA-seq Autopod cell A_34


title: single-cell RNA-seq Autopod cell A_33


title: single-cell RNA-seq Autopod cell A_32


title: single-cell RNA-seq Autopod cell A_31


title: single-cell RNA-seq Autopod cell A_41


title: single-cell RNA-seq Autopod cell A_30


title: single-cell RNA-seq Autopod cell A_38


title: single-cell RNA-seq Autopod cell A_29


title: single-cell RNA-seq Autopod cell A_28


title: single-cell RNA-seq Autopod cell A_27


title: RA-FLS_sample3_TL1A-stimulated

city: Kobe

first: Koji

last: Fukuda

address: 7-5-1 Kusunoki, Chuo

department: Department of Orthopaedic Surgery

institute: Kobe University Graduate School of Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 500.

source_name: RA-FLS stimulated by TL1A

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA (3' IVT Express Kit User Manual, 2008, Affymetrix).

growth_protocol: RA-FLS were cultured in DMEM supplemented with 10% fetal bovine serum (FBS; BioWhittaker, Walkersville, MD, USA) and 100 units/ml of penicillin/streptomycin at 37°C with 5% CO2.

extract_protocol: Total RNA was extracted using the QIAshredder and RNeasy Mini kit (Qiagen, Hilden, Germany) according to the manufacture’s protocol.

treatment_protocol: RA-FLS were incubated with either 1.0 μg/ml recombinant human TL1A protein (TL1A; R&D Systems, Minneapolis, MN, USA) or phosphate buffered saline (PBS) diluted with serum-free Opti-MEM medium as non-stimulated control for 12 hours at 37°C with 5% CO2.

tag: subject id

value: sample 3

tag: subject status

value: patient with rheumatoid arthritis (RA)

tag: ethnicity

value: Asian

value: Fibroblast like synoviocytes (FLS)

tag: treatment


title: RA-FLS_sample2_TL1A-stimulated

value: sample 2

value: 1.0 μg/ml recombinant human TL1A protein


title: RA-FLS_sample4_control

source_name: RA-FLS control

value: sample 4

value: none (non-stimulated)


title: single-cell RNA-seq Autopod cell A_26

tag: genotype/variation


title: RA-FLS_sample2_control


title: RA-FLS_sample1_TL1A-stimulated

value: sample 1


title: PIRINIXIC-ACID_364mg/kg_5d_NN_OG_Rep3

first: Pierre

middle: Robert

last: Bushel

department: Biostatistics and Computational Biology Branch

data_processing:
library strategy: TempO-Seq (Templated Oligo assay with Sequencing readout)
Sequencing was performed using a 50 cycle single-end read flow cell on a NextSeq 550 Sequencing System (Illumina, San Diego, CA, united States). Processing of sequencing data was conducted using Illumina’s BCL2FASTQ software employing default parameter settings.  Sequencing data were demultiplexed to generate fastq files.
We require that >=75% of the reads have an average quality score >=QC30.  The sequences were then filtered for Illumina p5 and p7 adaptors.
Bowtie2-2.1.0
Aligned to a pseudogenome (indexed probe fasta file reflecting the 50 nt sequences targeted by the detector oligos). Indels not allowed.  Up to 2 base pair mismatches  allowed. Multimapping sequences not allowed.
The counts were summarized using QuasR version 1.8.4.
Genome_build: pseudogenome (indexed probe fasta file reflecting the 50 nt sequences targeted by the detector oligos)
Supplementary_files_format_and_content: tab-delimited text file with read count per gene

organism: Rattus norvegicus

extract_protocol:
Livers were harvested 24 hours after the last dose as 100 mg punches using six millimeter disposable biopsy punches. An appropriately staggered schedule was employed so that the harvest times were accurate to ±30 min of the designed dose-to-harvest interval.  Automated RNA isolation was performed according to the manufacture’s protocol using the RNeasy Kit from Qiagen (Germantown, MD).
The sequencing library for the rat liver RNA samples was prepared by BioSpyder (BioSpyder Technologies, Inc., Carlsbad, CA, United States) according to their protocol  guidelines. One μl of each RNA sample (500-660 ng/uL) was hybridized with the S1500+ beta detector oligo pool mix (2 μl per sample) using the following thermocycler settings: 10 min at 70°C, followed by gradual decrease to 45°C over 49 min, and ending with 45°C for 1 min. Hybridization was followed by nuclease digestion (24 μl nuclease mix addition followed by 90 min at 37°C), ligation (24 μl ligation mix addition followed by 60 min at 37°C, then heat denaturation at 80°C for 30 min).. Ten microliters of each ligation product were then transferred to a 96-well PCR amplification microplate that also contained 10 μl of PCR mix per well. Through amplification well-specific, “barcoded” primer pairs were introduced to templates. Five microliters of the PCR amplification products from each well were then pooled into a single sequencing library. The TempO-Seq library was then processed with a PCR clean-up kit (Machery-Nagel, Mountain View, CA, United States) prior to sequencing.

treatment_protocol: Male Sprague-Dawley rats (aged 6–8 weeks and weighing 200–260 g) were dosed once daily in triplicate for 3, 5, or 7 days, depending on the test chemical.

value: Sprague-Dawley

tag: animal id

tag: Sex

value: Male

value: 6-8 weeks

value: Liver

tag: compound

value: PIRINIXIC ACID

tag: compound abbreviation

value: PIR

tag: moa

value: PPARA

tag: exposure

value: Treated

tag: dose (mg/kg)

tag: duration (days)

tag: vehicle

value: CMC %

tag: nutritive status

value: Non nutritive

tag: route

value: ORAL GAVAGE

tag: sample id


title: RA-FLS_sample3_control

tag: subject id

value: sample 3

value: patient with rheumatoid arthritis (RA)

value: Asian

tag: cell type

value: Fibroblast like synoviocytes (FLS)


title: RA-FLS_sample1_control

tag: subject status

tag: ethnicity

value: none (non-stimulated)


title: Panc-1-P in vivo#2

city: Tokyo

first: Taku

last: Sato

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

department: Department of Molecular Cytogenetics, Medical Research Institute

institute: Tokyo Medical and Dental University

description: Transplantation tumor in primary site

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K (G4851A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-107) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Panc-1-P in vivo#2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Panc-1-P and -CTC were maintained in appropriate media, D-MEM medium supplemented with 10%fetal bovine serum.

extract_protocol: RNA fractions were prepared using TRIsure (BIOLINE,London, UK) following the manufacturer's recommendations. The protocol includes clean up step after TURBO DNA-free™ Kit (Ambion, Austin, TX) digestion. RNAs were quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Panc-1-P and -CTC were injected to subcutaneous in mice.

tag: disease

value: pancreatic ductal adenocarcinoma

tag: cell line


title: Panc-1-CTC in vivo#1

description: Transplantation tumor in primary site

source_name: Panc-1-CTC in vivo#1


title: Panc-1-CTC in vitro#1

description: Dish culture

source_name: Panc-1-CTC in vitro#1


title: Panc-1-CTC in vitro#2

description: Dish culture

source_name: Panc-1-CTC in vitro#2


title: single-cell RNA-seq Autopod cell A_24

tag: strain background

value: mixed;  C57Bl6CBAF1 in which a tau-GFP knock-in was inserted in frame with Hoxd11 coding sequence

tag: genotype/variation

value: Hoxd11::GFP heterozygous

tag: developmental stage

value: embryonic day 12.5 (E12.5)

tag: tissue

value: dissociated forelimb

tag: run id


title: NCOA2_13_2

city: Iowa City

first: Miles

middle: A

last: Pufall

state: IA

address: 51 Newton Rd., BSB Rm 4-430

department: Biochemistry

institute: University of Iowa

description: untreat

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.32.0). It was vst transformed and quantile normalized.

source_name: B-ALL cell line

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

extract_protocol: Qiagen miRNAeasy

treatment_protocol: 1µM dexamethasone for 4 hours or vehicle (0.1% ethanol)

value: B-ALL cell line


title: single-cell RNA-seq Autopod cell A_25


title: RA-FLS_sample4_TL1A-stimulated

value: sample 4

tag: treatment

value: 1.0 μg/ml recombinant human TL1A protein


title: Panc-1-P in vitro #2

description: Dish culture

source_name: Panc-1-P in vitro #2


title: Panc-1-P in vitro #1

description: Dish culture

source_name: Panc-1-P in vitro #1


title: Panc-1-P in vivo#1

description: Transplantation tumor in primary site

source_name: Panc-1-P in vivo#1


title: Panc-1-CTC in vivo#2

description: Transplantation tumor in primary site

source_name: Panc-1-CTC in vivo#2


title: NCOA2_13_dex_2

description: 1uM dexamethasone


title: NCOA2_13_1

description: untreat


title: NCOA2_13_dex_1

description: 1uM dexamethasone


title: NCOA2_13_dex_3

description: 1uM dexamethasone


title: G9A_11_dex_3

description: 1uM dexamethasone


title: G9A_11_dex_2

description: 1uM dexamethasone


title: single-cell RNA-seq Autopod cell A_23


title: NCOA2_13_3

description: untreat


title: PIRINIXIC-ACID_364mg/kg_5d_NN_OG_Rep2

tag: strain

value: Sprague-Dawley

tag: animal id

tag: Sex

value: Male

tag: age

value: 6-8 weeks

value: Liver

tag: compound

value: PIRINIXIC ACID

tag: compound abbreviation

value: PIR

tag: moa

value: PPARA

tag: exposure

value: Treated

tag: dose (mg/kg)

tag: duration (days)


title: NAFENOPIN_338mg/kg_5d_NU_OG_Rep3

value: NAFENOPIN

value: NAF

tag: vehicle

value: CORN OIL %

tag: nutritive status

value: Nutritive

tag: route

value: ORAL GAVAGE

tag: sample id


title: single-cell RNA-seq Autopod cell A_22

tag: strain background

value: mixed;  C57Bl6CBAF1 in which a tau-GFP knock-in was inserted in frame with Hoxd11 coding sequence

tag: genotype/variation

value: Hoxd11::GFP heterozygous

tag: developmental stage

value: embryonic day 12.5 (E12.5)

tag: tissue

value: dissociated forelimb


title: G9A_11_3

description: untreat

tag: cell line

tag: cell type

value: B-ALL cell line


title: G9A_11_2

description: untreat


title: NAFENOPIN_338mg/kg_5d_NU_OG_Rep2

tag: strain

value: Sprague-Dawley

tag: animal id

tag: Sex

value: Male

tag: age


title: single-cell RNA-seq Autopod cell A_21

tag: run id


title: single-cell RNA-seq Autopod cell A_20


title: G9A_11_dex_1

description: 1uM dexamethasone


title: BEZAFIBRATE_617mg/kg_7d_NU_OG_Rep2

value: 6-8 weeks

value: Liver

tag: compound

value: BEZAFIBRATE

tag: compound abbreviation

value: BEZ

tag: moa

tag: exposure

tag: dose (mg/kg)


title: NAFENOPIN_338mg/kg_5d_NU_OG_Rep1

value: PPARA

value: Treated

tag: duration (days)

tag: vehicle

tag: nutritive status

tag: route

tag: sample id


title: BEZAFIBRATE_617mg/kg_7d_NU_OG_Rep1

tag: tissue


title: single-cell RNA-seq Autopod cell A_18

tag: strain background

tag: genotype/variation

tag: developmental stage


title: single-cell RNA-seq Autopod cell A_17


title: BEZAFIBRATE_617mg/kg_7d_NU_OG_Rep3

tag: strain

tag: animal id

tag: Sex


title: single-cell RNA-seq Autopod cell A_19

tag: run id


title: N-NITROSODIMETHYLAMINE_10mg/kg_5d_NN_IP_Rep2

tag: age

tag: compound

value: N-NITROSODIMETHYLAMINE

tag: compound abbreviation

value: NIT

value: SALINE %

value: Non nutritive

value: INTRAPERITONEAL


title: single-cell RNA-seq Autopod cell A_15

value: mixed;  C57Bl6CBAF1 in which a tau-GFP knock-in was inserted in frame with Hoxd11 coding sequence

value: Hoxd11::GFP heterozygous


title: N-NITROSODIMETHYLAMINE_10mg/kg_5d_NN_IP_Rep1

tag: moa

tag: exposure

tag: dose (mg/kg)


title: GLP_11_dex_2

description: 1uM dexamethasone

tag: cell line

tag: cell type


title: single-cell RNA-seq Autopod cell A_14

value: embryonic day 12.5 (E12.5)

value: dissociated forelimb


title: GLP_11_1

description: untreat

value: B-ALL cell line


title: H2452-antibody

city: Okayama

first: Shinichi

last: Toyooka

address: 2-5-1, shikatacho kitaku

department: School of medicine

institute: Okayama University

description: Gene expression profile in H2452 after treatment

hyb_protocol: 600ng of each labeled cRNA was fragmented by adding 5 μl 10 x blocking agent and 1 μl of 25 x fragmentation buffer, and then heated at 60°C for 30 min. Finally 25 μl 2 x GE hybridization buffer was added to dilute the labeled cRNA. 40μl of hybridization solution was dispensed into the gasket slide and assembled to the Agilent SurePrint G3 Human GE 8X60K, V2 Microarrays (Agilent®). The slides were incubated for 17 h at 65°C in an Agilent hybridization oven. then washed at room temperature by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010).

scan_protocol: The hybridized array was immediately scanned with an Agilent Microarray Scanner D (Agilent Technologies, Inc.)

data_processing: Microarray results were extracted using Agilent Feature Extraction software v11.0 (Agilent Technologies).   Quantile normalization was performed without baseline shift.

source_name: H2452 with antibody

label_protocol: RNA labeling and hybridization were performed by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010). Briefly, 100ng of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000(NanoDrop, Wilmington, USA).

growth_protocol: MPM cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum.

extract_protocol: total RNAs were extracted from cell lines using an RNeasy Mini Kit (Qiagen).

treatment_protocol: MPM cells were cultured with or without anti-S100A11 antibody (1 ug/ml) for 24 hours

value: malignant pleural mesothelioma (MPM)


title: Empty_dex_2

description: 1uM dexamethasone

value: scrambled


title: Empty_dex_3

description: 1uM dexamethasone


title: H2452-parent

description: Gene expression profile in H2452

source_name: H2452 without treatment


title: GLP_11_3

description: untreat


title: GLP_11_dex_1

description: 1uM dexamethasone


title: H2052-antibody

description: Gene expression profile in H2052 after antibody treatment

source_name: H2052 with antibody


title: H2052-parent

description: Gene expression profile in H2052

source_name: H2052 without treatment


title: GLP_11_2

description: untreat


title: single-cell RNA-seq Autopod cell A_13


title: Empty_dex_1

description: 1uM dexamethasone


title: Empty_3

description: untreat


title: single-cell RNA-seq Autopod cell A_16


title: Nalm6_dex_3

description: 1uM dexamethasone

value: wildtype


title: Empty_1

description: untreat


title: GLP_11_dex_3

description: 1uM dexamethasone


title: Nalm6_dex_2

description: 1uM dexamethasone


title: IFOSFAMIDE_143mg/kg_3d_NN_OG_Rep2

value: Sprague-Dawley

value: Male

value: 6-8 weeks

value: Liver

value: IFOSFAMIDE

value: IFO

tag: duration (days)

tag: vehicle

tag: nutritive status

tag: route

value: ORAL GAVAGE

tag: sample id


title: IFOSFAMIDE_143mg/kg_3d_NN_OG_Rep3

tag: strain

tag: tissue

value: Treated

value: SALINE %

value: Non nutritive


title: Empty_2

description: untreat

tag: genotype/variation


title: single-cell RNA-seq Autopod cell A_12

tag: strain background

value: mixed;  C57Bl6CBAF1 in which a tau-GFP knock-in was inserted in frame with Hoxd11 coding sequence

value: Hoxd11::GFP heterozygous

tag: developmental stage

tag: run id


title: N-NITROSODIMETHYLAMINE_10mg/kg_5d_NN_IP_Rep3

tag: animal id

tag: Sex

tag: age

tag: compound

value: N-NITROSODIMETHYLAMINE

tag: compound abbreviation

value: NIT

value: INTRAPERITONEAL


title: single-cell RNA-seq Autopod cell A_11

value: embryonic day 12.5 (E12.5)

value: dissociated forelimb


title: IFOSFAMIDE_143mg/kg_3d_NN_OG_Rep1

value: Sprague-Dawley

tag: moa

tag: exposure

tag: dose (mg/kg)


title: AFLATOXIN-B1_.3mg/kg_5d_NN_OG_Rep3

value: Male

value: AFLATOXIN B1

value: AFL

tag: duration (days)

tag: vehicle

value: CMC %

tag: nutritive status


title: single-cell RNA-seq Autopod cell A_10


title: single-cell RNA-seq Autopod cell A_9


title: AFLATOXIN-B1_.3mg/kg_5d_NN_OG_Rep2

tag: strain

value: 6-8 weeks

value: Liver

tag: route

tag: sample id


title: single-cell RNA-seq Autopod cell A_8

tag: strain background

tag: genotype/variation

tag: tissue


title: THIOACETAMIDE_200mg/kg_5d_NN_IP_Rep3

tag: animal id

value: THIOACETAMIDE

value: THI

value: Cytotox

value: Treated


title: THIOACETAMIDE_200mg/kg_5d_NN_IP_Rep2

tag: Sex

value: SALINE %

value: Non nutritive


title: AFLATOXIN-B1_.3mg/kg_5d_NN_OG_Rep1

tag: age

value: ORAL GAVAGE


title: single-cell RNA-seq Autopod cell A_7

value: mixed;  C57Bl6CBAF1 in which a tau-GFP knock-in was inserted in frame with Hoxd11 coding sequence

value: Hoxd11::GFP heterozygous

tag: developmental stage

tag: run id


title: THIOACETAMIDE_200mg/kg_5d_NN_IP_Rep1

tag: compound

tag: compound abbreviation

tag: moa

value: INTRAPERITONEAL


title: U87MG cells, miR-490 Rep 1

city: New Delhi

first: Dr. Ritu

last: Kulshreshtha

state: New Delhi

address: Room 134, Block I

department: Dept of Biochemical Engineering and Biotechnology

institute: Indian Institute of Technology

description: OM1 Avg (log2)

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45C on  GeneChip Human PrimeView Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000 7G.

data_processing: The data were analyzed with  Affymetrix Expression Analysis Console and Gene springGX 12.0 using Affymetrix default analysis settings for analysis type - Expression (Gene) and RMA as normalization method.

source_name: U87MG cells with miR-490 overexpression

label_protocol: Samples were labelled as per and using the 3'IVT PLUS reagent kit. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: U87MG cells grown in 6 well plates

extract_protocol: Total RNA prepared using RNA isolation kit according to manufacturer's instructions.

treatment_protocol: Transfected with either miR-490 overexpression vector PC-490 or its control vector PCDNA.

tag: cell line

tag: cell type

value: glioma cell line

value: miR-490 overexpression


title: Nalm6_dex_1

description: 1uM dexamethasone

value: B-ALL cell line

value: wildtype


title: U87MG cells, control Rep 2

description: OC2 Avg (log2)

source_name: U87MG cells with control vector

value: control vector


title: H4.V Input_1

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

description:
MNase ChIP
ws1ss1_ratio_L1800155_H4_V_Ty_MNase_Input_1_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800154_H4_V_Ty_MNase_ChIP_1_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig
ws2001ss501_ratio_L1800155_H4_V_Ty_MNase_Input_1_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800154_H4_V_Ty_MNase_ChIP_1_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig
ws501ss101_ratio_L1800155_H4_V_Ty_MNase_Input_1_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800154_H4_V_Ty_MNase_ChIP_1_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig

library_source: genomic

data_processing:
Demultiplexing: bcl2fastq v.20.0.422
Read trimming: cutadapt v.1.15 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
Read alignment: BWA-mem v.0.7.16 -t 20
Read filtering: samtools v.1.8 view -hSb, sort, view -bh -@4 -q10
COVERNANT v0.3.2
Genome_build: Tb427v9
Supplementary_files_format_and_content: wiggle files

organism: Trypanosoma brucei brucei

source_name: whole liquid cell culture

growth_protocol: All replicates were grown in HMI-11 (37 °C, 5% CO2) and drug selection was applied where necessary.

extract_protocol:
200 million cells were harvested by centrifugation and fixed in the presence of 1% formaldehyde. Cells were washed and permeabilized with digitonin and chromatin was digested using MNase. Mononucleosomes were collected from the supernatant and residual mononucleosomes were extracted from the cell pellet by sonication. An input sample was seperated from the chromatin and stored at -20 °C. The IP was performed by addition of Ig-coated magnetic beads (BB2 Antibody against the Ty1-tag) and incubation over night at 4°C. The DNA was subsequently washed and eluted from the beads. Crosslinks were reversed in both the ChIP and input sample. The samples were purified and the concentration was determined using Qubit.
ChIP and input samples were end-repaired using T4 DNA polymerase (NEB),
Klenow large Fragment (NEB) and T4 DNA Polynucleotide Kinase (NEB). Protruding A-bases were added to the 3` end using  Klenow fragment (3´ to 5´ exo minus) and dATP. TruSeq adapters were ligated to the cDNA fragments using Quick Ligase (NEB) and was purified using AMPure XP magnetic beads. Y-shaped adapters were converted to dsDNA with Illumina primers for 5 cycles, purified with magnetic beads  and library fragments of 200-500 bp were size selected from an agarose gel. The gel-purified library was further amplified for 10-17 cycles using Illumina primers and purified using magnetic beads. Libaries were quantified using Qubit and qPCR and were sequenced on an Illumina flow cell  in an Illumina NextSeq aparatus following the manufacturer's instructions

treatment_protocol: H4.V ectopic expression induced by addition of doxycycline.

value: Lister 427 MITat 1.2

tag: genotype

value: TetR, T7RNAP, H4.V-/-, Ty1-H4.V (EC)

tag: life cycle stage

value: Bloodstream form

tag: chip antibody


title: H4.V ChIP_2

description:
MNase ChIP
ws1ss1_ratio_L1800157_H4_V_Ty_MNase_Input_2_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800156_H4_V_Ty_MNase_ChIP_2_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig
ws2001ss501_ratio_L1800157_H4_V_Ty_MNase_Input_2_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800156_H4_V_Ty_MNase_ChIP_2_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig
ws501ss101_ratio_L1800157_H4_V_Ty_MNase_Input_2_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800156_H4_V_Ty_MNase_ChIP_2_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig

tag: strain


title: U87MG cells, miR-490 Rep 2

description: OM2 Avg (log2)


title: U87MG cells, control Rep 1

description: OC1 Avg (log2)


title: H4.V Input_2


title: MSC-3

city: Kyoto

first: Makoto

last: Ikeya

address: 53 kawahara-cho, shogoin

department: Center for iPS Cell Research and Application(CiRA)

institute: Kyoto University

description: Gene expression data of induced presomitic mesoderm derived from iPSC

hyb_protocol: Hybridisations were carried out with GeneChip® Hybridisation, Wash, and Stain Kit, with subsequent washing and staining of arrays on GeneChip® Fluid Station 450.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 TG system

data_processing: Expression values were calculated using the RMA16 algorithm, and the data obtained were analyzed by GeneSpring GX 14.5 (Agilent Technologies, Santa Clara, CA, USA).

source_name: induced somite-derived MSC

label_protocol: 500ng of total RNA from samples were reversed transcribed according to the Ambion® WT Expression Kit Protocol. Synthesized cDNA was then Labeled with GeneChip® Terminal Labeling Kit.

extract_protocol: Total RNA was extracted from each cells by using the RNeasy Mini Kit (Qiagen).

tag: time point

value: 20 days

value: induced somite-derived MSC


title: MSC-2


title: H4.V ChIP_1


title: MSC-1


title: Nalm6_3

description: untreat

tag: genotype/variation


title: Nalm6_1

description: untreat


title: single-cell RNA-seq Autopod cell A_5

source_name: Autopod cells E12.5

tag: strain background

value: embryonic day 12.5 (E12.5)

tag: tissue

value: dissociated forelimb


title: SYN-3

description: Gene expression data of induced syndetome derived from iPSC

source_name: hiPSC derived SYN

value: induced syndetome

tag: day of induction from ips

value: 32 days


title: SYN-2


title: CHLOROFORM_600mg/kg_5d_NU_OG_Rep3

value: Sprague-Dawley

tag: animal id

tag: Sex

value: Male

tag: age

value: 6-8 weeks

value: Liver

value: CHLOROFORM

value: CHL

value: Cytotox

tag: exposure

value: Treated

tag: dose (mg/kg)

tag: duration (days)

tag: vehicle

value: CORN OIL %

tag: nutritive status

value: Nutritive

tag: route

value: ORAL GAVAGE

tag: sample id


title: H3.V ChIP_2

description:
MNase ChIP
ws1ss1_ratio_L1800153_H3_V_Ty_MNase_Input_2_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800152_H3_V_Ty_MNase_ChIP_2_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig
ws2001ss501_ratio_L1800153_H3_V_Ty_MNase_Input_2_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800152_H3_V_Ty_MNase_ChIP_2_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig
ws501ss101_ratio_L1800153_H3_V_Ty_MNase_Input_2_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800152_H3_V_Ty_MNase_ChIP_2_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig

data_processing:
Demultiplexing: bcl2fastq v.20.0.422
cutadapt v.1.15 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
BWA-mem v.0.7.16 -t 20
samtools v.1.8 view -hSb, sort, view -bh -@4 -q10
COVERNANT v0.3.2
Genome_build: Tb427v9
Supplementary_files_format_and_content: wiggle files, ChIP data coverage

value: Lister 427 MITat 1.2

tag: genotype

tag: life cycle stage

value: Bloodstream form

tag: chip antibody


title: single-cell RNA-seq Autopod cell A_3

value: mixed;  C57Bl6CBAF1 in which a tau-GFP knock-in was inserted in frame with Hoxd11 coding sequence

tag: genotype/variation

value: Hoxd11::GFP heterozygous

tag: developmental stage

value: embryonic day 12.5 (E12.5)

tag: run id


title: single-cell RNA-seq Autopod cell A_4

tag: strain background

tag: tissue

value: dissociated forelimb


title: CHLOROFORM_600mg/kg_5d_NU_OG_Rep2

tag: strain

value: Sprague-Dawley

tag: animal id

tag: Sex

tag: compound

tag: compound abbreviation

tag: moa


title: H3.V Input_2


title: single-cell RNA-seq Autopod cell A_6


title: Nalm6_2

description: untreat

tag: cell line

tag: cell type

value: B-ALL cell line

value: wildtype


title: SYN-1

value: induced syndetome

tag: day of induction from ips

value: 32 days


title: H3.V Input_1

description:
MNase ChIP
ws1ss1_ratio_L1800151_H3_V_Ty_MNase_Input_1_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800150_H3_V_Ty_MNase_ChIP_1_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig
ws2001ss501_ratio_L1800151_H3_V_Ty_MNase_Input_1_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800150_H3_V_Ty_MNase_ChIP_1_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig
ws501ss101_ratio_L1800151_H3_V_Ty_MNase_Input_1_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800150_H3_V_Ty_MNase_ChIP_1_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig

tag: genotype


title: H3.V ChIP_1

tag: life cycle stage


title: single-cell RNA-seq Autopod cell A_2


title: single-cell RNA-seq Autopod cell A_1


title: SCL-3

description: Gene expression data of induced sclerotome derived from iPSC

source_name: hiPSC derived SCL

value: induced sclerotome

value: 11 days


title: CARBON-TETRACHLORIDE_1175mg/kg_7d_NU_OG_Rep3

value: Male

tag: age

value: 6-8 weeks

value: Liver

value: CARBON TETRACHLORIDE

value: CAR

value: Cytotox

tag: exposure

value: Treated

tag: dose (mg/kg)

tag: duration (days)

tag: vehicle

tag: nutritive status

tag: route

tag: sample id


title: CARBON-TETRACHLORIDE_1175mg/kg_7d_NU_OG_Rep1

tag: strain

tag: animal id

tag: Sex

tag: tissue

value: CORN OIL %

value: Nutritive

value: ORAL GAVAGE


title: CARBON-TETRACHLORIDE_1175mg/kg_7d_NU_OG_Rep2

value: Sprague-Dawley

tag: compound

tag: compound abbreviation

tag: moa


title: Vehicle_3d_NU_OG_Rep5

value: VEHICLE CONTROL

value: Control


title: Vehicle_3d_NU_OG_Rep4


title: PIRINIXIC-ACID_364mg/kg_5d_NN_OG_Rep1

value: PIRINIXIC ACID

value: PIR

value: PPARA

value: CMC %

value: Non nutritive


title: CHLOROFORM_600mg/kg_5d_NU_OG_Rep1

value: Male

value: 6-8 weeks

value: CHLOROFORM

value: CHL


title: ATACseq H3V-/- H4V-/-, 20 million cells

description:
ATACseq H3V-/- H4V-/-, 20 million cells
ws501ss101_ratio_L1800232_Nr05_Wt_20_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800235_Nr08_dKO_20_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig

data_processing:
Demultiplexing: bcl2fastq v.20.0.422
Read trimming: cutadapt v.1.15
Read alignment: BWA-mem v.0.7.16
Read filtering: samtools v.1.8
Coverage plots: COVERNANT v0.3.0
Genome_build: Tb427v9
Supplementary_files_format_and_content: wiggle files

extract_protocol:
Cells were harvested and washed in 30 ml cold 1x TDB, the pellet was resuspended in 300 µl permeabilization buffer with protease inhibitors, 3 µl of 4 mM digitonin was added and incubated for 5 minutes at RT. The cells were pelleted, resuspended in isotonic buffer with protease.
Adapters were integrated during the transposition reaction: 50 µl of transposition mix were added to the pellet (25 µl TD (2x reaction buffer from Nextera kit), 25 µl TDE1 (Tn5 transposase from Nextera kit), 22.5 µl nuclease-free water) and incubation was performed for 30 minutes at 37 °C. For the gDNA control, 200 ng of gDNA was treated in the same manner. The DNA samples were purified using Qiagen MinElute PCR Purification Kit and eluted in 10 µl EB (10 mM Tris-HCl, pH 8). The transposed DNA fragments were amplified using the NEBNext® High-Fidelity 2X PCR Master Mix (M0541) supplied with 2.5 µl of 25 µM barcoded primers and amplification for 13 cycles. The libraries were purified using AMPure XP beads (Beckman Coulter) following the manufacturer’s instructions. The library fragment sizes between 150 and 1000 bp were purified from a 6% polyacrylamide gel. Paired-end 76 bp sequencing was carried out using the Illumina NextSeq system with a mid-output NextSeq 500/550 kit according to the manufacturer’s instructions.

value: Lister 427 MITat 1.2

tag: genotype

value: Bloodstream form


title: ATACseq gDNA H3V-/- H4V-/-

description:
ATACseq on genomic H3V-/- H4V-/- DNA
ws501ss101_ratio_L1800236_Nr09_Wt_gDNA_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800237_Nr10_dKO_gDNA_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig

tag: life cycle stage


title: ATACseq gDNA wild type

description:
ATACseq on genomic wild type DNA
ws501ss101_ratio_L1800236_Nr09_Wt_gDNA_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800237_Nr10_dKO_gDNA_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig

value: wild type


title: ATACseq H3V-/-, 20 million cells

description:
ATACseq H3V-/-, 20 million cells
ws501ss101_ratio_L1800232_Nr05_Wt_20_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800233_Nr06_H3VKO_20_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig

value: TetR, T7RNAP, H3.V-/-


title: ATACseq H4V-/-, 20 million cells

description:
ATACseq H4V-/-, 20 million cells
ws501ss101_ratio_L1800232_Nr05_Wt_20_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800234_Nr07_H4VKO_20_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig

value: TetR, T7RNAP, H4.V-/-


title: ATACseq wild-type, 10 million cells

description:
ATACseq wild-type, 10 million cells
ws501ss101_ratio_L1800228_Nr01_Wt_10_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800229_Nr02_H3VKO_10_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig
ws501ss101_ratio_L1800228_Nr01_Wt_10_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800230_Nr03_H4VKO_10_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig
ws501ss101_ratio_L1800228_Nr01_Wt_10_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800231_Nr04_dKO_10_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig


title: ATACseq H4V-/-, 10 million cells

description:
ATACseq H4V-/-, 10 million cells
ws501ss101_ratio_L1800228_Nr01_Wt_10_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800230_Nr03_H4VKO_10_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig


title: ATACseq wild-type, 20 million cells

description:
ATACseq wild-type, 20 million cells
ws501ss101_ratio_L1800232_Nr05_Wt_20_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800233_Nr06_H3VKO_20_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig
ws501ss101_ratio_L1800232_Nr05_Wt_20_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800234_Nr07_H4VKO_20_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig
ws501ss101_ratio_L1800232_Nr05_Wt_20_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800235_Nr08_dKO_20_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig


title: SCL-1

tag: cell type

value: induced sclerotome

tag: day of induction from ips

value: 11 days


title: SCL-2


title: D-2

description: Gene expression data of induced dermatome derived from iPSC

source_name: hiPSC derived D

value: induced dermatome

value: 20 days


title: Vehicle_5d_NN_OG_Rep5

value: Sprague-Dawley

tag: age

value: Liver

value: VEHICLE CONTROL

value: Control

tag: exposure

tag: dose (mg/kg)

value: SALINE %

value: ORAL GAVAGE


title: D-1


title: MYO-3

description: Gene expression data of induced myotome derived from iPSC

source_name: hiPSC derived MYO

value: induced myotome

value: 41 days


title: MYO-2


title: ATACseq H3V-/- H4V-/-, 10 million cells

description:
ATACseq H3V-/- H4V-/-, 10 million cells
ws501ss101_ratio_L1800228_Nr01_Wt_10_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800231_Nr04_dKO_10_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig

value: Lister 427 MITat 1.2


title: MYO-1


title: D-3


title: G9A_11_1

description: untreat

source_name: B-ALL cell line

tag: cell line

value: B-ALL cell line

tag: genotype/variation


title: DM-1

description: Gene expression data of induced dermomyotome derived from iPSC

source_name: hiPSC derived DM

value: induced dermomyotome


title: ATACseq H3V-/-, 10 million cells

description:
ATACseq H3V-/-, 10 million cells
ws501ss101_ratio_L1800228_Nr01_Wt_10_to_HGAP3_Tb427v9_bwa.sorted.mapq10_vs_L1800229_Nr02_H3VKO_10_to_HGAP3_Tb427v9_bwa.sorted.mapq10.wig

value: TetR, T7RNAP, H3.V-/-

value: Bloodstream form


title: Vehicle_5d_NN_OG_Rep4

value: Male

value: 6-8 weeks

tag: duration (days)

tag: vehicle

tag: nutritive status

value: Non nutritive

tag: route

tag: sample id


title: DM-2

value: 11 days


title: Vehicle_5d_NN_IP_Rep6

tag: strain

value: Sprague-Dawley

tag: animal id

tag: Sex

tag: tissue

tag: compound


title: ΔH3.V/ΔH4.V R3 [Hi-C II]

description:
Hi-C library
H3V_H4V_dKO_2_Lib3
processed data file:
H3V_H4V_dKO_2_100000_homer_unjoined_merged.txt
H3V_H4V_dKO_2_10000_homer_unjoined_merged.txt
H3V_H4V_dKO_2_20000_homer_unjoined_merged.txt
H3V_H4V_dKO_2_50000_homer_unjoined_merged.txt

data_processing:
Sequencing: NextSeq 500
Demultiplexing: bcl2fastq v.20.0.422
Read trimming: cutadapt v.1.15
:-m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
Read pair filtering: HICUP v0.5.9 devel; truncation
Read alignment: BWA-mem v0.7.16; mapping, q>0
Normalization: HiC-Pro; v2.10.0; iterative correction
HiC analysis: Homer; custom python scripts (HiC sunt dracones v0.1.0)
Genome_build: Tb427v9, Tb427v9_without_allelic_variants and Tb427v9_Aforks_joined_without_allelic_variants (will be made available upon publication of the associated publication)
Supplementary_files_format_and_content: Hi-C interaction matrix; unjoined or  joined genome, separated or merged replicates, iced, matrix in homer format

growth_protocol: All replicates were grown in HMI-11 (37 °C, 5% CO2) to a maximum of 1x10^6 cells/ml. Drug selection after transfection was applied if necessary.

extract_protocol:
2x10^8 cells were harvested and fixed with 1% formaldehyde for 20 minutes at room temperature. The reaction was stopped by addition of glycine and incubation for 15 minutes on ice. Cells were snap frozen in liquid nitrogen. Nuclei were permeabilized with digitonin (200 µM final concentration, 5 minutes) and SDS and the chromatin was digested with MboI. Restriction fragments were biotinylated whilst being end-repaired and then re-ligated. Crosslinks were reversed and the DNA was fragmented by sonication and size selected with AMPure magnetic beads. DNA fragments were end-repaired using T4 polynucleotide kinase (NEB), T4 DNA polymerase (NEB) and DNA polymerase I, large Klenow fragment (NEB), thereby removing biotin from unligated ends. Biotinylated chimeric DNA fragments were enriched by addition of streptavidin coated magnetic beads and separation with a magnet.
DNA was reclaimed with a magnet, washed and subsequently polyadenylated at the 3` end using Klenow fragment (3´ to 5´ exo minus) and dATP. DNA fragments bound to the beads were reclaimed with a magnet, washed and annealed TruSeq adapters were ligated to the DNA fragments using Quick Ligase (NEB) and was purified by reclaiming with a magnet. The library was split in 8x 50 µl reactions, amplified using Illumina primers and 5 PCR cycles and the reactions were recombined. The library was purified using Agencourt XP beads (Beckman Coulter). Libraries were quantified using Qubit and qPCR and were sequenced on an Illumina flow cell in an Illumina NextSeq apparatus (500/550) following the manufacturer's instructions.

tag: life cycle stage


title: ΔH3.V/ΔH4.V R2 [Hi-C II]

description:
Hi-C library
H3V_H4V_dKO_2_Lib2
processed data file:
H3V_H4V_dKO_2_100000_homer_unjoined_merged.txt
H3V_H4V_dKO_2_10000_homer_unjoined_merged.txt
H3V_H4V_dKO_2_20000_homer_unjoined_merged.txt
H3V_H4V_dKO_2_50000_homer_unjoined_merged.txt


title: ΔH4.V R3 [Hi-C II]

description:
Hi-C library
H4V_Lib3
processed data file:
H4V_100000_homer_unjoined_merged.txt
H4V_10000_homer_unjoined_merged.txt
H4V_20000_homer_unjoined_merged.txt
H4V_50000_homer_unjoined_merged.txt

value: TetR, T7RNAP, H4.V-/-


title: DM-3

tag: cell type

tag: day of induction from ips


title: ΔH3.V/ΔH4.V R1 [Hi-C II]

description:
Hi-C library
H3V_H4V_dKO_2_Lib1
processed data file:
H3V_H4V_dKO_2_100000_homer_unjoined_merged.txt
H3V_H4V_dKO_2_10000_homer_unjoined_merged.txt
H3V_H4V_dKO_2_20000_homer_unjoined_merged.txt
H3V_H4V_dKO_2_50000_homer_unjoined_merged.txt


title: ΔH4.V R2 [Hi-C II]

description:
Hi-C library
H4V_Lib2
processed data file:
H4V_100000_homer_unjoined_merged.txt
H4V_10000_homer_unjoined_merged.txt
H4V_20000_homer_unjoined_merged.txt
H4V_50000_homer_unjoined_merged.txt


title: SM-3

description: Gene expression data of induced somitic mesoderm derived from iPSC

source_name: hiPSC derived SM

value: induced somitic mesoderm

value: 8 days


title: Vehicle_5d_NN_OG_Rep6

tag: age

value: Liver

value: VEHICLE CONTROL

tag: compound abbreviation

tag: moa

value: Control

tag: exposure

value: SALINE %


title: ΔH4.V R1 [Hi-C II]

description:
Hi-C library
H4V_Lib1
processed data file:
H4V_100000_homer_unjoined_merged.txt
H4V_10000_homer_unjoined_merged.txt
H4V_20000_homer_unjoined_merged.txt
H4V_50000_homer_unjoined_merged.txt

value: Lister 427 MITat 1.2

tag: genotype/variation


title: PSM-3

description: Gene expression data of induced presomitic mesoderm derived from iPSC

source_name: hiPSC derived PSM

value: induced presomitic mesoderm

value: 4 days


title: Vehicle_5d_NN_OG_Rep2

tag: dose (mg/kg)

tag: duration (days)

tag: vehicle

value: ORAL GAVAGE


title: Vehicle_3d_NU_OG_Rep2

value: CORN OIL %

tag: nutritive status

value: Nutritive

tag: route

tag: sample id


title: ΔH3.V R2 [Hi-C II]

description:
Hi-C library
H3V_Lib2
processed data file:
H3V_100000_homer_unjoined_merged.txt
H3V_10000_homer_unjoined_merged.txt
H3V_20000_homer_unjoined_merged.txt
H3V_50000_homer_unjoined_merged.txt

tag: strain

value: TetR, T7RNAP, H3.V-/-

value: Bloodstream form


title: ΔH3.V R3 [Hi-C II]

description:
Hi-C library
H3V_Lib3
processed data file:
H3V_100000_homer_unjoined_merged.txt
H3V_10000_homer_unjoined_merged.txt
H3V_20000_homer_unjoined_merged.txt
H3V_50000_homer_unjoined_merged.txt


title: ΔH3.V R1 [Hi-C II]

description:
Hi-C library
H3V_Lib1
processed data file:
H3V_100000_homer_unjoined_merged.txt
H3V_10000_homer_unjoined_merged.txt
H3V_20000_homer_unjoined_merged.txt
H3V_50000_homer_unjoined_merged.txt


title: PSM-2


title: PSM-1


title: Vehicle_5d_NN_OG_Rep1

tag: animal id

tag: Sex

value: Male

value: 6-8 weeks

tag: tissue

value: Non nutritive


title: SM-2

tag: cell type

value: induced somitic mesoderm


title: iPS-3

description: Gene expression data of iPSC

source_name: hiPSC

value: iPSC

tag: day of induction from ips

value: 0 days


title: SM-1

value: 8 days


title: Single-marker R3 [Hi-C II]

description:
Hi-C library
SM_Lib3
processed data file:
SM_100000_homer_unjoined_merged.txt
SM_10000_homer_unjoined_merged.txt
SM_20000_homer_unjoined_merged.txt
SM_50000_homer_unjoined_merged.txt

value: TetR, T7RNAP

tag: life cycle stage


title: PHENOBARBITAL_54mg/kg_5d_NN_OG_Rep3

value: Sprague-Dawley

tag: age

value: Liver

tag: compound

value: PHENOBARBITAL

tag: compound abbreviation

value: PHE

value: CAR/PXR

value: Treated

value: WATER %


title: iPS-2

description: Gene expression data of iPSC


title: Single-marker R2 [Hi-C II]

description:
Hi-C library
SM_Lib2
processed data file:
SM_100000_homer_unjoined_merged.txt
SM_10000_homer_unjoined_merged.txt
SM_20000_homer_unjoined_merged.txt
SM_50000_homer_unjoined_merged.txt

value: Lister 427 MITat 1.2

tag: genotype/variation


title: Single-marker R1 [Hi-C II]

description:
Hi-C library
SM_Lib1
processed data file:
SM_100000_homer_unjoined_merged.txt
SM_10000_homer_unjoined_merged.txt
SM_20000_homer_unjoined_merged.txt
SM_50000_homer_unjoined_merged.txt

value: Bloodstream form


title: Vehicle_5d_NN_OG_Rep3

value: Male

value: VEHICLE CONTROL

tag: moa

value: Control

tag: exposure

tag: dose (mg/kg)

value: SALINE %

value: ORAL GAVAGE


title: PHENOBARBITAL_54mg/kg_5d_NN_OG_Rep1

value: 6-8 weeks

tag: duration (days)

tag: vehicle

tag: nutritive status

value: Non nutritive


title: PHENOBARBITAL_54mg/kg_5d_NN_OG_Rep2

tag: strain

tag: route

tag: sample id


title: ΔH3.V/ΔH4.V R2 [Hi-C I]

description:
Hi-C library
H3V_H4V_dKO_Lib2
processed data file:
H3V_H4V_dKO_10000_homer_joined_merged.txt
H3V_H4V_dKO_10000_homer_unjoined_merged.txt
H3V_H4V_dKO_100000_homer_joined_merged.txt
H3V_H4V_dKO_100000_homer_unjoined_merged.txt
H3V_H4V_dKO_20000_homer_joined_merged.txt
H3V_H4V_dKO_20000_homer_unjoined_merged.txt
H3V_H4V_dKO_50000_homer_joined_merged.txt
H3V_H4V_dKO_50000_homer_unjoined_merged.txt

data_processing:
Sequencing: NextSeq 500
Demultiplexing: bcl2fastq v.20.0.422
Read trimming: cutadapt v.1.15
-m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
Read pair filtering: HICUP v0.5.9 devel; truncation
Read alignment: BWA-mem v0.7.16; mapping, q>0
Normalization: HiC-Pro; v2.10.0; iterative correction
HiC analysis: Homer; custom python scripts (HiC sunt dracones v0.1.0)
Genome_build: Tb427v9 and Tb427v9_joined_Aforks_without_allelic_variants (will be made available upon publication of the associated publication)
Supplementary_files_format_and_content: Hi-C interaction matrix; unjoined or  joined genome, separated or merged replicates, iced, matrix in homer format

extract_protocol:
2x10^8 cells were harvested and fixed with 1% formaldehyde for 20 minutes at room temperature. The reaction was stopped by addition of glycing and incubation for 5 minutes on ice. Cells were snap frozen in liquid nitrogen. Nuclei were permeabilized using with digitonin and SDS and the chromatin was digested with MboI. Restriction fragments were biotinylated whilst being end-repaired and then re-ligated. Crosslinks were reversed and the DNA was fragmented.Biotinylated chimeric DNA fragments were enriched by addition of strepavidin coated magnetic beads and separation with a magnet.
Biotinylated DNA was end-repaired using T4 polynucleotide kinase (NEB), T4 DNA polymerase (NEB) and DNA plymerase I, large Klenow fragment (NEB). DNA was reclaimed with a magnet, washed and subsequently polyadenylated at the 3` end using  Klenow fragment (3´ to 5´ exo minus) and dATP. DNA fragments bound to the beads were reclaimed with a magnet, washed and annealed TruSeq adapters were ligated to the DNA fragments using Quick Ligase (NEB) and was purified by reclaiming with a magnet. The DNA was eluted from the beads by heating at 98°C for 10 minutes. The library was amplified using Illumina primers and 10 or 15 PCR cycles. The libray was purified using Agencourt AMPure XP beads (Beckman Coulter). Libaries were quantified using Qubit and qPCR and were sequenced on an Illumina flow cell in an Illumina NextSeq aparatus following the manufacturer's instructions.

tag: genotype


title: iPS-1

description: Gene expression data of iPSC

tag: cell type

value: iPSC

value: 0 days


title: ΔH3.V/ΔH4.V R1 [Hi-C I]

description:
Hi-C library
H3V_H4V_dKO_Lib1
processed data file:
H3V_H4V_dKO_10000_homer_joined_merged.txt
H3V_H4V_dKO_10000_homer_unjoined_merged.txt
H3V_H4V_dKO_100000_homer_joined_merged.txt
H3V_H4V_dKO_100000_homer_unjoined_merged.txt
H3V_H4V_dKO_20000_homer_joined_merged.txt
H3V_H4V_dKO_20000_homer_unjoined_merged.txt
H3V_H4V_dKO_50000_homer_joined_merged.txt
H3V_H4V_dKO_50000_homer_unjoined_merged.txt


title: METHIMAZOLE_100mg/kg_3d_NN_OG_Rep3

value: Sprague-Dawley

tag: animal id

tag: Sex

tag: tissue

value: Liver

value: METHIMAZOLE

value: MET


title: 003_BAP-fused_macroH2A1_input_DNA_total_digested_chromatin

city: Astana

first: Pavel

last: Tarlykov

address: 13/5, Kurgalzhynskoye Road

country: Kazakhstan

institute: National Center for Biotechnology

description: ATCC number CCL-2.2

data_processing:
Base calls were generated with v5.0.5 of the Torrent Suite software.
The resulting reads were aligned to the Homo sapiens (human) genome assembly hg19 reference genome
Downstream analysis and visualization was performed using Seqmonk analysis tool (https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/). For visualization in genome browser images, the data were calculated as IP/input ratios of the reads per million values calculated on a log2 scale across 10kb windows across the entire human genome (version hg19).
Genome_build: hg19
Supplementary_files_format_and_content: txt

source_name: cervix

growth_protocol: Hela S3 cells obtained from American Type Culture Collection were grown in Dulbecco's modified Eagle's medium with high glucose (PAA) and 10% dialyzed fetal bovine serum (FCS, Thermofisher).

extract_protocol:
Extraction of total (nonbiotinylated) and biotinylated chromatin from Hela S3 stably coexpressing BirA-emerin and BAP-macroH2A1 fusion proteins. HeLa S3 and HeLa BirA-emerin and BAP-macroH2A1 expressing cells were pulse labeled with 5 ug/ml biotin for 1 hour with the addition of 50 mM final HEPES added to stabilize pH. After the removal of the biotin, cells were washed with PBS following the washing in HB buffer (10 mM TrisHCl, pH 7.3, 10 mM KCl, 1.5 mM MgCl2 , 0.2 mM PMSF, 10 mM beta mercaptoethanol). Next, cells were incubated in HB buffer on ice for 20 min and nuclei were released by breaking the cells with size B pestle in dounce homogenizer and spun at 800g for 15 min. Nuclei were resuspended in an equal amount of the TGME buffer (50% Glycerol, 0.5 M Tris pH 7.9, 1M MgCl2, 500 mM EDTA, pH 8.0 and 5 mM DTT). For micrococcal digestion, the nuclei were resuspended in 500 uL of TM2 buffer (10 mM Tris-HCl, 2 mM MgCl2, 0.1% Triton, 1 mM PMSF), 2.5 uL of 0.5 M CaCl2 and 25 uL of micrococcal nuclease (MNase) (0.2 U/uL; Sigma; N3755) were added before incubation at 37°C for 10 min. The reaction was stopped by adding 15 uL of 0.1 M EGTA. Nuclei were collected by spinning at 400g for 10 min at 4°C. After MNase digestion, the nuclei pellet was resuspended in 500 uL of prechilled 0.4 M salt extraction buffer (385 mM NaCl, 10 mM Tris-HCl [pH 7.4], 2 mM MgCl2, 2 mM EGTA, 0.1% Triton X-100, 1 mM PMSF). The tubes were rotated at 4°C for 30 min. Supernatant containing digested chromatin was separated from the remaining material by spinning at 400g for 10 min at 4°C. An equal volume of TM2 buffer was added to the extracted chromatin to arrive at a 0.2 M final salt concentration. The sample was centrifuged at maximum speed for 5 min at 4°C. For the preclearing, three hundred μL of a suspension of Protein A agarose beads (Pierce 20334, Thermo Fisher) were washed three times with 0.2 M salt extraction. The bead suspension was combined with chromatin and rotated for 30 min at 4°C. The sample was centrifuged at maximum speed and supernatant transferred to a new tube. 300 μL of a suspension of sepharose-streptavidin beads (GE Healthcare; 17-5113-01) were washed three times with 0.2 M salt extraction buffer. The bead suspension was combined with the supernatant containing chromatin and rotated for 3 h at 4°C. Afterward, the beads were washed twice in 500 μL of 0.4 M salt extraction buffer containing Triton for 5 min at 4°C. DNA fraction was eluted twice by adding 100 µL of 1.5 M Ammonium bicarbonate and SpeedVac’ed. Afterwards, DNA was resuspended in 200 µL TE and an equal volume of phenol was added to sample and centrifuged for 5 min at maximum speed. Upper phase with DNA was transferred to a new tube.
For library construction, DNA fragments (100 ng) were converted to blunt ends by end repair using Ion Xpress Plus Fragment Library Kit (Thermo Fisher Scientific) and ligated to Ion Xpress Barcode Adapters.

treatment_protocol: To generate HeLa S3 stable cell line expressing BirA-Emerin and BAP-macroH2A1 the retroviral transduction was performed.

tag: cell line

value: HeLa S3

value: cervix

tag: type

value: epithelial

tag: disease

value: adenocarcinoma

tag: age

value: 31 years


title: wild-type R2 [Hi-C I]

description:
Hi-C library
WT_Lib2
processed data file:
WT_10000_homer_joined_merged.txt
WT_10000_homer_unjoined_merged.txt
WT_100000_homer_joined_merged.txt
WT_100000_homer_unjoined_merged.txt
WT_20000_homer_joined_merged.txt
WT_20000_homer_unjoined_merged.txt
WT_50000_homer_joined_merged.txt
WT_50000_homer_unjoined_merged.txt

value: Lister 427 MITat 1.2

value: wild-type

tag: life cycle stage

value: Bloodstream form


title: wild-type R1 [Hi-C I]

description:
Hi-C library
WT_Lib1
processed data file:
WT_10000_homer_joined_merged.txt
WT_10000_homer_unjoined_merged.txt
WT_100000_homer_joined_merged.txt
WT_100000_homer_unjoined_merged.txt
WT_20000_homer_joined_merged.txt
WT_20000_homer_unjoined_merged.txt
WT_50000_homer_joined_merged.txt
WT_50000_homer_unjoined_merged.txt


title: METHIMAZOLE_100mg/kg_3d_NN_OG_Rep2

value: Male

tag: compound

tag: compound abbreviation

tag: moa

value: CAR/PXR

tag: exposure

value: Treated

tag: dose (mg/kg)

value: WATER %

value: ORAL GAVAGE


title: Vehicle_3d_NU_OG_Rep3

tag: strain

value: Sprague-Dawley

value: 6-8 weeks

value: VEHICLE CONTROL

value: Control

tag: duration (days)

tag: vehicle

value: CORN OIL %

tag: nutritive status

value: Nutritive

tag: route


title: 001_BAP-fused_macroH2A1_rep_1

description: ATCC number CCL-2.2

value: HeLa S3

value: cervix

value: epithelial


title: METHIMAZOLE_100mg/kg_3d_NN_OG_Rep1

tag: animal id

tag: Sex

value: Liver

value: METHIMAZOLE

value: MET

value: Non nutritive

tag: sample id


title: ECONAZOLE_334mg/kg_5d_NU_OG_Rep3

value: Male

tag: tissue

value: ECONAZOLE

value: ECO

value: CAR/PXR


title: LEFLUNOMIDE_60mg/kg_5d_NU_OG_Rep2

value: Sprague-Dawley

value: LEFLUNOMIDE

value: LEF

value: Ahr

value: Treated

value: ORAL GAVAGE


title: 002_BAP-fused_macroH2A1_rep_2

description: ATCC number CCL-2.2

tag: cell line

value: HeLa S3

tag: type

tag: disease

value: adenocarcinoma

value: 31 years


title: ECONAZOLE_334mg/kg_5d_NU_OG_Rep1

tag: age

value: 6-8 weeks

value: Liver

tag: compound

value: CORN OIL %

value: Nutritive


title: LEFLUNOMIDE_60mg/kg_5d_NU_OG_Rep1

value: Male

tag: compound abbreviation

tag: moa


title: BETA-NAPHTHOFLAVONE_1500mg/kg_5d_NN_OG_Rep1

value: BETA-NAPHTHOFLAVONE

value: NAP

tag: exposure

tag: dose (mg/kg)

value: CMC %

value: Non nutritive


title: Δset1:N+.2

city: Freising

first: Ulrich

last: Guldener

state: Bavaria

address: Maximus-von-Imhof-Forum 3

department: Chair of genome-oriented bioinformatics

institute: Technische Universität München

hyb_protocol: 1.5 ug of Cy3-labeled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60 °C for 30 minutes in a reaction volume of 250 mL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. Upon completion of the fragmentation reaction, 250 mL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Preprocessing steps including background correction, normalization and summarization of probe intensities were performed by employing the oligo R package (Carvalho 2010).

organism: Fusarium fujikuroi

source_name: Strain set1, 60mM Gln, replicate 2

growth_protocol: Strains were grown for 3 days in Darken medium and subsequently, an aliquot of 500 µL was transferred to liquid ICI medium with either 6 mM or 60 mM glutamine and grown for additional 3 days on a rotary shaker (180 rpm) at 28 °C.

extract_protocol: Total RNA was extracted using the TRI Reagent (Sigma-Aldrich, Steinheim, Germany) and DNA was removed using DNAse I (Roche Diagnostics, Mannheim, Germany). RNA quality and concentration was measured with an Bioanalyzer (Agilent Technologies Deutschland, Böblingen, Germany).

treatment_protocol: The mycelium was harvested, shock frozen with liquid nitrogen and lyophilized.

tag: treatment

value: 60mM Gln


title: Δkdm5:N+.2

source_name: Strain kdm5, 60mM Gln, replicate 2


title: Δkdm5:N+.1

source_name: Strain kdm5, 60mM Gln, replicate 1


title: BETA-NAPHTHOFLAVONE_1500mg/kg_5d_NN_OG_Rep3

tag: strain

value: Sprague-Dawley

tag: duration (days)

tag: vehicle


title: ECONAZOLE_334mg/kg_5d_NU_OG_Rep2

tag: animal id

value: ECONAZOLE

value: ECO

value: CAR/PXR

tag: nutritive status

tag: route


title: 3-METHYLCHOLANTHRENE_300mg/kg_5d_NN_OG_Rep3

tag: Sex

tag: tissue

value: Ahr

value: Treated

value: ORAL GAVAGE

tag: sample id


title: wt1:N+.2

source_name: Strain wt1, 60mM Gln, replicate 2


title: Δset1:N+.1

source_name: Strain set1, 60mM Gln, replicate 1


title: LEFLUNOMIDE_60mg/kg_5d_NU_OG_Rep3

value: 6-8 weeks

value: LEFLUNOMIDE

value: LEF


title: Δkdm5:N-.2

source_name: Strain kdm5, 6mM Gln, replicate 2

value: 6mM Gln


title: wt1:N+.1

source_name: Strain wt1, 60mM Gln, replicate 1


title: SAMPLE 11: NPB CD141high

city: Lund

first: Kristina

last: Lundberg

address: Medicon Village building 406, Scheelevägen 8

department: Immunotechnology

country: Sweden

institute: Lund University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 99° for 2 minutes, then 45° for 5 minutes. Centrifuge at max speed for 1 minute and then transfer 200μl on to the array. Hybridize 18 hours at 45° at 60rpm. Fluidics washing using the program FS450_0001.

scan_protocol: Signals were scanned by Affymetrix GeneChip Scanner 3000 7G

data_processing: Microarray signals were normalized using the RMA algorithm in the Affymetrix® Expression Console software (Affymetrix®).

source_name: Peripheral blood

label_protocol: Labeled with the Encore Biotin Module Kit (NuGEN) according to manufacturer’s protocols

extract_protocol: Total RNA isolated from FACS-sorted cells was amplified using the Ovation Pico WTA System V2 (NuGen, San Carlos, CA)

tag: cell type


title: Δset1:N-.1

source_name: Strain set1, 6mM Gln, replicate 1


title: SAMPLE 10: NPB CD1c


title: SAMPLE 9: NPB SlanDC

value: SlanDC


title: SAMPLE 12: NPB SlanDC


title: SAMPLE 7: NPB CD1c


title: BETA-NAPHTHOFLAVONE_1500mg/kg_5d_NN_OG_Rep2

value: Male

tag: age

value: Liver

value: BETA-NAPHTHOFLAVONE


title: Δkdm5:N-.1

source_name: Strain kdm5, 6mM Gln, replicate 1


title: Δset1:N-.2

source_name: Strain set1, 6mM Gln, replicate 2


title: SAMPLE 6: NPB SlanDC


title: SAMPLE 5: NPB CD141high


title: SAMPLE 8: NPB CD141high


title: SAMPLE 3: NPB SlanDC


title: SAMPLE 4: NPB CD1c


title: 3-METHYLCHOLANTHRENE_300mg/kg_5d_NN_OG_Rep2

tag: compound

value: CMC %

value: Non nutritive