title: BT-549 (16)

description: Corresponding sample number: 16

value: breast cancer cell line BT-549

value: treatment with doxycyline 72 hours


title: 1p7

status: Public on Dec 19 2018

type: SRA

city: Washington

first: Scott

middle: Nathan

last: Dean

state: DC

address: 4555 Overlook Ave SW

country: USA

institute: Naval Research Laboratory

description:
rpkm_0_AYR0M.txt
rpkm_1_AYR0M.txt
rpkm_2_AYR0M.txt
rpkm_3_AYR0M.txt

library_source: transcriptomic

data_processing:
Generated MiSeq reads were then analyzed via the RNAseq pipeline described by Li et al. (Li et al., 2018).
Read quality control was performed where Phred scores of <20 were trimmed using FastQC and Cutadapt as part of Trim Galore! (Krueger, 2015)
EDGE-pro (Estimated Degree of Gene Expression in PROkaryotes) (Magoc et al., 2013) for paired end reads was used with default settings on the remaining reads for alignment to the L. plantarum WCFS1 genome from NCBI (ftp://ftp.ncbi. nih.gov/genomes/Bacteria) generating RPKM files and count tables.
Each count table was read into R where DESeq2 (Love et al., 2014) was used for differential expression analysis and generating associated statistics as a function of treatment with 3OC12 and time.
Supplementary_files_format_and_content: Count tables
Supplementary_files_format_and_content: counts for all genes in files that begin with rpkm_0

molecule: total RNA

organism: Lactiplantibacillus plantarum

source_name: culture

extract_protocol:
Frozen sample aliquots thawed at room temperature and pelleted to remove residual RNA Later before treating with 400 µL Lysozyme Solution (1 mg mL-1 lysozyme, 40 mM EDTA, pH 8) for 1 h at 37 °C. Lysozyme treated cells were pelleted and resuspended in RNAzol RT following the manufacturer’s protocol for large RNA isolation.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: time

value: 1 h


title: BT-549 (27)

city: Groningen

first: Francien

last: Talens

address: Hanzeplein 1

department: Medical Oncology

country: Netherlands

institute: University Medical Center Groningen

description: Corresponding sample number: 27

data_processing:
The obtained cDNA fragment libraries were sequenced on an Illumina HiSeq2500 using default parameters (single read 1x50bp or Paired End 2 x 100 bp) in pools of multiple samples
The trimmed fastQ files where aligned to build b37 human reference genome using hisat/0.1.5-beta-goolf-1.7.20 (Dobin et al., Bioinformatics, 2013) allowing for 2 mismatches
Before gene quantification SAMtools/1.2-goolf-1.7.20 (Li et al., Bioinforma, 2009) was used to sort the aligned reads
The gene level quantification was performed by HTSeq/0.6.1p1 using --mode=union --stranded=no and, Ensembl version 75 was used as gene annotation database.
QC metrics are calculated for the aligned reads using Picard-tools picard/1.130-Java-1.7.0_80 CollectRnaSeqMetrics, MarkDuplicates, CollectInsertSize-Metrics and SAMtools/1.2-goolf-1.7.20 flagstat
Picard-tools picard/1.130-Java-1.7.0_80
Genome_build: b37 human reference genome
Supplementary_files_format_and_content: gene-level abundance measuremets

organism: Homo sapiens

source_name: epithelial cells

growth_protocol: BT-549 and HCC38 were cultured in Roswell Park Memorial Institute (RPMI) medium supplemented with 10% fetal calf serum (FCS) and penicillin/streptomycin (100 units/mL).

extract_protocol:
RNA was isolated using the mirVANA kit (Ambion, AM1561)
Sequence libraries were generated using the TruSeq RNA sample preparation kits (Illumina) using the Sciclone NGS Liquid Handler (Perkin Elmer)

treatment_protocol: Cells were treated with 72 hours with doxycycline (1 μg/mL) or left untreated.

tag: cell line

tag: tissue

value: Breast

tag: disease state

value: ductal carcinoma

tag: transduction with doxycycline-inducible shrna

tag: treatment

value: no treatment


title: 9d 1 DAC Rep1

city: Shanghai

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

country: China

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences

description: RNA-Seq of detached first-pair rosette leaves 1 day after culture (DAC)  from 9-day-old seedlings replicate 1

data_processing:
Raw RNA-seq reads were trimmed by quality using Trimmomatic and paired reads mapped to the Arabidopsis thaliana genome (TAIR10) using STAR 2.5.3.a with default settings.
The returned alignments were stringently filtered so as to remove duplicates, ambiguously mapped reads and read pairs with conflicting alignments.
RSEM v1.3.0 is used to quantitate gene abundance and the expression of individual gene is shown as the average of transcripts per million (TPM) in two biological replicates, all genes are filtered by the average of TPM in three developmental statuses < 0.5.
Differentially expressed genes were detected by EBSeq based on the combined criteria: |log2(fold change)| > 1 and false discovery rates < 0.05.
Genome_build: the Arabidopsis thaliana genome (TAIR10)
Supplementary_files_format_and_content: expression for genes(TAIR10) was provided. The format is tab delimited file format. Each row contains eight columns: gene_id, transcript_id, length, effective_length, expected_count,TPM and FPKM.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: leaves of 9-day-old seedlings

growth_protocol: 9-, 12- and 15-d-old A. thaliana Columbia-0 seeds were sterilized with 75% alcohol and kept at 4°C for 2d. The seeds were then germinated on 1/2 MS medium (half-strength of MS basal medium with 1% sucrose, 1% agar and 0.5 g/L MES, pH 5.7) at 22°C under 24-h constant light conditions. Detached leaf explants were cultured on B5 medium without sucrose (Gamborg B5 basal medium with 0.5 g/L MES and 0.8% agar, pH 5.7) at 22°C under 24-h light conditions.

extract_protocol:
RNA extraction using Trizol protocols.
Library construction and deep sequencing were performed by Genergy Biotechnology Co. Ltd. (Shanghai, China) using Illumina HiSeq 3000 following the manufacturer’s instructions (Illumina)

tag: developmental stage

tag: growth conditions

value: constant light

tag: ecotype

value: Columbia (Col-0)

value: cultured 1 day on B5 medium without sucrose.


title: Fibroblast NINF sample 3 from patient 2

type: genomic

city: Amsterdam

first: Peter

last: Henneman

state: Noord Holland

address: Meibergdreef 9

department: Clinical Genetics

institute: Academic Medical Center Amsterdam

hyb_protocol: bisulphite converted DNA was hybridised to Illumina Infinium Human Methylation EPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Minfi (v1.20.0) for reading the data; MethylAid (v1.8.0) for quality control
Unmethylated and methylated signal intensities in Series supplementary file

label: Cy5 and Cy3

molecule: genomic DNA

source_name: patient 2

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted from the fibroblasts using the QIAamp DNA mini kit (Qiagen, Valencia, CA), and bisulfite converted using the EZ DNA Methylation Kit (Zymo Research) according to manufacturer’s protocol. The bisulfite-converted DNA was subsequently analyzed on the Illumina HumanMethylation EPIC BeadChip Array at ServiceXS in Leiden, the Netherlands.

tag: gender

value: M

value: Crohn's Disease

tag: disease stage

value: non-inflamed

tag: montreal score

tag: age

tag: passage

tag: sampleID

tag: thiopurine usage

value: No

tag: atnf usage

value: Yes

tag: cell type

value: Ileal fibroblast


title: BT-549 (15)

description: Corresponding sample number: 15

tag: cell line


title: 9d time 0 Rep2

description: RNA-Seq of detached first-pair rosette leaves before culture (time 0) from 9-day-old seedlings replicate 2

value: No treatment applied.


title: 2m1b

description:
rpkm_0_ADTV7.txt
rpkm_1_ADTV7.txt
rpkm_2_ADTV7.txt
rpkm_3_ADTV7.txt

tag: strain

tag: time

value: 4 h


title: sO12

city: Beijing

first: Bing

last: Zhang

state: Beijing

address: Rm 437, School of Environment, Tsinghua University

department: School of Environment

institute: Tsinghua University

description:
GeoChip data for activated sludge sample collected at System OD, Day 12
raw data file: Activated sludge raw data1.txt

hyb_protocol: All labeled DNA was resuspended in 10 μl hybridization solution as previously described (Wu et al. 2006) and was hybridized with GeoChip 4.2 on a MAUI hybridization station (BioMicro, Salt Lake City, UT, USA) at 42℃ with 40% formamide for 16h.

scan_protocol: Microarrays were scanned by a ScanArray 5000 Microarray Analysis System (PerkinElmer, Wellesley, MA, USA) at 100% laser power.

data_processing: Signal intensities of the spots were measured with ImaGene 6.0 (Biodiscovery Inc., El Segundo, CA, USA). Data pretreatment was performed online (ieg.ou.edu). The percentages of thermophile probes (negative controls) in each sample were made less than 5% by the removal of low quality spots. The genes detected in only one out of three samples from the same system were removed.  The genes detected only in 3 or fewer samples out of 12 samples from the same system were removed to avoid potential noises. For each sample, intensities of the genes were then transformed to the natural logarithmic form and divided by the mean signal intensity.

organism: activated sludge metagenome

source_name: antibiotic resistance genes and virulence genes in activated sludge of full-scale wastewater treatment systems

label_protocol: As previously described (Lu et al. 2012), 1000 ng of each DNA sample was labeled were labeled with the fluorescent dye Cy-5 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA) and then dried.

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 12.

extract_protocol: Microbial genomic DNA was extracted from the pellets of activated sludge samples through joint use of freezing and sodium dodecyl sulfate (SDS) for cell lysis (Zhou et al. 1996). The extracted products were then purified employing the Wizard® SV Genomic DNA Purification Kit (Promega, Madison WI). DNA quality and quantity were measured using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA) and with PicoGreen using a FLUOstar Optima (BMG Labtech, Jena, Germany), respectively.

tag: tissue

tag: wastewater treatment system

value: Wastewater treatment system of OD in the short term


title: 9d time 0 Rep1

description: RNA-Seq of detached first-pair rosette leaves before culture (time 0) from 9-day-old seedlings replicate 1

tag: developmental stage

tag: treatment


title: BT-549 (2)

description: Corresponding sample number: 2

value: breast cancer cell line BT-549

tag: disease state

tag: transduction with doxycycline-inducible shrna

value: Luciferase

value: treatment with doxycyline 72 hours


title: BT-549 (26)

description: Corresponding sample number: 26

value: Breast

value: ductal carcinoma


title: sO11

description:
GeoChip data for activated sludge sample collected at System OD, Day 11
raw data file: Activated sludge raw data1.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 11.

value: activated sludge of full-scale wastewater treatment system


title: 2m4


title: Fibroblast Non_CD sample 4 from patient 3

source_name: patient 3

tag: gender

value: Non_Crohn's Disease

tag: disease stage


title: 1m4

value: 1 h


title: BT-549 (14)

description: Corresponding sample number: 14


title: sO10

description:
GeoChip data for activated sludge sample collected at System OD, Day 10
raw data file: Activated sludge raw data1.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 10.


title: 15d time 0 Rep1

description: RNA-Seq of detached first-pair rosette leaves before culture (time 0) from 15-day-old seedlings replicate 1

source_name: leaves of 15-day-old seedlings

tag: growth conditions

value: constant light

tag: ecotype

value: Columbia (Col-0)


title: 3p4

value: 7 h


title: sO9

description:
GeoChip data for activated sludge sample collected at System OD, Day 9
raw data file: Activated sludge raw data1.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 9.


title: BT-549 (25)

description: Corresponding sample number: 25

value: no treatment


title: sO8

description:
GeoChip data for activated sludge sample collected at System OD, Day 8
raw data file: Activated sludge raw data1.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 8.


title: 2p4


title: 1p4


title: sM1

description:
GeoChip data for activated sludge sample collected at System MBR, Day 1
raw data file: Activated sludge raw data1.txt

growth_protocol: MLSS samples were taken from the the membrane tanks of the MBR system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 1.

value: Wastewater treatment system of MBR in the short term


title: 3m4


title: BT-549 (1)

description: Corresponding sample number: 1


title: BT-549 (13)

description: Corresponding sample number: 13


title: sO7

description:
GeoChip data for activated sludge sample collected at System OD, Day 7
raw data file: Activated sludge raw data1.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 7.


title: 3m1


title: sO5

description:
GeoChip data for activated sludge sample collected at System OD, Day 5
raw data file: Activated sludge raw data1.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 5.


title: sO6

description:
GeoChip data for activated sludge sample collected at System OD, Day 6
raw data file: Activated sludge raw data1.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 6.


title: 1m1


title: sO4

description:
GeoChip data for activated sludge sample collected at System OD, Day 4
raw data file: Activated sludge raw data1.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 4.


title: Mouse 4- 3D- male

type: RNA

city: Northfield

first: Heather

middle: Elizabeth

last: Driscoll

state: VT

address: 158 Harmon Drive

department: Biology

institute: Norwich University

description: This is the fourth of five biological replicates of 3D silk scaffold bone marrow cell cultures from 16 week-old, C57BL/6J mice tibia and femurs.

hyb_protocol: Samples were combined with a hybridization mix, injected into Mouse ClariomTM S arrays, and place in the Affymetrix® GeneChip® Hybridization Oven 645 at 45° C and 60 RPM for 16.5 hours overnight.

scan_protocol: Arrays were stained using the Affymetrix® GeneChip® Fluidics Station 450 and scanned with the 7G Affymetrix® GeneChip® Scanner 3000. Raw image analysis was performed with Affymetrix® Expression ConsoleTM software. The raw data images produced from the scanner were processed into .CEL files, which contain measure intensities for each probe on the array.

data_processing: The .CEL files were imported into Partek® Genomics SuiteTM (GS) version 6.6 (Partek Inc., St. Louis, MO, USA, www.partek.com). Background correction, quantile normalization, log2 transformation, and probe set summarization were performed using default settings for the Robust Multichip Average (RMA) procedure (see Bolstad et al. Bioinformatics 19(2):185; Irizarry et al. Biostatistics 4(2):249; Nucleic Acids Res. 31:e15). A two-way Analysis of Variance (ANOVA) with factors matrix type and subject (paired design) was performed on the RMA-normalized probesets to assess differential expression.

label: Biotin

organism: Mus musculus

source_name: 3D silk scaffold culture of tibia and femur bone marrow stromal cells after 4 weeks of adipogenic differentiation

label_protocol: Approximately 5.5ug of single-stranded cDNA was fragmented using UDG (10U/uL) and APE1 (1000U/uL), provided in the GeneChip® WT PLUS Reagent Kit.  Samples were then labeled with biotin using TdT (30U/uL), also provided in the GeneChip® WT PLUS Reagent Kit.  Efficiency of the fragmentation and labeling reactions were verified using NeutrAvidin (10mg/mL) with a gel-shift assay.

growth_protocol: Cells were cultured in basal growth media (DMEM supplemented with 10% FBS and 1% antibiotic-antimycotic) for 12 days and then switched to an adipogenic differentiation media (basal supplemented with 0.5 mM IBMX, 1 uM Rosi, 1 uM Dex, 10 ug/mL insulin) for 4 days, and then a seocnd adipogenic media (basal supplemented with 1 uM Rosi and 10 ug/mL insulin) for 3 days and then maintained in a third adipogenic media (basal supplemented with 10 ug/mL insulin only).

extract_protocol: After 4 weeks of adipogenesis, total RNA was isolated from 10 samples using the Qiazol and miRNeasy isolation mini-kit (Qiagen) according to the manufacturer’s protocol. 100ng of RNA was used to synthesize cDNA through a first-strand reverse transcription reaction and second-strand RNA degradation reaction, using reagents from the GeneChip® WT PLUS Reagent Kit.  cRNA was then synthesized through an overnight (16-hour) In-vitro transcription reaction, which utilizes a T7 RNA polymerase.  The cRNA was purified using an Affymetrix® magnetic bead protocol.  Sample concentrations were determined using a 40ug/mL/A260 constant on a Nanodrop 1000 spectrophotometer.

treatment_protocol: See growth protocol.

value: male

tag: sample type

value: 3D silk scaffold


title: Mouse 3- 3D- male

description: This is the third of five biological replicates of 3D silk scaffold bone marrow cell cultures from 16 week-old, C57BL/6J mice tibia and femurs.


title: 2m1

description:
rpkm_0_AYR0M.txt
rpkm_1_AYR0M.txt
rpkm_2_AYR0M.txt
rpkm_3_AYR0M.txt

value: 4 h


title: Mouse 2- 3D- female

description: This is the second of five biological replicates of 3D silk scaffold bone marrow cell cultures from 16 week-old, C57BL/6J mice tibia and femurs.

value: female


title: Mouse 5- 3D- male

description: This is the fifth of five biological replicates of 3D silk scaffold bone marrow cell cultures from 16 week-old, C57BL/6J mice tibia and femurs.


title: 3p1


title: 2p1


title: sO3

description:
GeoChip data for activated sludge sample collected at System OD, Day 3
raw data file: Activated sludge raw data1.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 3.

value: Wastewater treatment system of OD in the short term


title: sO2

description:
GeoChip data for activated sludge sample collected at System OD, Day 2
raw data file: Activated sludge raw data1.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 2.


title: 1p1


title: Mouse 1- 3D- female

description: This is the first of five biological replicates of 3D silk scaffold bone marrow cell cultures from 16 week-old, C57BL/6J mice tibia and femurs.


title: Mouse 5- 2D- male

description: This is the fifth of five biological replicates of 2D bone marrow cell cultures from 16 week-old, C57BL/6J mice tibia and femurs.

source_name: 2D tissue culture of tibia and femur bone marrow stromal cells after 4 weeks of adipogenic differentiation

value: 2D bone marrow cell


title: Moch

status: Public on Dec 18 2018

city: Austin

first: Rebecca

middle: L

last: Young

state: TX

address: 2415 Speedway

department: Integrative Biology

institute: University of Texas at Austin

data_processing:
An aliquot of total RNA was then run on a Bioanalyzer Nano RNA chip (Agilent) to confirm RNA integrity score was above 7 for each sample
Trimmomatic was used to filter and trim reads using the following parameters: -phred33 ILLUMINACLIPadapters.fa:3:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
A transcriptome was assembled de novo using Trinity from the reads of each sample/species
de novo assembled contigs were annotated to reference genomes using blastx
Reads were mapped the the annotated de novo assembly using bwa mem
Raw reads were calculated as the sum of transcript counts using SAMtools and Reads Per Million of library size (RPM) were calculated as the reads mapping to de novo assembled contigs  of annotated as the same gene and normalized by the size the size of the library.
Supplementary_files_format_and_content: fasta files including the de novo assembled contigs annotated using closely related reference genomes for each Sample
Supplementary_files_format_and_content: csv files including raw reads and RPMs for each sample

organism: Microtus ochrogaster

source_name: fore- and mid-brain

extract_protocol:
fore- and mid-brains were rapidly dissected and flash frozen on dry ice or preserved in RNAlater and stored at -80C until RNA was extracted using Trizol
RNA libraries were prepared for sequencing using the NEB small RNA kit (cat #E6160L or #E6160S) Illumina protocols by the University of Texas at Austin Genome Sequencing and Analysis Facility (GSAF)

value: fore- and mid-brain

tag: Sex

tag: state

value: reproductive

tag: number of individuals pooled

tag: annotation genome


title: sO1

description:
GeoChip data for activated sludge sample collected at System OD, Day 1
raw data file: Activated sludge raw data1.txt

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 1.


title: TUM622 cells in 2D culture, biological rep3

city: Pearl River

first: Kenneth

last: Geles

state: New York

address: 401 N Middletown Rd

department: Oncology Research Unit

institute: Pfizer

description: Gene expression data from TUM622 cells grown in 2D culture

hyb_protocol: For each sample, 10 μg of biotin-labeled cRNA was fragmented and hybridized to Human Genome U133+2 GeneChip oligonucleotide arrays (Affymetrix) using buffers and conditions recommended by manufacturer. GeneChips were then washed and stained with Streptavidin R-phycoerythrin (Molecular Probes) using the GeneChip® Fluidics Station 450

scan_protocol: GeneChips were scanned using a Affymetrix GeneChip Scanner 3000

data_processing: The gene expression data was processed by GCRMA algorithm or MAS5.0 algorithm

label: biotin

source_name: TUM622 cells grown in 2D cell flasks

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: TUM622 cells were maintained in serum-free bronchial epithelial cell growth medium (BEGM, Lonza #CC-3170).

extract_protocol: TUM622 cells in 2D culture were collected by trypsinization (Gibco #12604013). TUM622 acini from 3D culture were extracted from the ECM via Cultrex® 3D-cell harvesting kit (Trevigen #3448-020-K) according to manufacturer’s recommendation. Single cell suspensions were then stained with DAPI, EpCAM (BD Bioscience #347198) or control IgG antibody and subjected to FACS sorting using a BD FACSAria II to obtain live, EpCAM+ epithelial cell populations. RNA from TUM622 cells (2D or 3D) was isolated using the RNEasy kit (#74104, Qiagen).

treatment_protocol: For 2D culture, cells were plated in cell culture flasks with 50% medium change once every two days and passaging once every week; For 3D culture, cells were embedded at single cell density in ECM (Trevigen Cultrex® #3443-005-01) and cultured for 10 days with medium change once every two days.

value: Lung squamous carcinoma

tag: derivation

value: human tumor sample was first established as a patient derived xenograft (PDX) model. PDX tumors were then used to derive TUM622 cells in serum-free medium.


title: Mouse 1- 2D- female

description: This is the first of five biological replicates of 2D bone marrow cell cultures from 16 week-old, C57BL/6J mice tibia and femurs.

tag: strain


title: Mouse 4- 2D- male

description: This is the fourth of five biological replicates of 2D bone marrow cell cultures from 16 week-old, C57BL/6J mice tibia and femurs.


title: Mouse 2- 2D- female

description: This is the second of five biological replicates of 2D bone marrow cell cultures from 16 week-old, C57BL/6J mice tibia and femurs.


title: TUM622 cells in 3D culture, biological rep2

description: Gene expression data from TUM622 cells grown in 3D culture

source_name: TUM622 cells grown in 3D extracellular matrix

tag: tissue


title: TUM622 cells in 3D culture, biological rep1


title: TUM622 cells in 3D culture, biological rep3


title: Mouse 3- 2D- male

description: This is the third of five biological replicates of 2D bone marrow cell cultures from 16 week-old, C57BL/6J mice tibia and femurs.


title: TUM622 cells in 2D culture, biological rep1


title: Preterm-5d-FOR.13-13

city: Shenzhen

first: Desheng

last: Gong

address: No.7 PengFei road

institute: Agricultural Genomes Institute at Shenzhen

library_source: genomic

data_processing:
Genomic DNA from the above 87 samples were extracted and were subjected to RRBS library preparation.
Libraries were then subjected to paired-end 100/125bp multiplex sequencing on the Hiseq 2500 platform.
Raw sequencing data were processed by the Illumina base-calling pipeline. Low-quality reads that contained more than 30% ‘N’s or more than 10% of the sequence with low quality value (quality value <20) per read were omitted from the data analysis.
The clean reads were aligned to the NCBI Sus scrofa reference genome (Sscrofa10.2) using the BSMAP(BSMAP v2.73), to identify methylcytosine (mC).
The uniquely mapped reads that contained at least one enzyme digestion site in the ends were used for further analysis.
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: Cout files include chromosome ID,C sites' coordinate, the number of methylated reads and non-methylated reads.

organism: Sus scrofa

source_name: middle small intestine

extract_protocol:
DNeasy Blood & Tissue Kit (Qiagen)
RRBS protocol

value: middle small intestine

tag: gestation

value: Preterm

tag: nutrition

value: FOR

tag: postnatal age


title: Colon-PXRKO_PCN-Rep1

city: Toulouse

first: Sandrine

last: Ellero-Simatos

address: 180 chemin de Tournefeuille

country: France

institute: INRAe

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 14 out of 17 microarrays or with a minimal weight of 3 per group from at least one experimental group. At this step, 39394 spots out of 62976 were selected.  The mean signal of the 9 first samples and 8 last ones were substracted to individuals signals to correct the batch effect of the 2 serials (characteristics:WashBatch) observed during the microarray washing procedure. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 36695 rows each corresponding to a unique ProbeName (provided as data Matrix).

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

extract_protocol: At sacrifice, the liver, the three parts of the small intestine (duodenum, jejunum, ileum), and the colon were removed and snap-frozen in liquid nitrogen and stored at -80°C until used for RNA extraction. Total RNA was extracted with TRIzol reagent (Invitrogen).

treatment_protocol: Twelve six-week old wild-type (WT) C57BL/6J male mice were purchased from Charles River and 12 Pxr-/- animals (backcrossed on the C57Bl/6J background) are bred for 10y in our animal facility. Mice were acclimatized for two weeks, then randomly allocated to the different experimental groups: wild-type control (WT CONT, n=6), wild-type PCN-treated (WT PCN, n=6), Pxr-/- control (Pxr-/- CONT, n=6), Pxr-/- PCN-treated (Pxr-/- PCN, n=6). PCN-treated mice received a daily intraperitoneal injection of PCN (100 mg/kg) in corn oil for 4 days while control mice received corn oil only. Mice were killed at ZT6, 6 hours after the last PCN injection, in the fed state.

tag: strain background

tag: genotype/variation

value: PXRKO

tag: treatment

value: PCN

value: Colon

tag: washbatch


title: Colon-WT_Ctl-Rep5

value: WT

value: Ctl


title: Colon-WT_PCN-Rep1

value: male


title: Preterm-5d-FOR.9-13


title: Colon-PXRKO_Ctl-Rep2


title: Colon-WT_PCN-Rep3


title: Colon-WT_Ctl-Rep4


title: Colon-WT_Ctl-Rep3


title: Colon-WT_PCN-Rep2


title: Term-5d-TPN.343-13

value: Term

value: TPN


title: Colon-PXRKO_Ctl-Rep1


title: Term-5d-TPN.341-13


title: Term-5d-ENT.342-13

value: COL


title: Colon-PXRKO_PCN-Rep4


title: Colon-PXRKO_PCN-Rep3


title: Colon-PXRKO_Ctl-Rep5


title: Colon-WT_PCN-Rep4


title: Colon-PXRKO_Ctl-Rep4


title: Term-5d-ENT.340-13


title: Term-0d.406-13


title: Preterm-26d-TPN.205-14


title: Colon-PXRKO_PCN-Rep2


title: Term-0d.405-13


title: Term-26d-TPN.345-13


title: 3m7

tag: time

value: 7 h


title: Preterm-5d-ENT.312-13


title: Preterm-5d-ENT.303-13


title: Preterm-5d-TPN.315-13


title: Preterm-0d.388-13


title: TUM622 cells in 2D culture, biological rep2


title: Preterm-5d-FOR.55-13


title: Colon-PXRKO_Ctl-Rep3


title: Term-26d-TPN.346-13


title: Preterm-0d.387-13


title: Preterm-5d-FOR.39-13


title: Preterm-5d-FOR.27-13


title: Preterm-5d-FOR.23-13


title: Preterm-5d-FOR.21-13


title: Preterm-5d-FOR.17-13


title: Term-26d-ENT.379-13


title: Term-26d-ENT.375-13


title: Term-26d-TPN.369-13


title: Term-26d-ENT.376-13


title: Colon-WT_Ctl-Rep2


title: Term-26d-TPN.374-13


title: Term-26d-ENT.350-13


title: Term-26d-TPN.349-13


title: Term-26d-TPN.377-13


title: Term-26d-TPN.368-13


title: Term-26d-ENT.370-13


title: Term-26d-TPN.352-13


title: Term-26d-ENT.351-13


title: Term-26d-ENT.347-13


title: Preterm-26d-TPN.200-14


title: Term-5d-ENT.421-13


title: Term-5d-ENT.426-13


title: Term-5d-TPN.422-13


title: Term-5d-ENT.419-13


title: Term-5d-ENT.360-13


title: Term-5d-TPN.416-13


title: Term-5d-TPN.355-13


title: Term-5d-ENT.358-13


title: Term-5d-TPN.359-13


title: Term-5d-TPN.357-13


title: Term-5d-ENT.354-13


title: Term-0d.413-13


title: Term-0d.412-13


title: Term-0d.411-13


title: Preterm-26d-TPN.384-13


title: Preterm-26d-TPN.385-13


title: Term-26d-ENT.344-13


title: Preterm-26d-TPN.210-14


title: Preterm-26d-ENT.212-14


title: Preterm-26d-TPN.215-14


title: Preterm-26d-ENT.206-14


title: Preterm-26d-ENT.383-13


title: Preterm-26d-ENT.382-13


title: Term-5d-TPN.425-13


title: Preterm-26d-TPN.213-14


title: Preterm-26d-ENT.209-14


title: Preterm-26d-ENT.204-14


title: Preterm-26d-ENT.202-14


title: Preterm-26d-ENT.203-14


title: Preterm-5d-ENT.403-13


title: Term-0d.410-13


title: Term-0d.407-13


title: Preterm-5d-TPN.400-13


title: Preterm-5d-TPN.398-13


title: Preterm-5d-TPN.397-13


title: Preterm-5d-ENT.399-13


title: Preterm-5d-TPN.363-13


title: Preterm-5d-ENT.396-13


title: Preterm-26d-TPN.208-14


title: Preterm-5d-ENT.365-13


title: Preterm-5d-TPN.309-13


title: Preterm-5d-TPN.361-13


title: Preterm-0d.394-13


title: Preterm-0d.386-13


title: Preterm-0d.390-13


title: Preterm-0d.395-13


title: Preterm-5d-TPN.404-13


title: Preterm-0d.389-13


title: Preterm-5d-ENT.401-13


title: Preterm-5d-ENT.362-13


title: Preterm-0d.391-13


title: THP-1 24h after 1,25D treatment, 3rd replicate CEBPA

city: Kuopio

first: Carsten

last: Carlberg

address: Yliopistonranta 1D

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description:
CEBPA VD 24 h N3
ChIPmentation

data_processing:
Alignment to hg19 using Bowtie v1.1 Parameters -n 1 -k 1 -m 1 -l 32 -t -q best
Peak calling using MACS2, parameters bw 150 min peak 3 max peak 50
EtOH treated merged and considered as a unique file.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files
Supplementary_files_format_and_content: THP1_CEBPA_2h_EtOH.tdf

source_name: Culture

growth_protocol: THP-1 cells were grown in RPMI 1640 medium, supplemented with 10% fetal calf serum (FCS), 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin at 37°C.

extract_protocol:
Cells were grown in culture as mentioned above, after which they were crosslinked with formaldehyde, lysed and the DNA was extracted. Then, ChIPmentation was performed.
The library was created using NEBNext Ultra II DNA Library Prep Kit for Illumina and the samples were barcoded using Nextera sequencing primers. The pooled libraries were sequenced on an Illumina HiSeq2000.

treatment_protocol: Cells were treated with either 100 nM of 1,25(OH)2D3 (Sigma-Aldrich) or solvent (0.1% ethanol).

tag: cell line

tag: time point

tag: chip antibody

value: anti-CEBPA (Diagenode, catalog number:C15410225)


title: THP-1 24h after EtOH treatment, 2nd replicate CEBPA

description:
CEBPA EtOH 24 h N2
ChIPmentation
processed data file: THP1_CEBPA_merged_ET.txt

value: EtOH


title: THP-1 24h after EtOH treatment, 1st replicate CEBPA

description:
CEBPA EtOH 24 h N1
ChIPmentation
processed data file: THP1_CEBPA_merged_ET.txt


title: THP-1 24h after EtOH treatment, 3rd replicate CEBPA

description:
CEBPA EtOH 24 h N3
ChIPmentation
processed data file: THP1_CEBPA_merged_ET.txt


title: THP-1 24h after 1,25D treatment, 1st replicate CEBPA

description:
CEBPA VD 24 h N1
ChIPmentation


title: THP-1 24h after 1,25D treatment, 2nd replicate CEBPA

description:
CEBPA VD 24 h N2
ChIPmentation


title: Vehicle_1

city: Rochester

first: Paige

last: Lawrence

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

description: Intranasally infected with 120 HAU influenza A virus (HKx31, H3N2)

data_processing:
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-1.8.4
CLEANING - Trimmomatic-0.32 "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
MAPPING - STAR_2.4.2a "--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
READ COUNTING - htseq-count v0.6.1 "-q -f bam -s no -r pos -i gene_name"
Differential expression analyses and data normalization were performed using DESeq2-1.12.4 (35, 36) R/Bioconductor package (37) with an adjusted p-value (Benjamini-Hochberg) threshold of 0.05 within the R version 3.2.3 environment (https://Ahr.R-project.org).
Genome_build: mm9
Supplementary_files_format_and_content: Raw read counts for each sample in tab-delimited text file

source_name: Vehicle Peanut Oil rep1

growth_protocol: Eight week old female C57BL/6 mice were used in this study

extract_protocol:
Lung dendritic cells were FACS purified on day three post influenza A virus infection. RNA was isolated by trizol extraction, purified, and submitted for RNA Seq
The total RNA concentration from sorted mouse DCs was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with an Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA). There were three independent DC samples for each treatment group. The TruSeq RNA Sample Preparation Kit V2 (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 100ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate amplicons of approximately 200-500bp in size.

treatment_protocol: Mice were treated with Vehicle Peanut Oil or 10 ug/mL of TCDD by oral gavage one day previous to infection.  Mice were intranasally infected with 120 HAU influenza A virus (HKx31, H3N2).

tag: age

value: Eight weeks


title: Vehicle_3

source_name: Vehicle Peanut Oil rep3


title: TCDD_1

source_name: 10 ug/mL of TCDD rep1


title: TCDD_2

source_name: 10 ug/mL of TCDD rep2


title: TCDD_3

source_name: 10 ug/mL of TCDD rep3


title: Vehicle_2

source_name: Vehicle Peanut Oil rep2


title: THP-1 8h after EtOH treatment, 3rd replicate CEBPA

description:
CEBPA EtOH 8 h N3
ChIPmentation
processed data file: THP1_CEBPA_merged_ET.txt


title: THP-1 8h after EtOH treatment, 2nd replicate CEBPA

description:
CEBPA EtOH 8 h N2
ChIPmentation
processed data file: THP1_CEBPA_merged_ET.txt


title: THP-1 8h after 1,25D treatment, 1st replicate CEBPA

description:
CEBPA VD 8 h N1
ChIPmentation


title: THP-1 8h after 1,25D treatment, 2nd replicate CEBPA

description:
CEBPA VD 8 h N2
ChIPmentation


title: THP-1 8h after EtOH treatment, 1st replicate CEBPA

description:
CEBPA EtOH 8 h N1
ChIPmentation
processed data file: THP1_CEBPA_merged_ET.txt


title: MDA-MB-231 cells overexpressing miR-145, rep3

city: rome

first: andrea

last: sacconi

address: via elio chianesi

country: Italy

institute: regina elena cancer institute

hyb_protocol: Labeled RNA was hybridized to slides for 17h at 65°C.

scan_protocol: Scanning and image analysis were performed using the Agilent DNA Microarray Scanner (P/N G2565BA). Feature Extraction Software (Version 10.5) was used for data extraction from raw microarray image files.

data_processing:
Data was extracted by Agilent Feature Extraction Software and quantile normalized.
Values lower than 1 were thresholded to 1 and log2-trasformed.

source_name: MDA-MB-231 mimic145

label_protocol: Total RNA (100 ng) was labeled using Low Input Quick Amp WT Labeling Kit, one-color, and hybridized to SurePrint G3 Human Exon 2X400K arrays (Agilent).

growth_protocol: MDA-MB-231 cell line was cultured in DMEM medium supplemented with 50 U/mL penicillin, 50 U/ml streptomycin and 10% heat-inactivated FBS at 37°C in incubator with humidified 5% CO2 atmosphere.

extract_protocol: Total RNA for microarray analyses was extracted using Trizol (Invitrogen, Carlsbad, CA, USA). Genomic DNA contamination was eliminated through a DNase I (Qiagen, Chatsworth, CA) digestion step. RNA was further purified on Qiagen RNeasy columns for gene expression profiling (Qiagen, Chatsworth, CA). The concentration and purity of total RNA were assessed using a Nanodrop TM 1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

treatment_protocol: Pre-miR-145-5p (PM11480 #AM17100, Ambion), or Pre-miRNA Negative Control (#AM17110, Ambion) were transfected at final concentration of 5nM using Lipofectamine RNAiMAX (Invitrogen) according to the manufacturer’s instructions. For gene silencing experiments, MDA-MB-231 were transfected with Dicer-substrate short interfering RNAs (DsiRNAs) for AGO2 (IDT, Belgium) and NC1 negative control (IDT, Belgium) at 500 pM for 72h.

tag: cell type

value: breast cancer cell line

value: Overexpressing miR-145


title: MDA-MB-231 cells overexpressing miR-145 and interfered for AGO2 expression, rep3

source_name: MDA-MB-231 sirnaAGO2+mimic145

value: Overexpressing miR-145 and interfered for AGO2 expression


title: MDA-MB-231 cells interfered for AGO2 expression, rep1

source_name: MDA-MB-231 sirnaAGO2

value: Interfered for AGO2 expression


title: MDA-MB-231 cells overexpressing miR-145, rep2


title: MDA-MB-231 cells interfered for AGO2 expression, rep2


title: MDA-MB-231 cells of control, rep1

description: cntrl

source_name: MDA-MB-231 cntrl

value: Control


title: THP-1 8h after 1,25D treatment, 3rd replicate CEBPA

description:
CEBPA VD 8 h N3
ChIPmentation


title: THP-1 2h after EtOH treatment, 2nd replicate CEBPA

description:
CEBPA EtOH 2 h N2
ChIPmentation
processed data file: THP1_CEBPA_merged_ET.txt
processed data file: THP1_CEBPA_2h_EtOH.tdf


title: THP-1 2h after 1,25D treatment, 3rd replicate CEBPA

description:
CEBPA VD 2 h N3
ChIPmentation


title: MDA-MB-231 cells of control, rep3

description: cntrl


title: THP-1 2h after 1,25D treatment, 1st replicate CEBPA

description:
CEBPA VD 2 h N1
ChIPmentation


title: THP-1 2h after EtOH treatment, 3rd replicate CEBPA

description:
CEBPA EtOH 2 h N3
ChIPmentation
processed data file: THP1_CEBPA_merged_ET.txt
processed data file: THP1_CEBPA_2h_EtOH.tdf


title: MDA-MB-231 cells of control, rep2

description: cntrl


title: MDA-MB-231 cells overexpressing miR-145 and interfered for AGO2 expression, rep2


title: THP-1 8h after EtOH treatment, 2nd replicate H3K4me3

description: H3K4me3 8 ET N2

data_processing:
Alignment to hg19 using Bowtie v1.1 Parameters -n 1 -k 1 -m 1 -l 32 -t -q best
Peak calling using Zinba v 2.02 Parameters -f 200
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: tdf, bed

extract_protocol:
Cells were grown in culture as mentioned above, after which they were crosslinked with formaldehyde, lysed and the DNA was extracted. Then, ChIP was performed using antibody against H3K4me3 (Millipore, cat.# 07-473, lot# 2557645).
ChIP DNA was sent to EMBL and the library was prepared there according to their protocol.

treatment_protocol: Cells were treated with 100 nM of 1,25(OH)2D3 (Sigma-Aldrich) or solvent (0.1% ethanol).

tag: treatment protocol

value: 8h with EtOH


title: THP-1 input


title: THP-1 8h after 1,25D treatment, 3rd replicate H3K4me3

description: H3K4me3 8 VD N3


title: THP-1 2h after 1,25D treatment, 2nd replicate CEBPA

description:
CEBPA VD 2 h N2
ChIPmentation


title: THP-1 2h after EtOH treatment, 1st replicate CEBPA

description:
CEBPA EtOH 2 h N1
ChIPmentation
processed data file: THP1_CEBPA_merged_ET.txt
processed data file: THP1_CEBPA_2h_EtOH.tdf


title: MDA-MB-231 cells overexpressing miR-145 and interfered for AGO2 expression, rep1


title: THP-1 2h after 1,25D treatment, 3rd replicate H3K4me3

description: H3K4me3 2 VD N3


title: THP-1 2h after EtOH treatment, 2nd replicate H3K4me3

description: H3K4me3 2 ET N2

value: 2h with EtOH


title: MDA-MB-231 cells interfered for AGO2 expression, rep3


title: THP-1 2h after EtOH treatment, 3rd replicate H3K4me3

description: H3K4me3 2 ET N3


title: THP-1 2h after 1,25D treatment, 2nd replicate H3K4me3

description: H3K4me3 2 VD N2


title: THP-1 8h after 1,25D treatment, 1st replicate H3K4me3

description: H3K4me3 8 VD N1


title: MDA-MB-231 cells overexpressing miR-145, rep1


title: THP-1 8h after EtOH treatment, 1st replicate H3K4me3

description: H3K4me3 8 ET N1


title: THP-1 2h after 1,25D treatment, 1st replicate H3K4me3

description: H3K4me3 2 VD N1


title: THP-1 8h after EtOH treatment, 3rd replicate H3K4me3

description: H3K4me3 8 ET N3


title: THP-1 24h after 1,25D treatment, 3rd replicate CEBPA siRNA

description:
CEBPA V N3
24h transfection with siRNA against CEBPA, followed by 24h treatment with 1,25(OH)2D3.
processed data file: abundance.csv
processed data file: differential_expression_CEBPA_V_E.csv

data_processing:
QC applied to remove low quality reads.
Abundance quantification using kallisto with parameters -b 100 --single -l 180 -s 20
Differential expression using DESeq2 with default parameters.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: abundance.csv: Semi-colon-separated text file includes abundance of genes.
Supplementary_files_format_and_content: differential_expression_CEBPA_V_E.csv: Semi-colon-separated text file includes pval obtained by DESeq2 for all genes. 'baseMeanA' and 'baseMeanB' are defined by DESeq as the mean of normalized counts of all samples treated (A) and untreated (B).

extract_protocol:
Cells were grown in culture as mentioned above, after which they were transfected and treated as described. After treatment, RNA was extracted using the Quick-RNA MiniPrep kit (Zymo Research, R1054), and RNA-seq was performed.
RNA-seq library was constructed using NEBNext Ultra II Directional RNA Library Prep kit for Illumina (E7765L), after which the samples were sent to EMBL for sequencing.

treatment_protocol: Cells were transfected with either 50nM of control Dicer Substrate siRNA (IDT) or 50nM Dicer Substrate siRNA against CEBPA (IDT), after which they were treated with100 nM of 1,25(OH)2D3 (Sigma-Aldrich) or solvent (0.1% ethanol).

tag: sirna

value: siRNA against CEBPA


title: THP-1 2h after EtOH treatment, 1st replicate H3K4me3

description: H3K4me3 2 ET N1


title: THP-1 24h after EtOH treatment, 3rd replicate CEBPA siRNA

description:
CEBPA E N3
24h transfection with siRNA against CEBPA, followed by 24h treatment with EtOH.
processed data file: abundance.csv
processed data file: differential_expression_CEBPA_V_E.csv

value: 24h with EtOH


title: THP-1 24h after 1,25D treatment, 2nd replicate CEBPA siRNA

description:
CEBPA V N2
24h transfection with siRNA against CEBPA, followed by 24h treatment with 1,25(OH)2D3.
processed data file: abundance.csv
processed data file: differential_expression_CEBPA_V_E.csv


title: THP-1 24h after 1,25D treatment, 3rd replicate NC1 siRNA

description:
NC1 V N3
24h transfection with neg control siRNA, followed by 24h treatment with 1,25(OH)2D3.
processed data file: abundance.csv
processed data file: differential_expression_CEBPA_V_E.csv

value: neg control siRNA


title: THP-1 24h after 1,25D treatment, 2nd replicate NC1 siRNA

description:
NC1 V N2
24h transfection with neg control siRNA, followed by 24h treatment with 1,25(OH)2D3.
processed data file: abundance.csv
processed data file: differential_expression_CEBPA_V_E.csv


title: THP-1 24h after 1,25D treatment, 1st replicate CEBPA siRNA

description:
CEBPA V N1
24h transfection with siRNA against CEBPA, followed by 24h treatment with 1,25(OH)2D3.
processed data file: abundance.csv
processed data file: differential_expression_CEBPA_V_E.csv


title: THP-1 24h after EtOH treatment, 1st replicate CEBPA siRNA

description:
CEBPA E N1
24h transfection with siRNA against CEBPA, followed by 24h treatment with EtOH.
processed data file: abundance.csv
processed data file: differential_expression_CEBPA_V_E.csv


title: THP-1 24h after EtOH treatment, 1st replicate NC1 siRNA

description:
NC1 E N1
24h transfection with neg control siRNA, followed by 24h treatment with EtOH.
processed data file: abundance.csv
processed data file: differential_expression_CEBPA_V_E.csv


title: THP-1 24h after 1,25D treatment, 1st replicate NC1 siRNA

description:
NC1 V N1
24h transfection with neg control siRNA, followed by 24h treatment with 1,25(OH)2D3.
processed data file: abundance.csv
processed data file: differential_expression_CEBPA_V_E.csv


title: THP-1 24h after EtOH treatment, 3rd replicate NC1 siRNA

description:
NC1 E N3
24h transfection with neg control siRNA, followed by 24h treatment with EtOH.
processed data file: abundance.csv
processed data file: differential_expression_CEBPA_V_E.csv


title: THP-1 24h after EtOH treatment, 2nd replicate CEBPA siRNA

description:
CEBPA E N2
24h transfection with siRNA against CEBPA, followed by 24h treatment with EtOH.
processed data file: abundance.csv
processed data file: differential_expression_CEBPA_V_E.csv


title: dCas9-KRAB_sgRNA1-H3K27ac

city: London

first: Miguel

middle: R

last: Branco

address: 4 Newark Street

country: United Kingdom

institute: Blizard Institute

data_processing:
Adaptors and low-quality base calls were trimmed using trim_galore! v0.4.5 with default parameters.
Trimmed reads were mapped to mm10 using bowtie2 v2.3.4 with default paramaters. Uniquely aligned reads were extracted using a custom perl script.
BigWig tracks were generated using the bamCoverage function of deepTools2.0, with CPM normalisation and 200 bp bin size.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: embryonic stem cells

growth_protocol: ESCs stably expressing dCas9-KRAB-mCherry from a lentiviral vector were cultured on gelatin-coated plates without feeders, in DMEM supplemented with 15% fetal bovine serum and 1,000 U/ml LIF.

extract_protocol:
Chromatin was extracted 8 days post-infection from cross-linked cells, and sonicated to 200-700 bp fragments. Immunoprecipitation was performed with 15 µg of chromatin and 2.5 µg of anti-H3K27ac antibody. DNA was purified using the GeneJET PCR purification kit (Thermo Fisher).
Libraries were prepared from 1-5 ng of DNA using the NEBNext ultra II DNA library prep kit.

treatment_protocol: Cells were infected with a pool of four lentiviruses, each carrying a sgRNA (or an empty control) and a BFP reporter. After 48 hours, cells were sorted for mCherry and BFP expression.

value: embryonic stem cells

tag: strain

tag: sgrna

value: RLTR13D6 set 1

tag: antibody

value: anti-H3K27ac (Active Motif 39133)


title: dCas9-KRAB_sgRNA2-H3K27ac

value: RLTR13D6 set 2


title: THP-1 24h after EtOH treatment, 2nd replicate NC1 siRNA

description:
NC1 E N2
24h transfection with neg control siRNA, followed by 24h treatment with EtOH.
processed data file: abundance.csv
processed data file: differential_expression_CEBPA_V_E.csv


title: dCas9-KRAB_empty-H3K27ac


title: dCas9-KRAB_empty-Input

value: Input


title: RNA-seq_dCas9-KRAB_sgRNA2-3

data_processing:
Adaptors and low-quality base calls were trimmed using trim_galore! v0.4.5 with default parameters.
Trimmed reads were mapped to mm10 using HISAT2 v2.0.5 with --no-softclip.
Raw read counts for each gene were generated in Seqmonk with the RNA-seq quantitation pipeline. Normalised gene expression values were calculated with the variance stabilizing transformation in DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing normalised gene expression values (log2) for each sample.

extract_protocol:
RNA was extracted using QIAzol (QIAGEN).
RNA-Seq libraries were generated from 400-600 ng of total RNA using the NEBNext rRNA depletion kit and NEBNext ultra II directional RNA library prep kit.


title: RNA-seq_dCas9-KRAB_sgRNA2-2


title: RNA-seq_dCas9-KRAB_sgRNA1-3


title: chicken forelimb bud_PBS_24hr_rep2

city: Loma Linda

first: Kerby

middle: Clyde

last: Oberg

state: CA

address: 24785 Stewart Street

department: Pathology and Human Anatomy

institute: Loma Linda University

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: The data was normalized using RMA

organism: Gallus gallus

source_name: chicken limb bud tissue after 24hrs of PBS treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Fertile chicken eggs were incubated in a humidified chamber for 4 days or until embryos reached desired developmental stage (HH23).

extract_protocol: RNA was extracted from treated and untreated tissue surrounding the FGF/PBS bead after 24hrs of incubation  using QIAGEN RNeasy kit in accordance with the prescribed protocol provided with the kit.

treatment_protocol: Using tungsten needle and forceps, FGF2 or PBS soaked beads were implanted in HH23 Chicken limb buds about 500microns from the distal tip. Embryos were incubated for 24hrs then treated tissue was harvested

tag: developmental stage


title: Bb dks mutant B31A3-2-dks in RPMI rep3

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_Bb dks mutant B31A3-1-dks  in RPMI rep3

hyb_protocol: All cRNAs were hybridized to a custom Affymetrix GeneChip

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.

data_processing: The data were analyzed with CC using Affymetrix default analysis with a scale filter for Bb genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1250.

organism: Borreliella burgdorferi

source_name: Bb dks mutant B31A3-1-dks in RPMI rep3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Incubation of spirochetes in RPMI and growth in semi-solid BSK-II medium were performed under microaerobic conditions (5% CO2, 3% O2, 34 °C)

extract_protocol: Total RNA was extracted from 14 ml cultures at 5 x 107 spirochetes ml-1 density in BSK-II or RPMI

value: dks mutant


title: Bb wt B31A3-2 in BSK rep1

description: Gene expression data from_Bb wt B31A3-2  in BSK rep1

source_name: Bb wt B31A3-2 in BSK rep1

value: wild type


title: chicken forelimb bud_PBS_24hr_rep3


title: Bb dks mutant B31A3-2-dks in BSK rep3

description: Gene expression data from_Bb dks mutant B31A3-2-dks  in BSK rep3

source_name: Bb dks mutant B31A3-2-dks in BSK rep3


title: Bb wt B31A3-2 in RPMI rep2

description: Gene expression data from_Bb wt B31A3-2  in RPMI rep2

source_name: Bb wt B31A3-2 in RPMI rep2


title: Bb wt B31A3-2 in BSK rep2

description: Gene expression data from_Bb wt B31A3-2  in BSK rep2

source_name: Bb wt B31A3-2 in BSK rep2


title: Bb wt B31A3-2 in BSK rep3

description: Gene expression data from_Bb wt B31A3-2  in BSK rep3

source_name: Bb wt B31A3-2 in BSK rep3


title: Bb wt B31A3-2 in RPMI rep3

description: Gene expression data from_Bb wt B31A3-2  in RPMI rep3

source_name: Bb wt B31A3-2 in RPMI rep3


title: chicken forelimb bud_FGF2_24hr_rep1

source_name: chicken limb bud tissue after 24hrs of FGF2 treatment


title: chicken forelimb bud_FGF2_24hr_rep2


title: Bb dks mutant B31A3-2-dks in BSK rep1

description: Gene expression data from_Bb dks mutant B31A3-2-dks  in BSK rep1

source_name: Bb dks mutant B31A3-2-dks in BSK rep1


title: Bb dks mutant B31A3-2-dks in BSK rep2

description: Gene expression data from_Bb dks mutant B31A3-2-dks  in BSK rep2

source_name: Bb dks mutant B31A3-2-dks in BSK rep2


title: Bb dks mutant B31A3-2-dks in RPMI rep1

description: Gene expression data from_Bb dks mutant B31A3-1-dks  in RPMI rep1

source_name: Bb dks mutant B31A3-1-dks in RPMI rep1


title: chicken forelimb bud_PBS_24hr_rep1


title: Bb dks mutant B31A3-2-dks in RPMI rep2

description: Gene expression data from_Bb dks mutant B31A3-1-dks  in RPMI rep2

source_name: Bb dks mutant B31A3-1-dks in RPMI rep2


title: chicken forelimb bud_FGF2_24hr_rep3


title: Bb wt B31A3-2 in RPMI rep1

description: Gene expression data from_Bb wt B31A3-2  in RPMI rep1

source_name: Bb wt B31A3-2 in RPMI rep1


title: RNA-seq_dCas9-KRAB_sgRNA1-2


title: RNA-seq_dCas9-KRAB_sgRNA1-1


title: RNA-seq_dCas9-KRAB_empty-2


title: RNA-seq_dCas9-KRAB_empty-1


title: RNA-seq_dCas9-KRAB_sgRNA2-1


title: ckit5000

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

data_processing:
Fastq files were created using Cellranger 1.3
Reads were mapped and UMIs counted using CellRanger 2.1
Genome_build: mm10
Supplementary_files_format_and_content: A raw count matrix was generated using Seurat v2.3.4. Genes in the rows, and cells across the columns. -1 in the cellID denotes ckit1000, -2 ckit3000, -3 ckit5000. -4 zsgreen, -5 HSC

extract_protocol:
BM isolation
Libraries were constructed according to 10x genomics Chromium Single Cell 3' Reagents Kit V2 Protocol

treatment_protocol: no treatment

tag: tissue

value: Bone Marrow

value: 20 weeks old


title: zsgreen


title: cKit1000


title: hsc

source_name: Lin-CD45.2+c-kit+ ZsGreen+


title: DNA_METH_RISP_Chimera_WT4

city: Chicago

first: Benjamin

middle: D.

last: Singer

state: Illinois

address: 303 E. Superior St., Simpson Querrey 5th floor

institute: Northwestern University Feinberg School of Medicine

data_processing:
Basecalls performed using Illumina RTA2 software.
Indexed samples were demultiplexed to fastq files with bcl2fastq v2.17.1.14.
Reads were  trimmed of 10 base pairs from the 5’ end with TrimGalore! v0.4.3 to remove primer and adapter sequences.
Sequence alignment to the GRCm38/mm10 reference genome and methylation extraction ignoring 1 base at the 3’ end (after reviewing the M-bias plots) were performed with Bismark v0.16.3.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Bismark tab-delimited "coverage" files for cytosines in CpG context with the following columns: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>

source_name: CD4+ YFP-Foxp3+ CD25+ Cells

extract_protocol:
Genomic DNA was isolated using the AllPrep DNA/RNA Micro Kit (Qiagen).
Genomic DNA was quantified with a Qubit 3.0 instrument. ~50-200 ng of genomic DNA was then digested with the restriction endonuclease MspI (New England BioLabs). Resulting fragments underwent size selection for fragments ~100-250-bp in length using SPRI beads (MagBio Genomics) and subsequent bisulfite conversion using the EZ DNA Methylation-Lightning Kit (Zymo Research) per the manufacturer’s protocol. Bisulfite conversion efficiency averaged 99.4% as estimated by the measured percent of unmethylated CpGs in λ-bacteriophage DNA (New England BioLabs N3013S) added at a 1:200 ratio to each sample. Libraries for Illumina-based sequencing were prepared with the Pico Methyl-Seq Library Prep Kit (Zymo Research) using Illumina TruSeq DNA methylation barcodes. Libraries were run on a High Sensitivity chip using an Agilent TapeStation 4200 to assess size distribution and overall quality of the amplified library. Fluorometric quantitation and TapeStation size distribution estimates permitted equimolar pooling, and 4-6 pooled libraries per run were sequenced on an Illumina NextSeq 500 instrument using the NextSeq 500/550 V2 High Output reagent kit (1 x 75 cycles).

tag: genotype

value: RISP WT

value: CD4+ YFP-Foxp3+ CD25+ Cells


title: DNA_METH_RISP_Chimera_KO2

value: RISP KO


title: DNA_METH_RISP_Chimera_KO4


title: DNA_METH_RISP_Chimera_KO1


title: RNA-seq_dCas9-KRAB_empty-3

source_name: embryonic stem cells


title: DNA_METH_RISP_Chimera_WT3


title: DNA_METH_RISP_Chimera_KO3


title: DNA_METH_RISP_KO2


title: DNA_METH_RISP_WT1


title: DNA_METH_RISP_WT2


title: DNA_METH_RISP_KO3


title: DNA_METH_RISP_Chimera_WT2


title: DNA_METH_RISP_Chimera_WT1


title: RNAseq_In_vitro_AntimycinA_2

data_processing:
Basecalls performed using bcl2fastq
RNA-seq reads were aligned to the mm10 genome assembly using Tophat
Reads were counted on the exons of mm10 genes using htseq
Differential gene expression analysis was performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file including raw counts values for each sample

extract_protocol:
NEB kit
Cells were lysed with RLT Buffer from the Qiagen RNeasy Plus Mini kit (Qiagen). Cell lysates were stored at -80°C until RNA was extracted. RNA isolations were performed using Qiagen RNeasy Plus Micro/Mini kit (Qiagen) (Extended Data Fig. 5) or the AllPrep DNA/RNA Micro Kit (Qiagen) (Figure 3 and 4) following the manufacturer’s protocol with an additional on-column DNase treatment using the RNase-Free DNase Set (Qiagen). RNA quality and quantity were measured using Agilent 4200 Tapestation using the high-sensitivity RNA ScreenTape System.  (Agilent Technologies).
mRNA libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA, Inc) +Nextera XT DNA sample preparation kit (Illumina Inc) (Extended Data Fig. 5) or the NEBNext Ultra I RNA Library Prep Kit for Illumina with poly (A) mRNA selection (NEB Inc) (Figure 3,4).

tag: exposure

value: 1µM AntimycinA


title: RNAseq_In_vitro_AntimycinA_3


title: DNA_METH_RISP_WT3


title: RNAseq_In_vitro_AntimycinA_1


title: DNA_METH_RISP_KO1


title: RNAseq_In_vitro_3-NPA_3

value: 500µM 3-NPA


title: RNAseq_In_vitro_3-NPA_2


title: RNAseq_In_vitro_Piericidin_3

value: 1µM Piericidin


title: RNAseq_In_vitro_Piericidin_1


title: RNAseq_In_vitro_3-NPA_1


title: RNAseq_In_vitro_Piericidin_2


title: RNAseq_In_vitro_Untreated_1

value: Untreated


title: RNAseq_RISP_Chimera_KO4

description: htseq.all.counts_TREG-RISP-Chimera-KO-vs-WT.txt


title: RNAseq_RISP_Chimera_KO3


title: RNAseq_RISP_Chimera_KO1


title: RNAseq_RISP_Chimera_KO2


title: RNAseq_RISP_Chimera_WT4


title: RNAseq_RISP_Chimera_WT2


title: RNAseq_RISP_Chimera_WT1


title: RNAseq_RISP_KO1

extract_protocol:
Takara kit
Cells were lysed with RLT Buffer from the Qiagen RNeasy Plus Mini kit (Qiagen). Cell lysates were stored at -80°C until RNA was extracted. RNA isolations were performed using Qiagen RNeasy Plus Micro/Mini kit (Qiagen) (Extended Data Fig. 5) or the AllPrep DNA/RNA Micro Kit (Qiagen) (Figure 3 and 4) following the manufacturer’s protocol with an additional on-column DNase treatment using the RNase-Free DNase Set (Qiagen). RNA quality and quantity were measured using Agilent 4200 Tapestation using the high-sensitivity RNA ScreenTape System.  (Agilent Technologies).
mRNA libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA, Inc) +Nextera XT DNA sample preparation kit (Illumina Inc) (Extended Data Fig. 5) or the NEBNext Ultra I RNA Library Prep Kit for Illumina with poly (A) mRNA selection (NEB Inc) (Figure 3,4).


title: RNAseq_RISP_Chimera_WT3


title: RNAseq_RISP_WT4


title: RNAseq_RISP_KO3


title: RNAseq_RISP_KO4


title: RNAseq_RISP_WT1


title: RNAseq_RISP_WT2


title: RNAseq_RISP_KO2


title: RNAseq_RISP_WT3


title: BMP910StimSmad4KDE

city: New Orleans

first: Stryder

last: Meadows

state: LA

address: 6400 Freret

department: Cell and Molecular Biology

institute: Tulane University

description:
Smad4 bound DNA from BMP9/10 stimulated Ms1
bmp910stim2_peaks.xls

data_processing:
ChIP-Seq App on Illuminia BaseSpace: MACS2 to identify enriched regions and HOMER for motif discovery
Genome_build: mm10
Supplementary_files_format_and_content: MACS2-peaks

source_name: MS1 Cell line

growth_protocol: Cells were grown in DMEM with 10% FBS and 1% antibiotics/antimycotics.

extract_protocol:
ChIP was performed using Cell Signaling SimpleChIP Plus Sonication Kit and Smad4 antibody (Cell Signaling 46535).
TruSeq ChIP Library Preparation Kit (Illumina IP-202-1012)
10 ng starting material was used for library prep. DNA quantity was measured using Qubit DNA HS kit (Thermo 32851). Libraries were sequenced using NextSeq 500 High Output v2 kit. Library quality and quantity was assessed using Agilent DNA 1000 chip (Agilent 5067-1504) and Qubit DNA HS kit respectively

treatment_protocol: Cells were serum starved for 24 hours before addition of fresh media or 1 ng/mL BMP9/10 recombinant protein

tag: stimulation

value: Yes, BMP9/10 recombinant protein

tag: antibody for ip

value: SMAD4 (Cell Signaling)


title: RNAseq_In_vitro_Untreated_3


title: BMP910StimSmad4KDD


title: NonstimulatedSmad4IPB

description:
Smad4 bound DNA from unstimulated Ms1
UnstimUn_peaks.xls

value: No


title: RNAseq_In_vitro_Untreated_2


title: Lit40s56

data_processing:
Used Illumina BaseSpace RNA-Seq Alignment App
Used Illumina BaseSpace DESeq2 App
STAR Aligner
Genome_build: Mus Musculus/mm10
Supplementary_files_format_and_content: csv and .pdf

source_name: P7 Isolated Retinal Endothelial Cells

growth_protocol: Tamoixfen injections were given at postnatal day 1 to induce deletion of Smad4 from the endothelium. Pups were sacrified at P7 and retinas were collected and isolated.

extract_protocol:
RNA was extracted using Thermofisher GeneJet RNA Purification Kit (K0732).
Library was constructed using Illumina TruSeq RNA Library Preparation Kit v2 (RS-122-2001).

treatment_protocol: No treatment.

value: P7 Isolated Retinal Endothelial Cells

value: Mixed background- BL6/CD1


title: Lit40s12


title: Lit38s45


title: Lit38s12


title: NonstimulatedInputB

description:
Input DNA from unstimulated Ms1
UnstimUn_peaks.xls


title: NonstimulatedSmad4IPA


title: BMP910StimInputD

description:
Input DNA from BMP9/10 stimulated Ms1
bmp910stim2_peaks.xls


title: Lit38s37


title: Lit38s6


title: BMP910StimInputE


title: NonstimulatedInputA


title: ag120_1390G3_AG-VT+

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: Transcriptome of amplified cDNA of ag120 PGCLC, reconstituted day 6 hPGCLC with fetal ovarian somatic cells from E12.5 mice, culture day 120 on a Trans-well, sorted AG-VT+ population

data_processing:
All reads were processed with cutadapt v1.9.1 program to remove low quality bases and adaptor sequences.
Reads with 30 bases or longer were mapped onto human genome (GRCh38.p2/hg38) genome and ERCC spike-in RNA sequences with Tophat v2.0.11/Bowtie v1.1.2 program with options of “--bowtie1”, “--library-type fr-secondstrand” and  “--no-coverage-search”.
Mapped reads were subsequently processed with cufflinks v2.2.0 program with options of “--compatible-hits-norm”, “--no-length-correction”, “--library-type fr-secondstrand”, and “--max-mle-iterations 50000” for abundance estimation of genes expressions.
Genome_build: GRCh38.p2
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample.

source_name: AG-VT+ population of ag120 PGCLC, from 1390G3-526 iPSC

growth_protocol: 585B1 hiPSCs (XY) and 1390G3 hiPSCs (XX) were cultured with AK03N medium on iMatrix coated plate as reported previously (Sasaki and Yokobayashi et al., 2015).

extract_protocol:
The cells were pelleted down and snap frozen until use.  RNA samples were extracted with RNeasy kit following manufacturer's protocol.
For 3'-seq analysis, cDNA synthesis / amplification from RNA samples and library construction from the cDNAs were performed as described previously (Nakamura et al. 2015, NAR, 43, e60).

treatment_protocol:
The iMeLC induction was induced from iPSC cultured in above condition, passaged to fibronectin coated plate with Activin A (50 ng/ml), CHIR99021 (3µM) and Y27632 (10µM) in GMEM containing 15% KSR, and cultured for 44 to 48 hours.
Above iMeLCs were then dissociated and replated to low-adherent V-bottom plates to form aggregates with BMP4 (200 ng/ml), SCF (100 ng/ml), EGF (50 ng/ml), LIF(1000U/ml), and Y27632 (10µM) in GMEM containing 15% KSR for 4 or 6 days.
d6 PGCLC were dissociated and reaggregate with fetal ovarian somatic cells from E12.5 mouse. After for 2days of floating culture with Y27632 (10µM) in GMEM containing 15% KSR, the reconstituted ovary were transferred on  Transwell-COL culture inserts soaked in a alpha-MEM containing 10%FBS, 2-melcaptoethanol (55µM), L-ascorbic acid (150µM), until the harvest day.

tag: markers

value: DDX4-tdTomato, TFAP2C-EGFP


title: ag120_1390G3_AG+VT+

description: Transcriptome of amplified cDNA of ag120 PGCLC, reconstituted day 6 hPGCLC with fetal ovarian somatic cells from E12.5 mice, culture day 120 on a Trans-well, sorted AG+VT+ population

source_name: AG+VT+ population of ag120 PGCLC, from 1390G3-526 iPSC

tag: cell line


title: ag77_1390G3_AG+VT+

description: Transcriptome of amplified cDNA of ag77 PGCLC, reconstituted day 6 hPGCLC with fetal ovarian somatic cells from E12.5 mice, culture day 77 on a Trans-well, sorted AG+VT+ population

source_name: AG+VT+ population of ag77 PGCLC, from 1390G3-526 iPSC


title: ag120_1390G3_AG+/-VT+

description: Transcriptome of amplified cDNA of ag120 PGCLC, reconstituted day 6 hPGCLC with fetal ovarian somatic cells from E12.5 mice, culture day 120 on a Trans-well, sorted AG+VT+ and AG-VT+ population

source_name: AG+VT+ and AG-VT+ populations of ag120 PGCLC, from 1390G3-526 iPSC


title: ag77_2

description: Transcriptome of amplified cDNA of ag77 PGCLC, reconstituted day 6 hPGCLC with fetal ovarian somatic cells from E12.5 mice, culture day 77 on a Trans-well, sorted BTAG population, rep2

source_name: ag77 PGCLC, from 585 B1-868 iPSC

value: BLIMP1-tdTomato, TFAP2C-EGFP


title: ag77_1

description: Transcriptome of amplified cDNA of ag77 PGCLC, reconstituted day 6 hPGCLC with fetal ovarian somatic cells from E12.5 mice, culture day 77 on a Trans-well, sorted BTAG population, rep1

value: wild type


title: ag120_1390G3_AG+VT-_1

description: Transcriptome of amplified cDNA of ag120 PGCLC, reconstituted day 6 hPGCLC with fetal ovarian somatic cells from E12.5 mice, culture day 120 on a Trans-well, sorted AG+VT- population, rep1

source_name: AG+VT- population of ag120 PGCLC, from 1390G3-526 iPSC


title: ag120_1390G3_AG+VT-_2

description: Transcriptome of amplified cDNA of ag120 PGCLC, reconstituted day 6 hPGCLC with fetal ovarian somatic cells from E12.5 mice, culture day 120 on a Trans-well, sorted AG+VT- population, rep2


title: ag63_2

description: Transcriptome of amplified cDNA of ag63 PGCLC, reconstituted day 6 hPGCLC with fetal ovarian somatic cells from E12.5 mice, culture day 63 on a Trans-well, sorted BTAG population, rep2

source_name: ag63 PGCLC, from 585 B1-868 iPSC


title: ag35_1

description: Transcriptome of amplified cDNA of ag35 PGCLC, reconstituted day 6 hPGCLC with fetal ovarian somatic cells from E12.5 mice, culture day 35 on a Trans-well, sorted BTAG population, rep1

source_name: ag35 PGCLC, from 585 B1-868 iPSC


title: ag21_1

description: Transcriptome of amplified cDNA of ag21 PGCLC, reconstituted day 6 hPGCLC with fetal ovarian somatic cells from E12.5 mice, culture day 21 on a Trans-well, sorted BTAG population, rep1

source_name: ag21 PGCLC, from 585 B1-868 iPSC


title: ag35_2

description: Transcriptome of amplified cDNA of ag35 PGCLC, reconstituted day 6 hPGCLC with fetal ovarian somatic cells from E12.5 mice, culture day 35 on a Trans-well, sorted BTAG population, rep2


title: THP1_IRF8 [TS-7_S7]

city: Boston

first: Trevor

last: Siggers

state: MA

address: 24 Cummington Mall

department: Department of Biology

institute: Boston University

description:
IRF8 (2 biological replicates)
MACS2_IDR_IRF8.txt

data_processing:
fastq files for HiSeq 4000 reads were generated using the Illumina pipeline (1.8). NextSeq 500 data (IRF8 and associated Input) fastq files were generated and pre-processed by Illumina BaseSpace
reads not demonstrating a minimal quality level (at least 60% of the read must have PHRED score of at least 20) were filtered prior to mapping using the fastx-toolkit (fastq_quality_filter -q 20 -p 60)
filtered reads were mapped to the reference genome (hg19) using bowtie2 (default parameters, --local)
mapped reads were filtered for high-quality, uniquely mappable reads using samtools (samtools view -b -F 1548 -q 30)
peaks were called on both biological replicates separately using MACS2 with relaxed parameters (-p 1e-3)
transcription factor peaks (PU.1, C/EBPa, IRF8) were then filtered for stringent reproducibility across biological replicates (IDR < 0.01) using IDR and used to design the nextPBM microarray. Peaks shared across the punctate histone mark (H3K4me1 and H3K27ac) replicates were also used
Genome_build: hg19
Supplementary_files_format_and_content: bigWig, narrowPeak (relaxed parameters from MACS2), bed (cross-replicate IDR format)

source_name: THP-1 cell line

growth_protocol: THP-1 cells were purchased from ATCC (cat # TIB-202) and cultured in RPMI 1640 media with 10% FBS supplemented by 50 unit/ml Penicillin and 50ug/ml Streptomycin

extract_protocol:
Soluble-chromatin was prepared from 40,000,000 THP-1 cells according to previously described protocols with some modifications (outlined below). Briefly, cells were crosslinked with 1% formaldehyde (final concentration) (Fisher Scientific, cat # F79-500) for 10 minutes at room temperature with gentle shaking. Crosslinking was stopped by adding 125 mM final concentration of glycine solution in PBS . Fixed cells were pelleted at 800xg for 5 minutes at 4˚Ϲ and washed twice with 10 ml of cold PBS in a 15 ml conical tube and pelleted at 800xg for 5 minutes at 4˚Ϲ.  Washed cell pellet was re-suspended in 10 ml of Lysis Buffer 133, nutated for 10 minutes at 4˚Ϲ,  and pelleted at 2000xg for 5 minutes at 4˚Ϲ. The same procedure was repeated with Lysis Buffer 233 at room temperature followed by pelleting at 2000xg for 5 minutes at 4˚Ϲ. To release nuclei from hard-to-disrupt THP-1 membranes, cells were re-suspended in 10 ml of Lysis Buffer 333 and were shaken vigorously (225 rpm) at room temperature for 30 minutes. Cells then were passed through an 18-gauge needle (VWR, cat # BD305195) for 25 times using a 10ml syringe. Nuclei were pelleted at 3000xg for 20 minutes at 4˚Ϲ and re-suspended in 500 μl of Lysis Buffer 3 and then transferred into a 1.5 ml microfuge tube placed in Benchtop 1.5 ml Tube Cooler (Active Motif, cat # 53076).  The nuclei were sonicated using Active Motif Q120AM sonicator with a 3.2 mm Probe (Active motif cat # 53053) at 25% amplitude for 15 minutes with 20 seconds ON and 30 seconds OFF cycles (45 cycles total). Cell-debris was pelleted at 21,000xg for 30 minutes at 4˚Ϲ. 50 μl of the combined soluble-chromatin was saved to be used as the input DNA upon reverse-crosslinking. For immunoprecipitation, 500 μl of the soluble chromatin was mixed with 30 μg of either PU.1, C/EBPα, H3K4me or H3K27ac antibodies (60 μg of IRF8 antibody was mixed with 1 ml of the soluble chromatin), and a tubes were rotated at 25 rpm for one hour at 4˚Ϲ using HulaMixer (ThermoFisher Scientific cat # 15920). 125 μl of the protein A Dynabead slurry (ThermoFisher Scientific cat # 10001D) per each rabbit antibody (PU.1. C/EBPα, H3K4me or H3K27ac), and 250 μl of the protein G Dynabead slurry (ThermoFisher Scientific cat # 10003D) for the goat-IRF8 antibody, were transferred into 1.5 ml microfuges and placed on DynaMag magnet (ThermoFisher Scientific, cat # 12321D) until all beads collected on the side of tubes. The solution was gently aspirated off from each tube and then the rack was removed from the magnet and beads were re-suspended in 1 ml of the Lysis Buffer 3 with several gentle inversions and then the rack was put back on the magnet and the buffer was aspirated off after all beads were collected on the side of the tube. Each bead then re-suspended in 50 μl of Lysis Buffer 3 and were added to the corresponding tube and returned to HulaMixer to rotate at 35 rpm for over-night at 4˚Ϲ. Dynabeads were collected with placing the tubes in the magnet. Beads were washed for 6 times with 1 ml of the Lysis Buffer 3 and two times with 1 ml of the Wash Buffer (RIPA). All ChIP samples along with the 50 μl of the soluble-chromatin were reverse-crosslinked by adding 200 μl of the Elution buffer and 3 μl of 20 mg/ml Proteinase K (ThermoFisher Scientific, cat # AM2546) and incubated at 65˚Ϲ for over-night. Beads were collected by magnets and the solutions were transferred into a new 1.5 microfuges containing 1 μl of 10 mg/ml RNase A (ThermoFisher Scientific, cat # EN0531) and left at room temperature for an hour. The ChIP and input DNA were purified using QIAquick PCR Purification Kit (QIAGEN, cat # 28104) and eluted in 50 μl of 50˚Ϲ Nuclease-Free Water (Thermo Fisher Scientific, AM9932). The concentration and size distribution of the ChIP-DNA samples were defined using Agilent 2100 Bioanalyser
DNA libraries were prepared using NEBNext Ultr II DNA Library Prep kit (NEB, E7645S) following the provider’s instruction manual. Amplified libraries were Bioanalyzed again to check the size selection efficiency and to define the concentrations of libraries before preparing the library pool involving the same molarity of each library

treatment_protocol: untreated

value: untreated monocytes

value: IRF8 (Santa Cruz sc-6058x)


title: ag7_2

description: Transcriptome of amplified cDNA of ag7 PGCLC, reconstituted day 6 hPGCLC with fetal ovarian somatic cells from E12.5 mice, culture day 7 on a Trans-well, sorted BTAG population, rep2

source_name: ag7 PGCLC, from 585 B1-868 iPSC


title: ag49

description: Transcriptome of amplified cDNA of ag49 PGCLC, reconstituted day 6 hPGCLC with fetal ovarian somatic cells from E12.5 mice, culture day 49 on a Trans-well, sorted BTAG population

source_name: ag49 PGCLC, from 585 B1-868 iPSC


title: ag21_2

description: Transcriptome of amplified cDNA of ag21 PGCLC, reconstituted day 6 hPGCLC with fetal ovarian somatic cells from E12.5 mice, culture day 21 on a Trans-well, sorted BTAG population, rep2


title: ag7_1

description: Transcriptome of amplified cDNA of ag7 PGCLC, reconstituted day 6 hPGCLC with fetal ovarian somatic cells from E12.5 mice, culture day 7 on a Trans-well, sorted BTAG population, rep1


title: iMeLC_3

description: Transcriptome of amplified cDNA of iMeLC induced from 585B1-868 iPSC, non-sorted, rep3

source_name: iMeLC, from 585B1-868 hiPSC line


title: THP1_INPUT [TS-6_S6]

description: Input DNA (3 biological replicates)


title: ag63_1

description: Transcriptome of amplified cDNA of ag63 PGCLC, reconstituted day 6 hPGCLC with fetal ovarian somatic cells from E12.5 mice, culture day 63 on a Trans-well, sorted BTAG population, rep1


title: iMeLC_1

description: Transcriptome of amplified cDNA of iMeLC induced from 585B1-868 iPSC, non-sorted, rep1


title: iPSC_2

description: Transcriptome of amplified cDNA of 585B1-868 iPSC, non-sorted, rep2

source_name: iPSC, from 585B1-868 hiPSC line


title: iPSC_1

description: Transcriptome of amplified cDNA of 585B1-868 iPSC, non-sorted, rep1


title: iPSC_3

description: Transcriptome of amplified cDNA of 585B1-868 iPSC, non-sorted, rep3


title: ag77_1390G3_AG+VT-

description: Transcriptome of amplified cDNA of ag77 PGCLC, reconstituted day 6 hPGCLC with fetal ovarian somatic cells from E12.5 mice, culture day 77 on a Trans-well, sorted AG+VT- population

source_name: AG+VT- population of ag77 PGCLC, from 1390G3-526 iPSC


title: THP-1 8h after 1,25D treatment, 2nd replicate H3K4me3

description: H3K4me3 8 VD N2

source_name: Culture


title: HC OA microRNA

city: Kaohsiung

first: Yi-Jen

last: Chen

address: 100, Shih-Chuan 1st Road

department: Graduate Institute of Clinical Medicine, College of Medicine

country: Taiwan

institute: Kaohsiung Medical University

description: Sample 4

data_processing:
Sequencing data was processed with the Illumina software
Initially, the sequences generated went through a filtering process to obtain qualified reads. Trimmomatic was implemented to trim or remove the reads according to the quality score.
Qualified reads were analyzed using miRDeep2 to clip the 3' adapter sequence and discarding reads shorter than 17 nucleotides
Only reads that mapped perfectly to the human genome five or less times were used for miRNA detection
Supplementary_files_format_and_content: excel files include gene ID, gene type, gene name, EntrezGene ID, locus and FPKM values for samples 1 and 2; miRNA, raw read counts and normalized values for samples 3 and 4.

source_name: Chondrocytes

growth_protocol: Chondrocytes were cultured in monolayer using chondrocyte growth medium and maintained in 37 °C incubator containing 5% CO2 until confluence.

extract_protocol:
total RNAs from HC and HC OA cells were extracted by Trizol Reagent according to the manufacturer’s instructions.
RNA library construction was carried out according to the manufacture’s protocol from Illumina, using Agilent's SureSelect Strand Specific RNA Library Preparation Kit for 75SE (Single-End or Paired-End) sequencing on Solexa platform.
Small RNA library construction and deep sequencing was carried out using Illumina sample preparation kit, according to the TruSeq Small RNA Sample Preparation Guide.

value: Cartilage

tag: gender

value: male

tag: diagnosis

value: osteoarthritis


title: HC OA mRNA

description: Sample 2

data_processing:
The sequence was directly determined using sequencing-by-synthesis technology via the TruSeq SBS Kit.
Raw sequences were obtained from the Illumina Pipeline software bcl2fastq v2.0
Trimmomatics was implemented to trim or remove the reads according to the quality score
Qualified reads were analyzed using TopHat/Cufflinks for gene expression estimation.
The gene expression level was calculated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
CummeRbund was employed to perform statistical analyses of gene expression profiles.
genome build: Human genome from Genome Reference Consortium Human GRCh38.p10
Supplementary_files_format_and_content: excel files include gene ID, gene type, gene name, EntrezGene ID, locus and FPKM values for samples 1 and 2; miRNA, raw read counts and normalized values for samples 3 and 4.

tag: age


title: HC microRNA

description: Sample 3

value: healthy


title: HC mRNA

description: Sample 1


title: iMeLC_2

description: Transcriptome of amplified cDNA of iMeLC induced from 585B1-868 iPSC, non-sorted, rep2


title: ckit3000

value: Bone Marrow

value: 20 weeks old


title: US-1622969: 43 4D mTeSR - 1

city: Seattle

first: Hannele

last: Ruohola-Baker

state: WA

address: 850 Republican Street

institute: Institute for Stem Cell and Regenerative Medicine

data_processing:
RNA-seq reads in fastq files were aligned to hg19 using Tophat (version 2.0.13).
Gene-level read counts were quantified using htseq-count 62 using Ensembl GRCh37 gene annotations.
FeatureCounts was used to do gene-level quantification.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file of gene-level read counts for each sample.

source_name: human dental pulp stem cell

growth_protocol: Dental pulp stem cells were isolated from human third molars or exfoliated deciduous teeth   from 300 patients ranging from 9 to 58 years old. Teeth were obtained from the University of Washington dental clinic after consent from the patient or legal guardian. This study was approved by the Human Subjects Division of the University of Washington (HSD#51634-EJ).  The teeth were stored in DMEM Glutamax® media (Gibco) with 10% Fetal Bovine serum (FBS) (VWR) solution immediately after tooth extraction. Each individual tooth was cut using a dremel at the cemento-enamel junction which exposed the pulp chamber. The pulp was then removed and minced into small pieces. The isolated pulp tissue underwent an enzymatic digestion with a solution of collagenase type I (92μM) (Sigma-Aldrich, 9001-12-1) and dispase (444μM) (Gibco, 17105-041) for an hour at 37°C with occasional vortexing. Digested pulp pieces were centrifuged to remove the enzyme solution and seeded into proliferation media containing DMEM Glutamax® media (Gibco), 10% FBS (Invitrogen), ascorbic acid (0.1mM) and 1X antibiotic antimycotic solution (Sigma-Aldrich) in a 35-mm cell culture plate. Pulp tissues from the deciduous teeth were isolated with the same protocol and seeded in proliferation media supplemented with insulin growth factor (IGF-1) to increase proliferation success. Once seeded, the pulp pieces were incubated at 37°C with 5% CO2 with media changed every 3 days until cells migrated out and optimal confluence was achieved. When the cells were ~70% confluent, they were trypsinized and passaged to allow expansion in a 10cm plate for cryopreservation or further experimentation. The passaged DPSCs were cultured and maintained in media containing 10% FBS and 1% Penicillin-Streptomycin (Invitrogen) in DMEM.

extract_protocol:
RNA was extracted using Trizol (Life Technologies) according to manufacturer’s instructions. RNA samples were treated with Turbo DNase (Thermo Fisher Scientific) and quantified using Nanodrop ND-1000. Reverse transcription was performed using iScript cDNA Synthesis Kit (Bio-Rad). 10 ng of cDNA was used to perform qRT-PCR using SYBR Green (Applied Biosystems) or TaqMan (Applied Biosystems) on a 7300 real time PCR system (Applied Biosystems). The PCR conditions were set up as the following: stage 1 50°C for 2mins, stage 2 as 95°C for 10mis, 95°C for 15sec, 60°C for 1min (40 Cycles). ß-actin was used as an endogenous control. The primer sequences used in this work are shown in Supplementary Table S5.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: DPSCs were cultred to specific passages (early v.s late) under the growth protocol described above

value: human dental pulp stem cell


title: US-1622982: 43 4D mTeSR - 3


title: US-1623017: LONZA MSC-3

source_name: human mesenchymal stem cell

value: human mesenchymal stem cell


title: Sox2 adenovirus infection rep2

city: Plymouth

first: Xinpeng

last: Dun

state: Devon

address: John Bull Building, Research Way

institute: University of Plymouth

description: Gene expression data from Sox2/GFP adenovirus infected Schwann cells

hyb_protocol: Hybridization was performed using 5 micrograms of biotinylated target, which was incubated with the GeneChip® Rat Exon 1.0 ST array (Affymetrix) at 45 dergrees for 16 hours. After hybridization, non-specifically bound aterial was removed by washing and specifically bound target was detected using the GeneChip Hybridization, Wash and Stain kit, and the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix) and .CEL intensity files were produced using GeneChip Operating Software version 1.4 (Affymetrix).

data_processing: The Affymetrix data was analysed using the Affymetrix Power Tools (APT) software. Transcript expression values were normalised using robust multi array (RMA) normalisation and the p-values for each transcript were calculated using the Detection Above Background (DABG) algorithm which indicates whether a probe is significantly expressed or not in comparison to the background noise.

organism: Rattus norvegicus

label_protocol: Biotin-labeled targets for the microarray experiment were prepared using 1µg of total RNA. Ribosomal RNA was removed with the RiboMinus Human/Mouse Transcriptome Isolation kit (Invitrogen), and cDNA was synthesized using the GeneChip® WT (Whole Transcript) Sense Target Labeling and Control Reagents kit as described by the manufacturer (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Schwann cells cultured in Defined Medium

extract_protocol: RNA was purified with miRNeasy mini-kit (Qiagen, 217004) and on-column DNase digestion was also performed

treatment_protocol: Schwann cells infected with control GFP or Sox2/GFP adenovirus

value: Wistar

value: postnatal day 3 pups


title: Sox2 adenovirus infection rep1

source_name: Sox2/GFP adenovirus infected Schwann cells


title: GFP adenovirus infection rep2

description: Gene expression data from GFP adenovirus infected Schwann cells

source_name: GFP adenovirus infected Schwann cells


title: GFP adenovirus infection rep1


title: US-1623025: LONZA MSC-2


title: US-1622967: LONZA MSC-1


title: US-1622963: LONZA DPSC-3


title: 50_Vehicle_Vehicle_0mpk_IP

city: Cambridge

first: Radhika

last: Goenka

address: 200 Sidney St.

institute: Abbvie

data_processing:
FastQC was applied on raw fastq files to examine the sequence quality
STAR v2.52 reads aligner
Apply featureCounts  of the subread v1.5.0 package to generate read counts
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw reads counts data matrix by featureCounts

source_name: Vehicle IP with Intraperitoneal dosing route

extract_protocol: Illumina stranded RNA-seq workflow (TruSeq Stranded Total RNA Library Prep Kit) was used followed by sequencing using Illumina HiSeq 2500

tag: agent

value: Vehicle IP


title: Genomic DNA from adult human whole blood [C480329844]

city: Kansas City

first: Devin

middle: Charles

last: Koestler

state: KS

address: 3901 Rainbow Boulevard

department: Biostatistics

institute: The University of Kansas Cancer Center

description: DNA methylation profiling of adult human whole blood (WB)

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: The methylation signal intensities were generated with minfi Bioconductor package. Functional normalization (e.g., Funnorm) was applied to normalized the between array technical variation. Poor quality samples and probes were excluded based on their detection p-values. The SNP-associated (reported SNPs at the queried CpG site and at the single-base extension (SBE) site) and cross-reactive CpGs were also removed. As we observed statistically significant association between beadchip and the first principal component, we conducted batch-effect correction using ComBat (implemented using the ComBat() function in the sva Bioconductor package).

source_name: Adult human whole blood

label_protocol: Standard Illumina Protocol

growth_protocol: Not applicable

extract_protocol: DNA extraction was conducted from buffy coats using QIAamp Blood Mini Kit

treatment_protocol: Not applicable

tag: individual id

tag: year of collection

tag: nk

tag: bcell

tag: mono

tag: gran


title: Genomic DNA from adult human whole blood [C480329290]


title: 67_Vehicle_Vehicle_0mpk_IP


title: US-1622978: LONZA DPSC-2

tag: tissue


title: Genomic DNA from adult human whole blood [C480331606]


title: Genomic DNA from adult human whole blood [C480337092]


title: Genomic DNA from adult human whole blood [C480340071]


title: 59_Vehicle_Vehicle_0mpk_IP


title: Genomic DNA from adult human whole blood [C480335884]


title: Genomic DNA from adult human whole blood [C480341833]


title: Genomic DNA from adult human whole blood [C480327419]


title: Genomic DNA from adult human whole blood [C480342487]


title: US-1622962: LONZA DPSC-1


title: Genomic DNA from adult human whole blood [C480345457]


title: Genomic DNA from adult human whole blood [C480326865]


title: Genomic DNA from adult human whole blood [C480333468]


title: Genomic DNA from adult human whole blood [C480346011]


title: Genomic DNA from adult human whole blood [C480332260]


title: Genomic DNA from adult human whole blood [C480330498]


title: Genomic DNA from adult human whole blood [C480331052]


title: 49_Vehicle_Vehicle_0mpk_IP


title: Genomic DNA from adult human whole blood [C480337646]


title: US-1622965: 45-3


title: Genomic DNA from adult human whole blood [C480328073]


title: Genomic DNA from adult human whole blood [C480338209]


title: 51_Vehicle_Vehicle_0mpk_PO

source_name: Vehicle PO with per os dosing route

value: Vehicle PO


title: US-1622950: 45-2


title: 4_Vehicle_Vehicle_0mpk_PO


title: Genomic DNA from adult human whole blood [C480332814]


title: US-1622946: 45-1


title: Genomic DNA from adult human whole blood [C480328636]


title: Genomic DNA from adult human whole blood [C480350298]


title: 33_Vehicle_Vehicle_0mpk_PO


title: Genomic DNA from adult human whole blood [C480344249]


title: Genomic DNA from adult human whole blood [C480341279]


title: US-1622941: 44-1


title: 27_Vehicle_Vehicle_0mpk_PO


title: Genomic DNA from adult human whole blood [C480325003]


title: 61_IL-23_Vehicle_0mpk_IP

source_name: IL-23 Vehicle with Intraperitoneal dosing route

value: IL-23 Vehicle IP


title: US-1623003: 43-2


title: Genomic DNA from adult human whole blood [C480325657]


title: US-1623022: 43-1


title: Genomic DNA from adult human whole blood [C480326211]


title: 31_IL-23_Vehicle_0mpk_IP


title: 28_IL-23_Vehicle_0mpk_IP


title: Genomic DNA from adult human whole blood [C480348436]


title: RCH-ACV ctrl repl. 3

city: Tampere

first: Saara

last: Laukkanen

address: Arvo Ylpön Katu 34

institute: University of Tampere

description:
RA_raw_read_counts
RCH-ACV_CTRL_3

data_processing:
The samples were sequenced with Illumina HiSeq 2500 instrument using Truseq v2 Rapid sequencing chemistry. The samples were normalized and pooled for the automated onboard cluster preparation in HiSeq 2500. The 18 libraries were pooled into one pool and run in 2 lanes. Single-read sequencing with 1 x 50 bp read length was used, followed by 8 + 8 bp dual index run. The base calling was performed using Illumina's standard bcl2fastq2 software, automatic adapter trimming was used.
The quality of the raw sequencing reads was ensured with FastQC (v0.10.1) and reads were quality filtered using FASTX Toolkit (0.0.14) (-q 15 -p 93,3).
Reads were mapped to human reference genome version hg19 using STAR aligner software (2.5.3a modified) and reads aligning to more than two locations were discarded
The alignment file was turned into tag directories and raw read counts were calculated using HOMER tool kit (v4.8).
Genome_build: hg19
Supplementary_files_format_and_content: raw counts of sequencing reads for the features of interest

source_name: RCH-ACV cell line

growth_protocol: Cells were cultured in RPMI (Gibco, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 2 mM L-glut, 100 U penicillin, 100 ug/ml streptomycin and 10% FBS (Gibco).

extract_protocol:
Total RNA extraction was performed with PureLink™ RNA Mini Kit and On-Column PureLink® DNase Treatment Protocol was used to avoid contamination by genomic DNA (Ambion® by Life Technologies and Invitrogen). The quality of the total RNA samples was ensured with Advanced Analytical Fragment Analyzer.
Library preparation was done according to Illumina TruSeq® Stranded mRNA Sample Preparation Guide (part # 15031047) (Illumina, San Diego, CA, USA). The high quality of the libraries was confirmed with Advanced Analytical Fragment Analyzer and the concentrations of the libraries were quantified with Qubit® Fluorometric Quantitation (Life Technologies). Good quality libraries were exclusively selected and sequenced.

treatment_protocol: Cells were transfected with 300nM of either SOX11 specific or non-specific control siRNA (SR30005, OriGene, Rockville, MD, USA) using 4D-Nucleofector™ (Lonza, Basel, Switzerland). Total RNA samples were harvested 48h hours after transfection.

tag: sirna

value: CTRL

tag: replicate

value: RCH-ACV cell line

tag: cell type

value: B-ALL cells


title: RCH-ACV ctrl repl. 2

description:
RA_raw_read_counts
RCH-ACV_CTRL_2


title: 26_IL-23_Vehicle_0mpk_PO

source_name: IL-23 Vehicle with per os dosing route

value: IL-23 Vehicle PO


title: Genomic DNA from adult human whole blood [C480343041]


title: RCH-ACV ctrl repl. 1

description:
RA_raw_read_counts
RCH-ACV_CTRL_1


title: 68_IL-23_Vehicle_0mpk_PO


title: Genomic DNA from adult human whole blood [C480324449]


title: Genomic DNA from adult human whole blood [C480334022]