title: Long-term PD_Peritoneal cells from patient 28

city: Praha 4

first: Petra

last: Hruba

address: Videnska 1958

department: Transplant Laboratory

country: Czech Republic

institute: Institute for Clinical and Experimental Medicine

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_28

hyb_protocol: For all samples a total of 950 ng of labeled cRNA was hybridized at 58°C for 17 hours to the Illumina HumanHT-12 v4.0 Expression BeadChips (Illumina) and subsequently washed.

scan_protocol: Fluorescence signals of the hybridized IlLumina Microarrays were detected using BeadStation 500 instrument (Illumina Inc). The raw data were extracted with the BeadStudio Data Analysis Software (Illumina).

data_processing: Bead level data were summarized by Illumina BeadStudio Software v3, imported into R and normalized using the quantile method in the Lumi package. Only probes with detectable signal intensity in at least five samples were filtered. Thus matrix contains only these filtered probes.

source_name: peritoneal cells

label_protocol: RNA was amplified and biotinylated  for hybridization using Ambion® Illumina® TotalPrep™ RNA Amplification Kit according to manufacturer´s instructions. For all samples 300 ng of total RNA was used for amplification. Yields of labeled cRNA were determined using the Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer (Agilent Technologies).

extract_protocol: Peritoneal effluent of the long-dwell (median 9, range 8-13 hours) was centrifuged to obtain peritoneal cells. Peritoneal cells were stored in RNA lysis buffer at -20°C untill analysis. Total RNA was isolated from peritoneal cells using the RNeasy Micro Kit (Qiagen, Hilden, Germany) according to manufacturer´s instructions.

treatment_protocol: Transcriptome of peritoneal cells in patients with long- and short- tem peritoneal dialysis was compared  using microarrays.

tag: patient id

tag: time (peritoneal dialysis)

value: long-term

value: peritoneal cells


title: IPF769_R4_T8h_TGFB

status: Public on Jan 24 2019

type: RNA

city: Allschwil

first: Axel

last: Klenk

address: Hegenheimermattweg 91

department: Research Informatics

country: Switzerland

institute: Idorsia Pharmaceuticals Ltd.

hyb_protocol: a pool of 300 ng of Cy3 labeled aRNA (examined sample) and 300 ng of Cy5 labeled aRNA rat reference (Agilent, Austin TX, USA) were hybridized using the Agilent Hybridization kit (Agilent, Austin TX, USA) according to the manufacturer's instructions. Hybridization was performed for 17 hours and washed according to Agilent's instructions.

scan_protocol: Scanned on an Agilent G2505B scanner using Agilent scan control (version 8.5.1) Images were quantified using Agilent Feature Extraction Software (version 11.5.5.1).

data_processing: BioConductor package vsn was used for variance-stabilizing normalization and glog transformation

molecule: total RNA

organism: Homo sapiens

label_protocol: 100 ng of totRNA were labeled using the Low Input Quick Amp Labeling kit (Agilent, Austin TX, USA) following the manufacturer's instructions.

extract_protocol: total RNA extracted  using MagMAX-96 for microarrays kit (Life technologies, Foster City CA, USA ) following the manufacturer's instructions

tag: cell line

tag: treatment

value: TGFB

tag: timepoint

source_name: Stratagene Reference

tag: tissue

value: Pool of 10 human cell lines


title: Short-term PD_Peritoneal cells from patient 33

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_33

value: short-term

tag: cell type


title: Short-term PD_Peritoneal cells from patient 27

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_27


title: HIP_UCMS1_S1

type: SRA

city: Guildford

first: Emma

last: Laing

address: Stag Hill

country: United Kingdom

institute: University of Surrey

library_source: transcriptomic

data_processing:
Quality control (QC) of sequencing reads, read alignment and feature quantification were performed using a RNA-Seq workflow developed by Eli Lilly and Company.
FASTQ files were checked for integrity and potential transfer errors prior to QC. QC was performed on both pre-aligned reads (base quality, base composition, heterologous organisms, rRNA/mitochondrial/viral and adaptor content) and post-alignment.
Location type count summary, template length, species, DNA genotype/RNA genotype match, sample relatedness/intermixing, and 3’-bias were assessed. No samples were excluded from the alignment analysis based on these QC measures.
Alignment of reads was performed against the genome of the Mus musculus strain C57BL/6J (assembly GRCm38.p4) with GSNPA.
Feature quantification was performed at the exon level and a counting algorithm using the NCBI-based gene models. Exons defined by these gene models served as the base feature to which counts are attributed. Count data were subsequently normalized at the gene level.
Data were normalized using Robust Linear Model (RLM) and quartile normalization (75% quartile; QM) following visual inspection of the distribution curves.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: comma-delimited text files (csv) include read counts for each Sample (one file per tissue)

organism: Mus musculus

source_name: Brain

extract_protocol:
Tissues were collected 14-16 hours after the last stress exposure (between ZT12.5 and ZT14.5). Brain tissues were immediately immersed in RNAlater® (Sigma-Aldrich) and stored at -20°C, while trunk blood was collected in RNAprotect Animal Blood tubes (Qiagen). Total RNA was extracted from dissected brain tissue using the RNeasy® Fibrous Tissue Mini Kit (Qiagen), and from whole blood samples using the RNeasy® Protect Animal Blood Kit (Qiagen).
RNA libraries were prepared using the NEBNext® rRNA Depletion Kit and the NEBNext® Ultra Directional RNA library preparation kit with 100 ng of total RNA from each sample, according to manufacturer's protocols.

treatment_protocol: Mice were subjected to a 9-week paradigm of Unpredictable Chronic Mild Stress (UCMS), a model of major depressive disorder, while control animals remained unstressed.

tag: strain

value: BALB/c

tag: Sex

value: Male

tag: age

value: 28 weeks

tag: group

value: UCMS

value: Hippocampus


title: Short-term PD_Peritoneal cells from patient 31

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_31


title: IPF769_R1_T8h_TGFB


title: Short-term PD_Peritoneal cells from patient 30

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_30


title: Long-term PD_Peritoneal cells from patient 32

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_32


title: Short-term PD_Peritoneal cells from patient 29

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_29


title: Short-term PD_Peritoneal cells from patient 26

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_26


title: IPF769_R2_T8h_TGFB


title: Short-term PD_Peritoneal cells from patient 25

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_25


title: Short-term PD_Peritoneal cells from patient 24

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_24


title: Short-term PD_Peritoneal cells from patient 23

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_23


title: IPF769_R3_T8h_TGFB_ACT


title: HIP_Control8_C8

value: Control


title: HIP_Control7_C7


title: S. sclerotiorum 1980 grown in Minimum medium rep3

city: Castanet tolosan

first: Sylvain

last: Raffaele

address: 28 chemin de borde rouge

country: France

institute: INRAE

description:
Sample 6
HDX18

data_processing:
HiSeq control software 2.2.38 or 2.2.58, RTA 1.18.61.0 or RTA 1.18.64.0, Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genomes using the RNA-seq analysis function of the CLC genomics software with default settings.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using the RNA-seq analysis function of the CLC genomics software with default settings.
Genome_build: S. sclerotiorum version 2.0: https://www.ncbi.nlm.nih.gov/genome/487?genome_assembly_id=290987
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Sclerotinia sclerotiorum

source_name: 4-days old culture

growth_protocol: Samples1-6: S. sclerotiorum was grown in liquid potato dextrose medium (P6685 - Sigma) for 4 days at 24°C under shaking at 180 rpm. Cultures were filtered using vacuum and a fritted glass column protected with a doubled miracloth membrane and ground in liquid nitrogen.

extract_protocol:
The edge and center of developed mycelial colonies (15 to 30 mm diameter) was harvested and stored in liquid nitrogen. Samples were ground with metal beads (2.5 mm) in a Retschmill apparatus (24hertz for 2x1min) before solubilizing in 1mL Trizol reagent (ThermoFisher) and left for 5 min at RT. Chloroform (200 µL) was added and mixed thoroughly before incubating for 3 min at RT. After centrifugation at ~12,000g (4°C) for 15min, the upper aqueous phase was recovered and nucleic acids were precipitated by adding 2µL GlycoBlue (Ambion) and 500µL isopropanol (10 min at -20°C). After centrifugation at ~15,000g (4°C) for 15min, pellets were washed twice with 70% ethanol before drying and resuspended in RNAse-free water. To eliminate chloroform traces, water resuspended nucleic acids were further cleaned using an RNA extraction kit (Quiagen) following manufacturer’s instructions. Genomic DNA was removed by DNase treatment (TURBO DNase; Ambion) following manufacturer’s instructions. The quality and concentrations of RNAs preparations were assessed with an Agilent apparatus and chips (nano).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: S. sclerotiorum strain 1980 was subcultured on Potato Dextrose Agar plates at 22°C. For inoculations, a 5-mm wide agar plug containing actively growing S. sclerotiorum mycelium was placed at the center of a Petri dish or on the adaxial surface of leaves and plants. The border (ring of ~5mm wide) and center of colonies were collected with a scalpel and frozen in liquid nitrogen.

value: control

tag: culture medium

value: Minimum medium


title: S. sclerotiorum 1980 grown in Minimum medium rep2

description:
Sample 5
HDX17


title: HIP_Control5_C5


title: HIP_Control6_C6


title: IPF769_R2_T8h_ACT

value: ACT


title: HIP_Control4_C4


title: S. sclerotiorum 1980 grown in Minimum medium rep1

description:
Sample 4
HDX16


title: Long-term PD_Peritoneal cells from patient 22

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_22


title: IPF769_R3_T8h_ACT


title: PFC_UCMS8_BS2

value: Prefrontal cortex


title: HIP_Control1_C1


title: HIP_Control3_C3


title: PFC_UCMS7_S8


title: HIP_Control2_C2


title: PFC_UCMS6_S7


title: PFC_UCMS5_S5


title: PFC_UCMS3_S3


title: Short-term PD_Peritoneal cells from patient 19

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_19


title: PFC_UCMS2_S2


title: Short-term PD_Peritoneal cells from patient 21

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_21


title: Long-term PD_Peritoneal cells from patient 16

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_16


title: Long-term PD_Peritoneal cells from patient 14

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_14


title: Short-term PD_Peritoneal cells from patient 18

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_18


title: IPF769_R1_T8h_ACT


title: PFC_UCMS1_S1


title: Long-term PD_Peritoneal cells from patient 17

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_17


title: Short-term PD_Peritoneal cells from patient 20

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_20


title: PFC_UCMS4_S4


title: PFC_Control7_C7


title: Short-term PD_Peritoneal cells from patient 11

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_11


title: IPF769_R4_T8h_ACT


title: Long-term PD_Peritoneal cells from patient 13

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_13


title: Long-term PD_Peritoneal cells from patient 10

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_10


title: Short-term PD_Peritoneal cells from patient 12

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_12


title: Long-term PD_Peritoneal cells from patient 8

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_8


title: PFC_Control5_C5


title: Short-term PD_Peritoneal cells from patient 9

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_9


title: Short-term PD_Peritoneal cells from patient 5

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_5


title: PFC_Control6_C6


title: Long-term PD_Peritoneal cells from patient 7

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_7


title: Long-term PD_Peritoneal cells from patient 2

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_2


title: PFC_Control3_C3


title: Short-term PD_Peritoneal cells from patient 4

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_4


title: PFC_Control2_C2


title: Long-term PD_Peritoneal cells from patient 6

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_6


title: Long-term PD_Peritoneal cells from patient 15

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_15


title: PFC_Control1_C1


title: Short-term PD_Peritoneal cells from patient 1

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_1


title: Short-term PD_Peritoneal cells from patient 3

description:
RNA was extracted using RNeasy Micro Kit (QIAgen)
PRAGUE_3


title: D3 Bach2-WT replicate 1

city: Birmingham

first: Hui

last: Hu

state: ALABAMA

address: 845 19th Street South,BBRB Rm859

department: Microbiology

country: USA

institute: University of Alabama at Birmingham

data_processing:
Sequencing adapters were trimmed from reads using TrimGalore! (Babraham Bioinformatics).
Trimmed reads were aligned to Mm10 using STAR (Dobin 2013) and reads mapping to individual genes were counted using HTSeq-Count.
Raw read counts were normalized, and differential expression analyzed using DESeq2 (Love 2014).
Genome_build: Mm10
Supplementary_files_format_and_content: raw read counts of each genes for each samples

source_name: donor OT-II cells isolated from recipient spleen

extract_protocol:
For sample preparation, total RNA from purified naive Bach2-WT, naive Bach2-cKO,  day 3 Bach2-WT donor or day 3 Bach2-cKO donor cells from recipient mice spleen after NP-OVA/alum immunization was isolated with miRNeasy Mini Kit (QIAGEN). RNA quality was assessed with Agilent Bioanalyzer. Only samples with RNA-integrity numbers of ≥ 9.5 were used for further studies.
RNA was sent to La Jolla Institute functional genomics sequencing core for their standard library construction.

treatment_protocol: To circumvent any potential thymocyte development issue, we generated OT-IITgBach2f/fCre-ERT2+RosaYFP mice in which the conditional deletion of Bach2 alleles in OT-II T cells will be mediated by Cre recombinase expressed from the gene encoding a tamoxifen-sensitive estrogen receptor variant (Cre-ERT2), and Bach2-deleted OT-II cells will express yellow fluorescent protein (YFP) from the ubiquitously expressed Rosa26 locus. We sorted CD44lowYFP+ Bach2-deficient naïve OT-II (OT-II Bach2-cKO) or wild-type naïve OT-II (OT-II Bach2-WT) T cells from tamoxifen-treated OT-IITgBach2f/fCre-ERT2+RosaYFP mice or from control OT-IITgBach2f/fRosaYFP mice, respectively. Sorted cells were then transferred into lymphocytic choriomeningitis virus (LCMV) epitope gp66-77-specific (SMARTA) TCR transgenic recipient mice followed by immunization with NP-OVA in alum. SMARTA mice were used as recipients to reduce the competition between transferred donor OT-II T cells and host T cells in response to NP-OVA challenge. Naive OT-II Bach2-WT and naive OT-II Bach2-cKO, total donor OT-II Bach2-WT and OT-II Bach2-cKO cells were purified using BD FACSAria III.

tag: genotype

value: Spleen

value: OT-II

tag: time point

value: Day 3


title: D3 Bach2-cKO replicate 1


title: D3 Bach2-WT replicate 2


title: PFC_Control4_C4


title: D3 Bach2-cKO replicate 2


title: D0 Bach2-cKO replicate 2

source_name: naive CD4+ T cells isolated from spleen

value: Day 0


title: Donor3_24H_I

city: Baltimore

first: yang

last: song

state: MD

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

description: Gene expression data  in the present of immobilized IgG1 for 24 hours,replicate2

hyb_protocol: cDNA were hybridized for 16 hr on Illumina Human HT-12 v 4.0 Expression BeadChips

scan_protocol: The arrays were scanned in a 3000 7G scanner.

data_processing: Probe level analysis was performed on the illumina raw data (.idat files) with the limma quantile method implemented in the R package 'limma' to obtain a log2 expression value for each gene probe set.

label: biotin

source_name: Human natural killer cells

label_protocol: cDNA were prepared according to the standard Illumina protocol.

growth_protocol: Human natural killer cells were negatively selected from peripheral blood mononuclear cells.

extract_protocol: Total RNA was extracted following 4 or 24 hours of stimulation using a standard TRIzol-based extraction method and Direct-zol RNA Miniprep.

treatment_protocol: One day prior to NK cell stimulation, 96-well cell flat bottom culture plates were coated with human IgG1 (50 μg/ml) at 37°C. Wells were washed with PBS at least three times before experimentation. Isolated NK cells were stimulated for 4 or 24 hours in the presence or absence of immobilized IgG1 in AIM V media.

value: Human natural killer cells

value: immobilized IgG1

value: 24 Hours


title: D0 Bach2-WT replicate 2


title: Dlx1/2 -/- mutant LGE rep3

city: Shanghai

first: Guoping

last: Liu

address: 138 Yi Xue Yuan Road

country: China

institute: Fudan University

description:
E16-DLx-LGE3
Dlx1/2-/- mutant
processed data file: Processed_data_Dlx12_mut.txt

data_processing:
Illumina Casava1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome (version:GRCm38.p4) using Hisat2 (version:2.0.4).
Stringtie (version: 1.3.0) was used to count the read numbers mapped to each gene, and standardized the counts using TMM (Trimmed mean of M values).
edgeR was used to find the differential expression genes.
To identify most differentially expressed genes, we ranked genes according to their size and sequencing coverage normalized FPKM (fragments per kilo base of exon per million). The log2 fold changes of gene FPKM between two genotypes were tested statistically to determine whether an individual gene expression was altered significantly or not.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Processed_data_Dlx12_mut.txt: Tab-delimited text file includes FPKM values for each sample.

source_name: E16.5 LGE

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Cat#74106, QIAGEN) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: LGE from E16.5 WT mice and Dlx1/2 -/- mutant mice were dissected in ice-cold HBSS. These tissues were flash frozen in the nitrogen and then stored into -80 oC.

tag: strain/background

value: mixed genetic background (C57BL/6J, 129S6, CD1)

tag: genotype/variation

value: Dlx1/2 -/- mutant

value: LGE

tag: developmental stage

value: Embryonic day 16.5


title: Dlx1/2 -/- mutant LGE rep1

description:
E16-DLx-LGE1
Dlx1/2-/- mutant
processed data file: Processed_data_Dlx12_mut.txt


title: Donor3_4H_I

description: Gene expression data  in the present of immobilized IgG1 for 4 hours,replicate2

value: 4 Hours


title: Wild type LGE rep3

description:
XZJ-control-3
Wild type littermate
processed data file: Processed_data_Dlx12_mut.txt

value: wild type


title: Wild type LGE rep2

description:
XZJ-control-2
Wild type littermate
processed data file: Processed_data_Dlx12_mut.txt


title: D0 Bach2-cKO replicate 1


title: Wild type LGE rep1

description:
XZJ-control-1
Wild type littermate
processed data file: Processed_data_Dlx12_mut.txt


title: Pax6 mutant cortex rep1

description:
Pax6 mutant
processed data file: Pax6_Mutants_E16_Neocortex.txt

data_processing:
Illumina Casava1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome (version:GRCm38.p4) using TopHat (version:2.0.9).
Cufflinks (version:2.2.1) was used to count the read numbers mapped to each gene, and standardized the counts using TMM (Trimmed mean of M values).
edgeR was used to find the differential expression genes.
To identify most differentially expressed genes, we ranked genes according to their size and sequencing coverage normalized FPKM (fragments per kilo base of exon per million). The log2 fold changes of gene FPKM between two genotypes were tested statistically to determine whether an individual gene expression was altered significantly or not.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Pax6_Mutants_E16_Neocortex.txt: Tab-delimited text file includes FPKM values for each sample.

source_name: E16.5 cortex

treatment_protocol: Cortex from E16.5 WT mice and Pax6 sey/sey mutant mice were dissected in ice-cold HBSS. These tissues were flash frozen in the nitrogen and then stored into -80 oC.

value: Pax6 sey/sey mutant

value: brain cortex


title: D0 Bach2-WT replicate 1


title: Donor1_24H_M

description: Gene expression data  in the absence of immobilized IgG1 for 24 hours, replicate1

value: control


title: Donor1_24H_I

description: Gene expression data  in the present of immobilized IgG1 for 24 hours,replicate1


title: Pax6 mutant cortex rep2


title: Wild type cortex rep2

description:
Wild type littermate
processed data file: Pax6_Mutants_E16_Neocortex.txt


title: Donor3_4H_M

description: Gene expression data  in the absence of immobilized IgG1 for 4 hours, replicate2


title: Dlx1/2 -/- mutant LGE rep2

description:
E16-DLx-LGE2
Dlx1/2-/- mutant
processed data file: Processed_data_Dlx12_mut.txt


title: Donor3_24H_M

description: Gene expression data  in the absence of immobilized IgG1 for 24 hours, replicate2


title: Wild type cortex rep1


title: Donor1_4H_I

description: Gene expression data  in the present of immobilized IgG1 for 4 hours,replicate1


title: BPA group mRNA

city: Wuhan

first: Huimin

last: Li

address: 13th Hangkong Road

institute: Huazhong University of Science and Technology

data_processing:
Hiseq2500 platform was used to sequence mRNA in 6G depth. Clean reads were aligned to reference genome (mouse GRCm38/mm10) with STAR software. And StringTie and Cuffcompare were used for transcription assembly and novel transcription prediction.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: txt files including name, genome location, normalized counts, compared fold changes, P value, etc.

growth_protocol: GC-2 spd(ts) (ATCC # CRL-2196)were purchased from ATCC (Manassas, VA, USA) and cultured in DMEM high glucose medium (Hyclone, Logan, UT, USA), supplement with 10% fetal bovine serum (Sijiqing, Hangzhou, China) and 1% Penicillin-Streptomycin (Hyclone, Logan, UT, USA) at 37°C and 5% CO2.

extract_protocol:
Strand-specific library construction with TruSeq RNA LTPrep Kit (Illumina, San Diego, CA, USA).
Cells were harvested by Trizol and subject to convention RNA extraction procedures. And RNAs from the same sample were shared to three aliquot for the subsequent circRNA, miRNA and mRNA high-throughput sequencing. For circRNA sequencing, total RNA was depleted of rRNA and then linear RNAs by RNase R digestion.

treatment_protocol: After synchronized by cultured in DMEM without FBS for 12h, the cells were treated with BPA (Sigma-Aldrich, St.Louis, MO, USA) for 48h. BPA was dissolved in DMSO and diluted with complete medium to the 120 μM concentration before use. Cells treated with complete medium with 0.1% (v/v) DMSO were used as a control. The cells treated with 120 μM BPA and complete medium with 0.1% DMSO were harvested and subject to circRNA/miRNA/mRNA deep sequencing.

value: mouse spermatocyte derived cell line

value: 120μM BPA for 48 h

tag: molecule subtype

value: mRNA


title: Donor1_4H_M

description: Gene expression data  in the absence of immobilized IgG1 for 4 hours, replicate1


title: CON group mRNA

value: 0 μM BPA for 48 h


title: BPA group miRNA

data_processing:
Small RNA sequencing was performed on Hiseq2500 in 10M sequence depth. After adaptor trimming by FASTXToolkit (0.0.14), reads were aligned to the mouse genome (GRCm38/mm10) with Bowtie software (version 1.1.0).miRBase v21 and miRDeep2 were used to annotate or forecast new miRNAs respectively.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: txt files including name, genome location, normalized counts, compared fold changes, P value, etc.

extract_protocol:
Regular small RNA library preparation.
Cells were harvested by Trizol and subject to convention RNA extraction procedures. And RNAs from the same sample were shared to three aliquot for the subsequent circRNA, miRNA and mRNA high-throughput sequencing. For circRNA sequencing, total RNA was depleted of rRNA and then linear RNAs by RNase R digestion.

value: miRNA


title: CON group miRNA


title: Helios pos 5

city: Hamilton

first: Craig

last: Martens

state: MT

address: 903 S. 4th St

department: DIR

institute: NIAID

description:
HS132_normalized_counts.txt
Processed data file column: 9436

data_processing:
Illumina Casava1.8.2 software was used for basecalling
Reads were processed using fastx toolkit to trim for adapter and low quality bases and filter for low quality reads.
Processed reads were mapped to the Mus musculus  genome using hisat2 version 2.0.4
Reads mapping to genes were counted using htseq-count
Deseq2 was used to filter the genes based on raw counts prior to normalization.  Genes that had less than 10 counts total in the 10 samples were filtered out.
Gene normalization and differential expression analysis were performed using Deseq2 and a paired T-test
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab delimited text file containing deseq2 normalized values in a single matrix format.

source_name: Treg cells

extract_protocol:
RNA was extracted using Qiagen AllPrep DNA/RNA kit with an additional on-column Dnase I treatment
Total RNA libraries were prepared using theClontech SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian (Takara Bio)

value: Treg cells

tag: cell subpopulation

value: CD4+RFP+GFP+ (Helios+Treg)

tag: replicate


title: Helios neg 5

description:
HS132_normalized_counts.txt
Processed data file column: 9435

value: CD4+RFP+GFP- (Helios-Treg)


title: dGR 6h DEX_repeat1

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Arabidopsis Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.42.0).

organism: Arabidopsis thaliana

source_name: 4-day-old seedlings, transfered to DEX for 6h, harvested root tips

label_protocol: Purified total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: All seeds were surface sterilized in liquid bleach/EtOH mixture (25%/75%), sown on solid MS plates and vernalized for two days before growing at a constant temperature of 22°C in a growth room.

extract_protocol: Total RNA was isolated using Trizol-Chlorophorm extraction followed by clean-up using the RNeasy Plant Mini kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: 4-day-old seedlings were transferred to MS medium supplemented with dexamethasone (DEX) for the indicated time. Next, root meristems were harvested and used for total RNA extraction.

tag: treatment time (hrs)

tag: treatment

value: DEX

value: root meristems

tag: genetic background (ecotype)

tag: introduced construct

value: pRPS5A::TMO5:GR x pRPS5A::LHW:GR


title: Helios pos 4

description:
HS132_normalized_counts.txt
Processed data file column: 9434

tag: cell type


title: Helios neg 4

description:
HS132_normalized_counts.txt
Processed data file column: 9433


title: Helios pos 3

description:
HS132_normalized_counts.txt
Processed data file column: 9432


title: dGR 6h DEX_repeat2

tag: tissue


title: PFC_Control8_C8

tag: strain

value: BALB/c

tag: Sex

value: Male

tag: age

value: 28 weeks

value: Control

value: Prefrontal cortex


title: dGR 6h DEX_repeat3


title: dGR 5h DEX_repeat2

source_name: 4-day-old seedlings, transfered to DEX for 5h, harvested root tips


title: dGR 5h DEX_repeat3


title: dGR 3h DEX_repeat3

source_name: 4-day-old seedlings, transfered to DEX for 3h, harvested root tips


title: dGR 4h DEX_repeat3

source_name: 4-day-old seedlings, transfered to DEX for 4h, harvested root tips


title: Helios neg 3

description:
HS132_normalized_counts.txt
Processed data file column: 9431


title: dGR 5h DEX_repeat1


title: dGR 3h DEX_repeat2


title: dGR 4h DEX_repeat1


title: Helios neg 2

description:
HS132_normalized_counts.txt
Processed data file column: 9429


title: Helios pos 1

description:
HS132_normalized_counts.txt
Processed data file column: 9428


title: H6_2 [miRNA]

city: Beijing

first: Su-Ren

last: Chen

address: 1Beichen West Road, Chaoyang District

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Experiment Pipeline Steps for Small RNA Sequencing: 1) Filter small RNA: separate 18-30nt RNA segment by PAGE gel. 2) 3' adaptor ligation: link 5-adenylated, 3-blocked single-stranded DNA adapter to 3' end of selected small RNAs from step 1. 3) Reverse primer annealing: the RT primer is added to the solution from step 2, and is cross-linked to the 3' adapter of RNAs and excessive free 3' adapter. 4) 5' adaptor ligation: the 5' adaptor is linked to the 5' end of the product from step 3. The connection (5' adaptor) will be attached to the 5' end only, but it is not connected to the 3' adaptor or RT primer hybrid chain. This greatly reduces self-ligation. 5) Strand cDNA synthesis: reverse extend the RT primer in step 3 to synthetize strand cDNA. 6) PCR amplification: use high-ping polymerase to amplify cDNA, enrich cDNA with both 3' and 5' adaptor. 7) Library fragment selection: separate the PCR product of 100~120bp by PAGE gel to eliminate primer-dimer and other byproducts. 8) Library quantitative and pooling cyclization.
Bioinformatics Analysis Pipeline for Small RNA Sequencing: 1) Eliminate the low-quality reads, adaptors and other contaminants to get clean reads. 2) Summarize the length distribution of the clean tags, common and specific sequences between samples. 3) Annotate the clean tags into different categories. 4) Predict the novel miRNA. 5) Function annotation of known miRNAs.
Data Filtering: 1) Remove low quality tags. 2) Remove tags with 5' primer contaminants. 3) Remove tags without 3' primer. 4) Remove tags without insertion. 5) Remove tags with poly A. 6) Remove tags shorter than 18nt. 7) Summarize the length distribution of the clean tags. After filtering, the remaining tags are called 'clean tags' and stored in FASTQ format.
Reads Mapping: Bowtie2 : -q -L 16 --phred64 -p 6 cmsearch: --cpu 6 --noali
sRNA Classification: MiRbase > pirnabank > snoRNA(human/plant) > Rfam > other sRNA. sRNA Prediction: miRDeep2, Piano,
DEGseq: Fold Change >= 2 and Adjusted Pvalue <= 0.001
Genome_build: mm10
Supplementary_files_format_and_content: Including RPKM values for each sample

source_name: Mouse testicular peritubular myoid (PTM) cells

growth_protocol: The isolated PTM cells were cultured in DMEM/F12 containing 10% fetal bovine serum (FBS) at 37°C with 5% CO2.

extract_protocol:
Total RNA (including small RNA) was extracted from the NC, H1, and H6 PTM cells using TRNzol (Tiangen, Beijing, China).
Small RNA libraries were prepared for sequencing using standard BGI protocols.

treatment_protocol: Cell culture dishes of peritubular myoid cells were placed in 42℃ sterile water bath for 30 min and then put back in cell culture incubator. Cells were collected 1 hour and 6 hours after heat treatment.

value: heat 6hr after

tag: passage

value: Primary


title: Helios neg 1

description:
HS132_normalized_counts.txt
Processed data file column: 9427


title: Helios pos 2

description:
HS132_normalized_counts.txt
Processed data file column: 9430


title: dGR 2h DEX_repeat3

source_name: 4-day-old seedlings, transfered to DEX for 2h, harvested root tips


title: dGR 3h DEX_repeat1


title: IL-2C rep 3

city: Minneapolis

first: Sara

middle: Elizabeth

last: Hamilton Hart

state: MN

department: Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN

institute: University of Minnesota

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were aligned to mm10 with TopHat v. 2.0.13 using the parameters  -r 0 --mate-std-dev 135 and a gtf of RefSeq transcripts downloaded from the UCSC Table Browser (https://genome.ucsc.edu/cgi-bin/hgTables) on July 8, 2015.
FPKM and differential expression were calculated using Cufflinks v 2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files for each sample contain FPKM values, tab-delimited file for IL15C vs. IL2C contains differential expression results

extract_protocol:
RNA was isolated from sort-purified NK cells (NK1.1 + NKp46 + CD3 - CD1d tetramer - ) using a RNAeasy kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: NK cells

value: IL-2 cytokine complex


title: dGR 2h DEX_repeat2


title: dGR 1h DEX_repeat3

source_name: 4-day-old seedlings, transfered to DEX for 1h, harvested root tips


title: dGR 4h DEX_repeat2


title: dGR 1h DEX_repeat2


title: dGR 2h DEX_repeat1


title: IL-2C rep 1

source_name: sort-purified NK cells (NK1.1 + NKp46 + CD3 - CD1d tetramer - )


title: H1_2 [miRNA]

value: heat 1hr after

value: Mouse testicular peritubular myoid (PTM) cells


title: dGR 1h DEX_repeat1


title: dGR 30' DEX_repeat3

source_name: 4-day-old seedlings, transfered to DEX for 30', harvested root tips


title: H1_3 [miRNA]


title: dGR 30' DEX_repeat2


title: NC_3 [miRNA]


title: NC_2 [miRNA]


title: iHPC_donor2_d34_iMSC

type: genomic

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

description:
SAMPLE 8
iHPCs cultivated for additional 14 days on iMSCs in co culture medium after initial 20 days of differentiation

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium MethylationEPIC BeadChip using standard Infinium HD Methylation Assay protocol.

scan_protocol: Standard Infinium HD Methylation Assay protocol

data_processing: Initial analysis was performed by the Genomestudio 2010.3 (Modul M Version 1.8.5). Data were normalized with internal controls according to Illumina´s standard procedures. Methylation level at each locus was calculated with the GenomeStudio Methylation module as beta-value (ranging from 0 to 1). The number of beads per feature varies between chips and beta-values were calculated as average of at least three technical replica. The signal_intensities.txt contains ynmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

source_name: iPSC from bone marrow MSC

growth_protocol: For differentiation of induced pluripotent stem cells towards hematopoietic progenitor cells, iPSC colonies were harvested and aggregated into embryoid bodies (EBs), which were cultured in basal differentiation medium consisting of StemPro34 supplemented with 100 U/ml penicillin, 100 µg/ml streptomycin, 2 mM L glutamine (all Thermo Fisher Scientific), 0.4 mM monothioglycerol, and 50 µg/ml L ascorbic acid (all Sigma Aldrich, St. Louis, Missouri, USA). The following growth factors were added: 8 ng/ml bone morphogenic protein 4 (BMP4; day 0-4), 10 ng/ml human basic fibroblast growth factor (bFGF; day 1-6),10 ng/ml vascular endothelial growth factor (VEGF), 100 ng/ml interleukin 6 (IL 6), 25 ng/ml insulin like growth factor 1 (IGF1; all day 2-6), 100 ng/ml stem cell factor (SCF; day 2-20), 30 ng/ml interleukin 3 (IL-3), 20 ng/ml thrombopoietin (TPO) and 10 ng/ml fms-related tyrosine kinase 3 ligand (FLT3L; all day 4-20). BMP4, IL-3, IL 6 and SCF were purchased from Miltenyi Biotech GmbH, and all other cytokines from Peprotech (Hamburg, Germany). Between day 0 and day 7 cells were cultured in a 5 % O2 and 5 % CO2 atmosphere. On day 6 cells were moved to 0.1 % gelatin coated tissue culture plastic and on day 8 cultures were transferred to a 5 % CO2 and normoxia atmosphere. On day 20 the iHPCs were harvested for analysis or additional co-culture.    Mesenchymal stromal cells were isolated from bone marrow (caput femoris) of patients undergoing orthopedic surgery after written consent and the study was approved by the Ethic Committee of the Use of Human Subjects at the University of Aachen (permit number: EK128/09). iPSCs were generated from two MSC preparations with episomal plasmids. iPSCs were cultured on tissue culture plastic coated with vitronectin (0.5 mg/cm2) in StemMACS iPS-Brew XF (all Miltenyi Biotec GmbH, Bergisch Gladbach, Germany). Generation of iPSC-derived MSCs (iMSCs) was performed by switching to standard hPL medium and then passaged on 0.1 % gelatin-coated plates.  Mesenchymal stromal cells, iPSCs, and iMSCs were generated from the same two donors. MSCs and iMSCs were irradiated (30 Gy) and used as feeder layers at a density of 50,000 cells/cm2 on 0.1 % gelatin coated dishes. After differentiation, iHPCs were seeded at 50,000 cells/ml onto MSCs, iMSCs or tissue culture plastic StemSpan SFEM (Stemcell Technologies, Cologne, Germany) supplemented with 10 ng/ml fibroblast growth factor 1 (FGF-1), 10 ng/ml SCF, 10 ng/ml TPO (all purchased from Peprotech), and 1 % penicillin/streptomycin.

extract_protocol: Genomic DNA of iHPCs was harvested with the NucleoSpin Tissue kit (Macherey-Nagel, Düren, Germany).

tag: subject id

value: donor 2

value: Induced pluripotent stem cell derived hematopoietic progenitor cells

tag: co-culture

value: co-culture with syngenic induced pluripotent stem cell derived mesenchymal stem cells


title: dGR 0h DEX_repeat3

source_name: 4-day-old seedlings, transfered to DEX for 0h, harvested root tips

value: DEX


title: dGR 30' DEX_repeat1

value: root meristems


title: NC_1 [miRNA]


title: IL-2C rep 2


title: IL-15C rep 2

value: IL-15 cytokine complex


title: dGR 0h DEX_repeat1

value: pRPS5A::TMO5:GR x pRPS5A::LHW:GR


title: dGR 0h DEX_repeat2


title: MeJA2

city: Oldenburg

first: Sascha

last: Laubinger

address: Carl-von-Ossietzky-Str. 9-11

institute: University of Oldenburg

description: Replicate 2

data_processing:
Ribosomal and tRNA sequence filtering with Bowtie2  (version 2.2.9, parameters --fr --un-gz),  using unaligned forward and reverse reads later.
Aligning to A. thaliana genome to  expression data: TopHat2 (version 2.1.1, parameters: -p 10 -i 10 -I 1000 --library-type fr-secondstrand). Or BWA
Collecting unnormalized read counts from alignment with featureCounts (Subead package, version 1.5.2, parameters: -T 6  -F GTF -J -O -G ), using the Ensembl 34 annotation.
Running perl ../CIRI_v2.0.3/CIRI_v2.0.3.pl -I -F -A using the Ensemble 34 release reference files.
Genome_build: Arabidopsis thaliana: Ensembl Plants release 34(ftp://ftp.ensemblgenomes.org/pub/release-34/plants/) genome fasta and GTF files, for rRNA/tRNA filering:  Arabidopsis thaliana sequences from tRNA collections (http://gtrnadb2009.ucsc.edu/download/tRNAs/GtRNAdb-all-tRNAs.fa.gz),  Arabidopsis thaliana genes for 5.8S rRNA and 25S rRNA with 18S rRNA fragment (geneBank ID: X52320.1);  sequences from arabidopsis.org: AT2G01010.1 – 18SrRNA, AT2G01020 – 5.8sRNA, ATCG00920 – 16SrRNA, ATCG00950 – 23SrRNA, ATCG00960 – 4.5SrRNA, ATCG01160.1 – 5SrRNA, ATMG00020.1 – 26SrRNA
Supplementary_files_format_and_content: counts_all_e34.txt” oread count utput file from featureCounts, “*.ciri” output file reporting circRNA hits from CIRI2, SAF files for simplified annotation format, *.txt files decribing features of circRNA candidates

source_name: Methyl-jasmonate (MeJa) treated plant

growth_protocol: Plant material for RNA Seq library construction was coming from Arabidopsis thaliana Col-0 seeds. Sterilized seeds were sowed on 1 ⁄ 2 MS plates. For plant liquid cultures, 25 mg of sterilized seeds were stratified for 3 days in dark in a volume of 50 ml 1 ⁄ 2 MS medium in flasks. Plants were grown in flasks, shaking at 130 rpm under continuous light conditions.

extract_protocol:
RNA was extracted using RNeasy Plant Mini Kit (Qiagen) according to manufacturer’s instructions. 6 ug of extracted RNA were used for RiboZero treatment and subsequent purification using Clean and Concentrator Kit (). Additionally, all samples were treated with RNAse R (1 U per ug RNA) in order to enrich circular RNAs by depleting linear RNAs specifically followed by additional purification with Clean and Concentrator Kit.
Library preparation was performed with ScriptSeq TM v2 RNA-Seq Library Preparation Kit Protocol (Epicentre, Madison, WI 53719, US).

treatment_protocol: Sterilized seeds were sowed on 1 ⁄ 2 MS plates, and after 10 days continuous light conditions plants were treated with 80 uM methyl-jasmonate (MeJa), 1 mM salicylic acid (SA) and ethanol mock, respectively and were used for RNA Seq library construction.

value: whole plant

tag: ecotype

value: Methyl-jasmonate (MeJa)


title: MeJA3

description: Replicate 3


title: iHPC_donor2_d34_TCP

description:
SAMPLE 6
iHPCs cultivated for additional 14 days on tissue culture plastic in co culture medium after initial 20 days of differentiation

label_protocol: Standard Infinium HD Methylation Assay protocol

value: culture expansion without co-culture


title: MeJA1

description: Replicate 1


title: iHPC_donor1_d34_iMSC

description:
SAMPLE 4
iHPCs cultivated for additional 14 days on iMSCs in co culture medium after initial 20 days of differentiation

value: donor 1


title: H1_1 [miRNA]


title: SA2

description: Replicate 2

source_name: Salicylic acid (SA) treated plant

value: Salicylic acid (SA)


title: SA1

description: Replicate 1


title: IL-15C rep 1


title: iHPC_donor1_d20

description:
SAMPLE 1
iHPCs after 20 days of differentiation

value: no additional culture expansion


title: iHPC_donor2_d34_MSC

description:
SAMPLE 7
iHPCs cultivated for additional 14 days on MSCs in co culture medium after initial 20 days of differentiation

value: co-culture with syngenic bone marrow derived mesenchymal stem cells


title: Mock2

description: Replicate 2

source_name: Mock treated plant

value: Mock


title: serous-patient58-batch1-left-ear

city: Midlothian

first: Michael

last: Cheeseman

address: Easter Bush

department: Developmental Biology

institute: Roslin Institute

description:
Serous ear effusion, left ear, patient 58
58L

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on a HuGene-2_0-st. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner.

data_processing: CEL files were processed and normalized using AromaAffymetrix and a chip definition file provided by Brainarray (v19) and differentially expressed genes were found using limma with an adjusted P-value cut-off of 0.01 and a minimal difference of a factor 2 (ie absolute value of the log2 of the fold change equal or greater than 1). Full script available at https://github.com/gdevailly/oitis_array_analysis .

label_protocol: Labelled sense single-stranded DNA for hybridization was generated from 100 ng of RNA with the Affymetrix GeneChip WT PLUS Reagent Kit.

extract_protocol: Intracellular RNA from blood was isolated with PAXgene Blood RNA kit (PreAnalytiX, Qiagen) following manufacturer’s instructions and its quality was assessed using a bioanalyzer (Agilent Tecnologies). RNA from middle ear effusions was extracted using the NucleoSpin® kit (Macherey-Nagel) following manufacturer’s instructions. Due to the large volume of some effusions the initial volume of lysis buffer and β-mercaptoethanol was increased to 1 ml and the sample run through the tube through several rounds of centrifugation. Due to the larger sample volumes at this initial stage, flow-through was collected in 15 ml tubes. cDNA was generated following manufacturer’s instructions using a high capacity cDNA reverse transcriptase kit containing MultiScribe™ Reverse Transcriptase (Applied Biosystems).

value: serous

tag: batch

tag: patient


title: blood-patient58-batch1

description:
Whole blood RNA, patient 58
58+blood

source_name: Whole blood RNA, patient 58

value: blood


title: serous-patient58-batch1-right-ear

description:
Serous ear effusion, right ear, patient 58
58R


title: serous-patient53-batch1

description:
Serous ear effusion, left ear, patient 53
53L


title: Mock1

description: Replicate 1


title: EC-IL1b-IBET762, biological replicate-3

city: Pittsburgh

first: Vijay

last: Yechoor

state: PA

address: 200 Lothrop street,

department: Vascular Medicine Institute

institute: University of Pittsburgh

description: Time of treatments - 48h

hyb_protocol: Following fragmentation and end label, 2.4 ug of ss-cDNA were hybridized for 16 hr at 45C on GeneChip Human Clariom S. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner with 7G upgrade.

data_processing: The data were analyzed with Gene Expression Console using Gene level SST-RMA  with default settings.

label_protocol: Biotiny end labeled ss-cDNA were prepared according to  Affymetrix WT pico protocol from 4 ng total RNA (GeneChip WT pico Reagent kit P/N 703262 rev 4).

growth_protocol: HPAECs were cultured in endothelial cell growth medium from Lonza. All the experiments were done in the cells with passage number 4-8.

extract_protocol: Total RNA was isolated using Qiazol extraction method from Qiagen according to manufacturer's instructions.

treatment_protocol: The cells were treated with IL-1b (10ng/ml) either with vechicle control (DMSO) or I-BET762 (500nM) for 48 h in complete media.

value: Human pulmonary artery endothelial cells


title: 7.047

first: Lei

last: Zheng

state: Maryland

address: 1650 Orleans St; CRB1

department: Oncology

institute: Johns Hopkins University School of Medicine

data_processing:
The Human samples sequencing was done using Illumina HiSeqX platform. TruSeq RNA Access Library Prep Kit was used to perform RNA sequencing. cDNA is generated from the cleaved RNA fragments using random priming during first and second strand synthesis and sequencing adapters are ligated to the resulting double-stranded cDNA fragments. The coding regions of the transcriptome are then captured from this library using sequence-specific probes to create the final stranded RNA-Seq library.
Reads mapping to ribosomal and mitochondrial genome were removed before performing alignment.
After QC for fastq files, trim sequence read where necessary to only retain high quality sequence for further analysis. For the RNA-Seq analysis, remove the unwanted sequences, especially nonpolyA tailed RNAs from the sample. Contamination removal was performed using Bowtie2 (version - 2.2.4).
The paired-end reads are aligned to the reference human genome Feb. 2009 release downloaded from UCSC database (GRCh37/hg19). Alignment was performed using STAR (version - 2.4.1) 2-pass approach where splice junctions detected in a first alignment run are used to guide the final alignment.
The aligned reads are used for estimating expression of the genes. The raw read counts were estimated using HTSeq (version - 0.6.1). Read count data were normalized using DESeq2.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: raw and DESeq2-normalized read counts

source_name: pancreatic adenocarcinoma

extract_protocol:
Approximately 20, 5-mm sections of FFPE tissue from each subject were anonymized and stained with H&E immediately before the stroma were microdissected by a pathologist using a dissecting microscope. RNA was purified using the RecoverAll Total Nucleic Acid Isolation Kit for FFPE (Ambion) and amplified by the WT-Ovation FFPE System (NuGEN Technologies) as per the manufacturers’ protocols. RNA was quantified with NanoDrop ND-1000 followed by quality assessment with 2100 Bioanalyzer (Agilent Technologies) according to manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1 dose of GM-CSF expressing whole cell pancreatic vaccine (GVAX) 2 weeks prior to resection.

value: microdissected tumor stroma

tag: treamtment


title: 7.056

value: 1 dose of GM-CSF expressing whole cell pancreatic vaccine (GVAX) 2 weeks prior to resection


title: 7.022


title: blood-patient53-batch1

description:
Whole blood RNA, patient 53
53+blood

source_name: Whole blood RNA, patient 53


title: iHPC_donor1_d34_TCP

description:
SAMPLE 2
iHPCs cultivated for additional 14 days on tissue culture plastic in co culture medium after initial 20 days of differentiation

value: Induced pluripotent stem cell derived hematopoietic progenitor cells


title: mucoid-patient44-batch2

description:
Mucoid ear effusion, left ear, patient 44
E44L

value: mucoid


title: blood-patient44-batch2

description:
Whole blood RNA, patient 44
B44

source_name: Whole blood RNA, patient 44


title: EC-IL1b-IBET762, biological replicate-1

description: Time of treatments - 48h


title: iHPC_donor2_d20

description:
SAMPLE 5
iHPCs after 20 days of differentiation

value: donor 2


title: 7.036


title: iHPC_donor1_d34_MSC

description:
SAMPLE 3
iHPCs cultivated for additional 14 days on MSCs in co culture medium after initial 20 days of differentiation


title: IL-15C rep 3

value: NK cells

value: IL-15 cytokine complex


title: SA3

description: Replicate 3

value: whole plant


title: blood-patient41-batch2

description:
Whole blood RNA, patient 41
B41

source_name: Whole blood RNA, patient 41


title: EC-IL1b-VC, biological replicate-3

description: Time of treatments - 48h

source_name: HPAECs-IL1b-vehicle control


title: 7.03


title: EC-IL1b-VC, biological replicate-2

description: Time of treatments - 48h


title: EC-IL1b-VC, biological replicate-1

description: Time of treatments - 48h


title: 7.02


title: mucoid-patient38-batch2

description:
Mucoid ear effusion, left ear, patient 38
E38L


title: 7.019


title: EC-Un-I-BET762, biological replicate-3

description: Time of treatments - 48h


title: H6_3 [miRNA]

value: heat 6hr after

value: Mouse testicular peritubular myoid (PTM) cells

value: Primary


title: EC-Un-I-BET762, biological replicate-2

description: Time of treatments - 48h


title: 7.012


title: blood-patient38-batch2

description:
Whole blood RNA, patient 38
B38

source_name: Whole blood RNA, patient 38


title: EC-Un-I-BET762, biological replicate-1

description: Time of treatments - 48h


title: 7.027


title: mucoid-patient41-batch2

description:
Mucoid ear effusion, right ear, patient 41
E41R


title: EC-Un-VC, biological replicate-3

description: Time of treatments - 48h

source_name: HPAECs-unstimulated-vehicle control


title: EC-Un-VC, biological replicate-2

description: Time of treatments - 48h


title: 7.001


title: H6_1 [miRNA]

source_name: Mouse testicular peritubular myoid (PTM) cells


title: blood-patient25-batch2

description:
Whole blood RNA, patient 25
B25

source_name: Whole blood RNA, patient 25


title: serous-patient31-batch1

description:
Serous ear effusion, right ear, patient 31
31R


title: blood-patient37-batch1

description:
Whole blood RNA, patient 37
37+blood

source_name: Whole blood RNA, patient 37


title: mucoid-patient25-batch2

description:
Mucoid ear effusion, right ear, patient 25
E25R


title: 7.002


title: EC-Un-VC, biological replicate-1

description: Time of treatments - 48h


title: 7.011


title: blood-patient24-batch2

description:
Whole blood RNA, patient 24
B24

source_name: Whole blood RNA, patient 24


title: serous-patient37-batch1

description:
Serous ear effusion, right ear, patient 37
37R


title: Blood-B05-T52_2

status: Public on Jan 23 2019

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

country: Spain

institute: IDIBAPS

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

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: The data were analyzed with Bioconductor tools in R (http://www.r-project.org) using GC-RMA as normalization method. Next we employ a conservative probe-filtering step excluding those probe sets not reaching a log2 expression values of 5 in at least 1 sample.

source_name: Peripheral blood of Crohn's Disease patient collected at 52 weeks after HSCT

label_protocol: Biotin

extract_protocol: Total RNA was extracted by Rneasy Kit (Qiagen) according to the manufacturer's instructions.

value: Peripheral blood

tag: diagnosis

value: Crohn’s disease (CD)

tag: disease location

value: Colonic

tag: disease phenotype

value: Inflammatory

tag: timepoint

tag: response

value: Yes

tag: cdai

tag: ses-cd

tag: gender

value: Female


title: Blood-F09-T13_3

source_name: Peripheral blood of Crohn's Disease patient collected at 13 weeks after HSCT

tag: tissue


title: mucoid-patient5-batch2

description:
Mucoid ear effusion, right ear, patient 5
E5R


title: blood-patient8-batch1

description:
Whole blood RNA, patient 8
8+blood

source_name: Whole blood RNA, patient 8

value: blood


title: serous-patient8-batch1

description:
Serous ear effusion, right ear, patient 8
8R

value: serous


title: Blood-A09-T0_2

source_name: Peripheral blood of Crohn's Disease patient collected at baseline

tag: age


title: Blood-G09-T52_3

value: Fistulating


title: blood-patient5-batch2

description:
Whole blood RNA, patient 5
B5

source_name: Whole blood RNA, patient 5


title: blood-patient31-batch1

description:
Whole blood RNA, patient 31
31+blood

source_name: Whole blood RNA, patient 31


title: Blood-H05-T13_3


title: Blood-G07-T52_3


title: Blood-G05-T26_2

source_name: Peripheral blood of Crohn's Disease patient collected at 26 weeks after HSCT


title: Blood-F07-T26_3


title: 7.007

source_name: pancreatic adenocarcinoma

value: microdissected tumor stroma

value: 1 dose of GM-CSF expressing whole cell pancreatic vaccine (GVAX) 2 weeks prior to resection


title: Blood-F07-T0_1


title: Blood-E09-T26_2

value: Stenosing


title: Blood-H05-T0_2

value: Ileocolonic


title: Blood-C07-T13_3


title: mucoid-patient24-batch2

description:
Mucoid ear effusion, right ear, patient 24
E24R

value: mucoid


title: EC-IL1b-IBET762, biological replicate-2

description: Time of treatments - 48h

value: Human pulmonary artery endothelial cells


title: 7.044


title: Blood-G05-T0_1


title: Blood-G07-T13_1


title: Blood-C05-T0_3


title: Blood-B09-T13_3

value: No


title: Blood-H07-T26_3


title: G15FN-109-1

city: Saint Paul

first: Robert

middle: M

last: Stupar

address: 411 Borlaug Hall, 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

description: Fast-neutron mutant/ wild-type parent comparison

hyb_protocol: Arrays are hybridized at 67C for approximately 72 hours at a rotation speed of 20rpm. Arrays are washed in Wash Buffer 1 for 5 minutes at room temperature, Wash Buffer 2 for 1.5 minutes at 37C, followed by a 1minute wash in room temperature Acetonitrile. All other processing follow Agilent Protocol version 7.3 March 2014 entitled “Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis”.

scan_protocol: Arrays are immediately and individually scanned using Roche NimbleGen MS200 array scanner using NimbleGen MS200 v1.2 acquisition software. The array is inserted “active side up” with a Scan Resolution of 2micons, Gain at 100% for both channels, Laser Intensity at 100% for both channels, Autogain is deselected and a Multi Tiff File Setting.

data_processing: Image extraction and grid alignment is done using Agilent Feature Extraction (FE) 12.0.0.7.  The CGH module portion of Agilent Genomic Workbench (AWB) 7.0.4.0 software is used to generate data.  Analysis settings include: Aberration Algorithm is ADM-2, Threshold is 6.0, Fuzzy Zero is selected, GC correction is selected with a window size of 2 Kb, Legacy is selected with a bin size of 10, Diploid Peak is deselected, Manually Reassign Peaks is deselected and Combine Intra-Array Replicates is selected. The Aberration Filter is set to call amplification or deletion as having 2 consecutive probes with an absolute log ratio greater or equal to +/- 1.

organism: Glycine max

source_name: Fast neutron mutant individual G15FN-109-1

label_protocol: Individual reactions with 500ng of Soybean DNA are labeled with Cy3 and Cy5 following Agilent Protocol version 7.3 March 2014 entitled “Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis”.

extract_protocol: Soybean DNA is extracted from approximately 90 mg of fresh, young tissue disrupted with mortar and pestle and liquid nitrogen. The tissue is processed using Qiagen DNeasy Plant Mini Kit catalog number 69106. The Qiagen protocol is followed with 2 elution’s of DNA from the column using 60uL – 50% AE / 50% Water.

value: Leaf

tag: genotype/variation

value: Fast neutron mutant

value: wildtype


title: Blood-E09-T26_3

value: Peripheral blood

value: Crohn’s disease (CD)

value: Male


title: Blood-C07-T52_1

value: Inflammatory

value: Female


title: Blood-D07-T52_1

value: Yes


title: Blood-D05-T52_2


title: Blood-F09-T52_2

value: Fistulating


title: Blood-A07-T52_2


title: Blood-A07-T26_3


title: Blood-B07-T13_2


title: Blood-A07-T0_1


title: G15FN-12-1

source_name: Fast neutron mutant individual G15FN-12-1


title: Blood-D05-T0_1


title: Blood-E07-T0_1


title: G15FN-54-3

source_name: Fast neutron mutant individual G15FN-54-3


title: Blood-A05-T13_3


title: Blood-F09-T13_1


title: Blood-F05-T26_3


title: Blood-E05-T13_3


title: Mock3

description: Replicate 3

source_name: Mock treated plant

value: whole plant

tag: treatment

value: Mock


title: Blood-B09-T0_2


title: Blood-H09-T0_3


title: Blood-H05-T26_1

value: Colonic


title: Blood-D09-T13_2


title: Blood-E05-T0_2


title: Blood-A09-T52_3


title: G15FN-23-3

source_name: Fast neutron mutant individual G15FN-23-3


title: Blood-E09-T0_1


title: CD5

first: Yongjie

address: 1665 kongjiang road

institute: Xinhua Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw reads were cleaned by removing adapter sequences and low quality sequences (reads with over 5% undetermined base pairs‘N’). Then, the high quality reads were assembled using Trinity and further mapped to the human genome (hg19) using TopHat v2.0.11 with the default parameters.
Count files of the aligned sequencing reads were generated by the htseq-count script from the Python package HTSeq with union mode, using the GTF annotation file.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include counts for each Sample

source_name: cord blood

extract_protocol:
Total RNA was isolated using Trizol reagent
The purified mRNA was fragmented (200bp-300bp) using divalent cations under elevated temperature. These short fragments were copied into the first-strand cDNA using random hexamer primers and reverse transcriptase (Invitrogen, Carlsbad, CA, USA). Second-strand cDNA was synthesized with adding of DNA Polymerase I and RNase H. The products were then enriched by PCR amplification for 15 cycles, separated by Certified Low Range Ultra Agarose (Bio-Rad, USA) gel electrophoresis, and further analyzed for quality on an Agilent 2100 Bioanalyzer (Agilent technologies). The amplicons in the sizes of 300–400 bps were collected and purified.

treatment_protocol: The cord blood of newborns was collected into a sterilized heparin anticoagulant tube, and then centrifuged for the separation of leukocytes.

value: cord blood

tag: cell type

value: leukocytes

tag: developmental stage

value: newborn

tag: condition

value: cesarean delivery


title: VD5

value: vaginal delivery


title: CD2


title: CD3


title: VD4


title: VD8


title: VD7


title: VD2


title: CD6


title: VD3


title: Sample_2-R (SI)

city: Catania

first: Viviana

last: Cafiso

state: Italy

address: Via Santa Sofia,97

department: Biometec

country: Italy

institute: University of Catania

description:
SI_2R-2S vs ATCC.xlsx
SI_2R-2S vs ACICU.xlsx

data_processing:
Basecalls performed using CASAVA version 1.8.2
Raw reads quality has been checked using FastQC v0.11.2
Sequences were trimmed using Trimmomatic 0.32.  Minimum base quality 15 over a 4 bases sliding window was required. Only sequences with longer than 36 nucleotide were considered
Sequence mapping and quantification was performed using Rockhopper v2.0.2
Genome_build: Acinetobacter baumannii ATCC17978 and Acinetobacter baumannii  ACICU (NC_010611)
Supplementary_files_format_and_content: Excel files derived from Rockhopper include for both the COL-R/COL-S isogenic couple mRNAs: Trancription Start, Translation Start, Translation Stop, Transcription Stop, Strand, Name, Synonym, Product, Raw Counts, Normalized Count, RPKM, Expression, pValue and qValue.

organism: Acinetobacter baumannii

source_name: bronchial aspirate

extract_protocol:
A single colony was used to inoculate 7 ml of BHI liquid culture and incubated at 37 °C  for 24h. Total RNA was extracted with TRIzol reagent (Invitrogen) according to the manufacturer's protocol.
Sequencing libraries were prepared using the Illumina mRNA-seq sample preparation kit following  the supplier's instructions except that (a) total RNA was not fragmented and (b) double-stranded cDNA was size-selected (100 to 400 bp) to maximize the recovery of small RNAs. The prepared libraries were evaluated with the High sensitivity D1000 screen Tape (Agilent Tape Station 2200). The indexed libraries were quantified in triplicates with the ABI7900 qPCR instrument using the KAPA Library Quantification Kit, according to the manufacturer’s protocol (KapaBiosystems, Woburn, MA, USA). Five μL of the pooled library at a final concentration of 4 nM were used for sequencing using Illumina Miseq with a A single end stranded library with reads of 50bp. After sequence data generation, raw reads were processed using FastQC v0.11.2 to assess data quality. Reads were then trimmed using Trimmomatic v.0.33.2 to remove sequencing adapters for Single End reads, requiring a minimum base quality of 15 (Phred scale) and a minimum read length of 15 nucleotides. Only trimmed reads were included into downstream analysis.

value: Colistin resistant A.baumannii


title: CD1


title: CD7


title: Sample_1-S (SI)

description:
SI_1R-1S_vs ATCC.xlsx
SI_1R-1S vs ACICU.xlsx

value: Colistin sensitive A.baumannii


title: Sample_2-S (SI)


title: Sample_1-R (SI)


title: MCF7 WGBS

city: Darlinghurst

first: Qian

last: Du

state: NSW

address: 384 Victoria St

country: Australia

institute: Garvan Institute of Medical Research

library_source: genomic

data_processing:
Adaptor sequences and poor quality bases were removed using Trim Galore (v0.2.8) in paired-end mode with default parameters. bwa-meth (v0.10) was used to align reads to hg19 using default parameters. PCR duplicates were removed using Picard (v1.91). Count tables of the number of methylated and unmethylated bases sequenced at each CpG site in the genome were constructed using the ‘tabulate’ module of bwa-meth and BisSNP (v0.82.2) with default parameters.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *bw: BigWig files containing counts of methylated (C) and coverage (cov, C + T) at each CpG site assayed.

source_name: MCF7 cancer breast cell

growth_protocol: Cell lines were cultured according to manufacturer's instructions.

extract_protocol:
Genomic DNA was extracted from cells using QIAamp Mini Kit (QIAGEN, #51304).
Library preparation was performed using the CEGX TrueMethyl Whole-Genome kit (v2.1) with minor improvements as described in Nair et al., 2018. The resulting libraries were sequenced on the Illumina X Ten platform.

value: Breast

tag: cell line


title: Sample_2-R (TS)

description:
TS_2R-2S vs ATCC.xlsx
TS_1R-1S and 2R-2S vs ACICU.xlsx

extract_protocol:
RNAs were extracted from the samples after 12h of incubation using the NucleoSpin RNA (Macherey-Nagel, Dueren, Germany) kit following manufacturer’s protocol with minor modifications. Bacterial cell pellets were lysed by bead-beating procedure in the presence of 50 μL Buffer RA1. Then 3.5 μL ß-mercaptoethanol were added and the lysate was filtrate through NucleoSpin Filters (violet rings). RNA binding condition was adjusted by adding 350 μL of ethanol (70%) to the lysate and the RNA was then extracted with TRIzol reagent (Invitrogen) according to the manufacturer's protocol. The quality of the total RNA was verified using a 2200 TapeStation RNA Screen Tape device (Agilent, Santa Clara, CA, USA) and its concentration ascertained using an ND-1000 spectrophotometer (NanoDrop, Wilmington, DE). Ribosomal RNA was removed using the Ribo-Zero rRNA Removal Kit (Bacteria) from 2 microgram of Total RNA, and the depleted RNA was used as input in the Illumina TruseqRNA stranded kit without PolyA-enrichment.
The prepared libraries were evaluated with the High sensitivity D1000 screen Tape (Agilent Tape Station 2200). The indexed libraries were quantified with the ABI9700 qPCR instrument using the KAPA Library Quantification Kit in triplicates, according to the manufacturer’s protocol (Kapa Biosystems, Woburn, MA, USA). Five μL of the pooled library at a final concentration of 2 nM were used for sequencing using Illumina Miseq with a 150 Paired end-Read sequencing module.


title: Blood-D07-T52_2

value: Peripheral blood

value: Crohn’s disease (CD)


title: Sample_1-S (TS)

description:
TS_1R-1S vs ATCC.xlsx
TS_1R-1S and 2R-2S vs ACICU.xlsx


title: Sample_1-R (TS)


title: Sample_2-S (TS)


title: VD6


title: CD8


title: VD1


title: CD4


title: hfd:KO:13561X11_11_146_hfd

city: Salt Lake City

first: Morgan

last: Nelson

state: Utah

address: 15 North Medical Drive

department: Pathology

institute: University of Utah

data_processing:
Reads were aligned to mm10 + splice junctions using NovoAlign
Spliced alignments were converted back to genomic coordinates using USeq SamTranscriptomeParser
Reads mapping uniquely to features were counted using USeq DefinedRegionDifferentialSeq (DRDS)
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with FPKMs

growth_protocol: Adipose tissue macrophage were harvested from 20 week old mice fed either NCD or HFD.

extract_protocol:
Stromal Vascular Fraction was separated from adipocytes. SVF was then FACS sorted for CD45+ CD11b+ F4/80+ cells. RNA was extracted from these sorted cells in preparation for RNA-seq.
Library preparation used Illumina TruSeq Stranded RNA Kit with Ribo-Zero Gold.

value: Adipose Tissue macrophage

tag: diet

value: high fat


title: hfd:KO:13561X10_10_146_hfd


title: hfd:WT:13561X7_7_wt_hfd

source_name: WT HFD 1

value: wt


title: nc:KO:13561X5_6_146_nc

value: normal chow


title: nc:KO:13561X5_5_146_nc


title: hfd:WT:13561X9_9_wt_hfd

source_name: WT HFD 3


title: gBT_TGF-β_IL-2_rep1

city: Melbourne

first: Artika

middle: Praveeta

last: Nath

state: VIC

address: 75 commerical road

institute: Baker Heart and Diabetes Institute

data_processing:
Base calling and quality scoring were done with the standard Illumina pipeline, Real-Time Analysis (RTA) version 1.18.64 software.
The qualities of the raw sequence reads were assessed using FastQC version 0.11.3
The 100bp paired-end reads were aligned to the mouse (mm10) reference genome using Tophat2 version 2.1.1. All mappings were performed with the default options, except the mate pair inner distance and standard deviation parameters, which were set to 0 and 65, respectively
Transcript assembly and quantification was carried out with Cufflinks2 version 2.2.1. Gene-level abundance was expressed as fragments per kilobase of exons per million fragments mapped (FPKM) values
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.

source_name: Spleen

extract_protocol:
Total RNA was isolated using Trizol reagent and Qiagen RNAeasy Columns
All 12 RNA samples were processed with the Illumina TruSeq Stranded mRNA sample prep protocol to make cDNA libraries
Sequencing was performed on the Illumina HiSeq 2500 system with the HiSeq SBS Kit v4 reagents

tag: strain

tag: Sex

value: Female

value: 8 - 15 weeks

value: Spleen


title: gBT_unstimulated_rep1


title: gBT_IL-2_rep3


title: gBT_TGF-β_rep3


title: gBT_unstimulated_rep2


title: gBT_TGF-β_rep2


title: gBT_TGF-β_L-2_rep3


title: gBT_unstimulated_rep3


title: gBT_IL-2_rep2


title: nc:KO:13561X4_4_146_nc


title: gBT_TGF-β_IL-2_rep2


title: gBT_IL-2_rep1


title: gBT_TGF-β_rep1


title: hfd:KO:13561X12_12_146_hfd


title: hMADS-d0_miR-29a_vs_miR-C_rep3

city: Vienna

last: Karbiener

address: Benatzkygasse 2-6 / G

department: Global Pathogen Safety

country: Austria

institute: Takeda

description: Biological replicate 3, cells harvested 2 days after transfection

hyb_protocol: Shortly before hybridization, microarrays were washed in 0.2% SDS (3 times, 2 min each) and ddH2O (4 times, 1 min each), then incubated in prehybridization buffer (5x SSC, 0.1% SDS, 1% BSA) at 42°C for 45 min, again washed with ddH2O (five times, 30 sec each), finally dipped in isopropanol, and dried by immediate centrifugation. Immediately before applying the labeled cDNA samples to the microarray, the samples were heated at 95°C for 3 min, snap cooled on ice for 30 sec and centrifuged for 1 min at maximum speed. The sample was pipetted onto the microarray surface, and a rectangular coverslip was gradually lowered, distributing the sample across the spotted area of the microarray. Hybridization was performed by incubation at 42°C for 16-20 h. Subsequently, microarrays were submerged in wash buffer I (2x SSC, 0.1% SDS, preheated to 42°C) for 2 min, leading to separation of the microarray and the coverslip. Three washing steps (each 5 min at room temperature with gentle rotation) were performed using wash buffer I (2x SSC, 0.1% SDS, preheated to 30°C), wash buffer II (1x SSC), and wash buffer III (0.5xSSC). Finally, the microarray was dipped into ddH2O and dried by immediate centrifugation.

scan_protocol: Scanning of microarrays was performed with a GenePix 4000B microarray scanner (Axon Instruments) at 10 µm resolution using GenePix Pro 4.1 software (Axon Instruments).

data_processing: GenePix Pro 4.1 was used to filter out spots of suboptimal quality prior to further analysis. High intensity spots were filtered out if more than 20% of spot pixels were saturated in either of the two channels. Inhomogenity of spots was estimated by comparing (for either of the two channels) the median of pixel intensities to the mean; if the difference was greater than 20%, the spot was considered as inhomogenous and thus filtered out. Low intensity spots were defined by two distinct approaches: (i) if the sum of the medians/means of the pixel intensities in both channels was lower than 700, or (ii) if not more than 55 percent of the pixels within a spot had intensities higher than the intensity of the surrounding background plus one standard deviation of the background pixels. Subsequently, the filtered raw data was background corrected (by estimation and subtraction of local background), normalized by global mean and dye-swap pairs using ArrayNorm (PMID: 15073026). Finally, features detecting the same transcript were combined by averaging and the data was exported as text-file containing log2 transformed ratios of gene expression.

source_name: hMADS cells, transfected with miR-29a mimic

label_protocol: Concentration of total RNA samples was determined by UV/VIS photospetrometry on a NanoDrop-1000 device, and aliquots of 15 µg total RNA in 16.5 µL RNase-free H2O were prepared. For reverse transcription (RT), 2 µL random primers (3 mg/ml, lifetechnologies # 48190-011) were added to the RNA sample, followed by incubation at 70°C for 10 min and snap-freezing on ice for 30 sec. Subsequently, the following agents were added to complete the RT reactions: 0.6 µL aminoallyl-dNTP mix (25 mM dATP, 25 mM dCTP, 25 mM dGTP, 15mM dTTP (all lifetechnologies #10297-018), 10mM aminoallyl-dUTP (Sigma #A0410)), 6 µL 5x first strand buffer, 3 µL 0.1 M DTT, 2 µL SuperScript II Reverse Transcriptase (all lifetechnologies #18064-014). After mixing, RT reactions were incubated at 42°C for ~18 h. RNA was then hydrolyzed by adding 10 µL 1  M NaOH and 10 µL 0.5 M EDTA, followed by incubation at 65°C for 15 min. Subsequently, pH was neutralized by adding 10 µL 1 M HCl. To remove unincorporated aminoallyl-dUTP, reactions were purified based on the QIAquick PCR purification kit (QIAGEN #28106). Briefly, 300 µL of buffer PB were added to each sample before transfer to a QIAquick column and centrifugation (13000 x rcf, 1 min). Flowthrough was discarded and the cDNA (captured in the column matrix) was washed twice by addition of 750 µL phosphate wash buffer (5 mM potassium phosphate (prepared from 1M potassium phosphate buffer, pH 8.5), 80% EtOH) and subsequent centrifugation and discarding of flowthrough as above. Finally, the column matrix was dried by additional centrifugation for 1 min at maximum speed, and elution of purified cDNA was performed with 60 µL 4 mM potassium phosphate (diluted from 1M potassium phosphate buffer, pH 8.5). Samples were dried completely in a SpeedVac for 45 min and then resuspended in 4.5 µL of 0.1 M Na2CO3 buffer. To label the samples with fluorescent dyes, 4.5 µL of Cy5 or Cy3 NHS-ester (GE healthcare #PA25001 and #PA23001, one aliquot dissolved in 73 µL DMSO and stored at -80°C) were added and the samples were mixed and incubated at room temperature in the dark for 1 h. To remove uncoupled NHS-ester dyes, labeled cDNA samples were purified using the QIAquick PCR purification kit (QIAGEN #28106) according to the manufacturer’s instructions. After elution of the purified labeled cDNA in 60 µL Buffer EB, samples were again completely dried in a SpeedVac for 45 min. Subsequently, samples were resuspended in 24 µL hybridization buffer (50% N,N-Dimethylformamide (Sigma #D4551), 5xSSC, 0.1% SDS) and 1 µL human COT-1 DNA (lifetechnologies #15279-011, 20µg/µL, prepared according to the manufacturer’s instructions) as well as 1 µL poly(A)-DNA (20µg/µL, lifetechnologies primer service) were added to block nonspecific hybridization.

growth_protocol: For experiments, hMADS cells (Rodriguez et al., 2005, PMID: 15867092) were used between passage (P) 19 and P25. Medium for proliferation of hMADS cells was termed Medium I and consisted of (DMEM 1 g/l Glc (Lonza #BE12-707F), 2mM L-Gln (Invitrogen/ Gibco #25030-024), 10mM HEPES (Invitrogen/ Gibco #15630-056), 100ug/ml Normocin (InVivogen #ant-nr-2), 10% FBS (Lonza, #14-801F, Lot.no. 9SB031; or Pan-Biotech, #P30-3300, Lot.no.250330), supplemented with 2.5 ng/mL human Fibroblast Growth Factor 2 (hFGF2, Sigma #F0291). In this medium, hMADS cells had population doubling times of 48-96 h (depending on the passage number, i.e. the replicative age of cells). At densities in the range of 50–80% of optical confluence, passaging of cells was performed at passaging ratios between 1:2 and 1:5, depending on the actual population doubling time. Cells were cultivated in 100 mm dishes (Greiner Bio-One #664160), with 10 ml Medium I per dish, at 37°C in a humidified atmosphere with 5% CO2. For passaging, old medium was aspirated and cells were washed with Phosphate Buffered Saline (PBS, Invitrogen / Gibco #10010015) before incubation with 0.05% Trypsin with EDTA in PBS (Invitrogen / Gibco #15400054; 1mL per 100 mm dish) for 3–5 min at 37°C. Subsequently, Trypsin was inactivated by addition of Medium I (prewarmed to 37°C), and the cell suspension was transferred to new culture dishes according to the desired passaging ratio.

extract_protocol: Two days after transfection (= day 0), as well as at day 3 after induction of adipocyte differentiation, cells were harvested with TRIzol reagent (lifetechnologies, #15596-026). Total RNA was isolated according to the manufacturer's instructions and dissolved in RNase-free H2O.

treatment_protocol: Transient transfection of hMADS cells (when cells had reached confluence, designated day –2) with miRNA mimics (purchased from Dharmacon; miRIDIAN Mimic C-300504-07, hsa-miR-29a, and as non-targeting control miRIDIAN microRNA Mimic Negative Control #1 #CN-001000-01-20) was performed using HiPerFect transfection Reagent (QIAGEN #301707). Briefly, Medium I was changed 1 h before transfection (12 ml per 100 mm dish). The final oligonucleotide concentration was 5.4 nM. Therefore, previously established stock solutions of oligonucleotides (20 µm in sterile PBS, stored at -80°C) were thawed on ice. Subsequently, transfection mixtures were generatedby mixing 3.7 uL oligonucleotide stock solution, 1230 uL DMEM (without any additives) and 74.2 uL HiPerFect transfection reagent (for one 100 mm dish). The reactions were incubated at room temperature for 10 min and finally added dropwise onto the cells while gently swaying the dish. Adipocyte differentiation was induced two days later (designated day 0) by changing the medium to Medium II, consisting of DMEM(1 g/L Glc, Lonza Lonza #BE12-707F)/ Ham’s F12 (Lonza # BE12-615F) (50:50), 2mM L-Gln (Invitrogen/ Gibco #25030-024), 10mM HEPES (Invitrogen/ Gibco #15630-056), 100 µg/mL Normocin (InVivogen #ant-nr-2), 10 nM human insulin (Sigma #I9278), 10 µg/mL apo-transferrin (Sigma #T2252), 0.2 nM T3 (Sigma #T6397), 100 nM rosiglitazone (Cayman Chemicals / BRL49653), 100 µM IBMX (Sigma #I7018) and 1 µm Dexamethasone (Sigma #D4902). 12 ml Medium II were used for 1 100mm dish.

tag: differentiation stage

value: two-day postconfluent cells in growth medium

value: Multipotent Adipose-Derived Stem (hMADS) cells

source_name: hMADS cells, transfected with control siRNA

tag: differentiation


title: adipo-d3_miR-29a_vs_miR-C_rep3

description: Biological replicate 1, cells harvested 3 days after start of adipocyte differentiation

value: cells at early stage of adipocyte differentiation


title: adipo-d3_miR-29a_vs_miR-C_rep1


title: hMADS-d0_miR-29a_vs_miR-C_rep2

description: Biological replicate 2, cells harvested 2 days after transfection


title: hMADS-d0_miR-29a_vs_miR-C_rep1

description: Biological replicate 1, cells harvested 2 days after transfection


title: adipo-d3_miR-29a_vs_miR-C_rep2


title: hfd:WT:13561X8_8_wt_hfd

source_name: WT HFD 2


title: hMADS-d0_miR-29a_vs_miR-C_rep4

description: Biological replicate 4, cells harvested 2 days after transfection


title: nc:WT:13561X3_3_wt_nc

source_name: WT NCD 3


title: nc:WT:13561X2_2_wt_nc

source_name: WT NCD 2


title: nc:WT:13561X1_1_wt_nc

source_name: WT NCD 1


title: mBcells_KMT2D_HOM_H3K4me1_REP2

city: Sydney

first: Ksenia

last: Skvortsova

address: 384 Victoria St, Darlinghurst

department: Genomics and Epigenetics

institute: Garvan Institute

data_processing:
Sequenced reads from H3K4me1 ChIP-seq and input control WT, HET and HOM KMT2D mutant B cells samples were mapped to the reference mouse genome (mm10) with bowtie v.1.1.058 (Langmead et al, Genome Biol, 2009) allowing up to three mismatches
Differential H3K4me1 binding between WT, HET and HOM KMT2D mutant B cells was calculated using csaw package (Lun et al, Nucleic Acids Res, 2016)
H3K4me1 enrichment counts were calculated per 1000bp windows (200bp sliding) normalised against input ChIP-seq signal with minimum of 5 reads per window
Blacklisted regions as specified by ENCODE were excluded from window read counts
Windows were filtered to retain the ones with the average abundance of ≥3-fold increase above the background
Genome_build: mm10
Supplementary_files_format_and_content: bw

source_name: mouse spleen B cells with the homozygous chr15: 98,835,228 A>T  mutation in KMT2D (Ile5482Asn)

growth_protocol: A single cell suspension of the spleen was obtained by gently mashing the solid tissue through a 70 μm nylon mesh filter. Bulk B cell purification was performed by cell staining based on the Miltenyi Biotec Pan-B Cell Isolation Kit Mouse II protocol, followed by manual MACS cell separation by negative depletion

extract_protocol:
Sorted splenic B cells were fixed with 1% formaldehyde at room temperature for 10 mins followed by quenching with 0.125M glycine (final concentration).  The cells were washed twice with ice cold PBS containing protease inhibitors (1mM phenylmethylsulfonyl fluoride (PMSF), 1 g/ml aprotinin and 1g/ml pepstatin A), harvested and treated with SDS lysis buffer for 10 min on ice.  Resulting lysates were sonicated to shear the DNA to fragment lengths of 200 to 500bp.
10 ng chromatin immunoprecipitated DNA was used for each library prep using Illumina Truseq Chip Library Prep Kit according to the manufacturer’s instructions

treatment_protocol: no treatment

value: Spleen bulk B cells

tag: genotype

value: HOM

tag: ip antibody

value: histone H3K4me1 polyclonal antibody (Active Motif, cat no 39297, lot no 01714002)


title: mBcells_KMT2D_HET_H3K4me1_REP2

source_name: mouse spleen B cells with the heterozygous chr15: 98,835,228 A>T  mutation in KMT2D (Ile5482Asn)

value: HET


title: Blood-D09-T26_3

source_name: Peripheral blood of Crohn's Disease patient collected at 26 weeks after HSCT

tag: diagnosis

tag: disease location

tag: disease phenotype

value: Fistulating

tag: timepoint

tag: response

value: Yes

tag: cdai

tag: ses-cd


title: TK4L_AP_12_2

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
MBD-seq reads were trimmed for adapters and low-quality flanking ends using Trim Galore v0.3.7 and Cutadapt v1.4.2
Processed reads were mapped to mm10 using Rsubread
Consensus peaks (p-value < 0.05) were called using Macs2 on the full assemble of samples, including all four intestinal sections of both germ-free and conventionally raised mice
The sample specific read coverage of each consensus peak was computed with featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: methylation peaks (in bed format), sample by sample counts of reads in methylation peaks (in csv format)

source_name: intestine

extract_protocol:
DNA samples were sheared with a Bioruptor Plus sonication device (Diagenode) to obtain average DNA size of 250 bp which was checked on a Bioanalyzer instrument (DNA 2100 kit, Agilent Genomics). Methylated DNA was isolated using the MethylMiner Methylated DNA Enrichment Kit (Invitrogen). This method uses the properties of the methyl-CpG-binding domain (MBD) to capture DNA fragments with CpG methylation.
The total amount of captured DNA fraction was used for preparation of sequencing libraries (NEBNext Ultra DNA Library Prep Kit for Illumina, New England Biolabs) using the protocol described in (Nylander et al., Diabetes, 2016). Libraries were quality-controlled on a Bioanalyzer instrument (Agilent Technologies) and subjected to 100-bp single-end sequencing on HiSEq 2500 system (Illumina) at the Danish National High-Throughput DNA Sequencing Centre.

tag: mouse model

value: GermFree

tag: tissue

value: intestine

tag: instestine section

value: Jejunum

tag: mouse


title: TK4L_AP_10_3

value: Ileum


title: TK4L_AP_10_2


title: TK4L_AP_12_4

value: Colon


title: TK4L_AP_12_1

value: Duodenum


title: REXQ_AP_9_3


title: REXQ_AP_9_2


title: TK4L_AP_10_1


title: REXQ_AP_9_4


title: REXQ_AP_9_1


title: TK4L_AP_10_4


title: REXQ_AP_4_4

value: ConvR


title: REXQ_AP_4_3


title: REXQ_AP_4_1


title: NHSY_AP_8_2


title: NHSY_AP_3_4


title: NHSY_AP_8_4


title: NHSY_AP_8_1


title: NHSY_AP_3_3


title: NHSY_AP_8_3


title: NHSY_AP_3_2


title: TK4L_AP_12_3


title: mBcells_KMT2D_WT_H3K4me1_REP2

source_name: mouse spleen B cells with the wild type KMT2D

tag: cell type

value: WT


title: FUAQ_AP_6_3


title: NHSY_AP_3_1


title: FUAQ_AP_6_4


title: FUAQ_AP_6_2


title: FUAQ_AP_6_1


title: FUAQ_AP_1_3


title: FUAQ_AP_1_2


title: FFRV_AP_7_3


title: FFRV_AP_7_1


title: FFRV_AP_2_4


title: FFRV_AP_7_2


title: REXQ_AP_4_2


title: FUAQ_AP_1_1


title: FFRV_AP_2_2


title: FFRV_AP_2_3


title: FFRV_AP_2_1


title: ELNP_AP_5_4


title: ELNP_AP_5_3


title: ELNP_AP_5_1


title: ELNP_AP_11_4


title: ELNP_AP_11_2


title: ELNP_AP_11_1


title: ELNP_AP_5_2


title: ELNP_AP_11_3


title: FUAQ_AP_1_4


title: FFRV_AP_7_4


title: mBcells_KMT2D_HOM_H3K4me1

extract_protocol:
Sorted splenic B cells were fixed with 1% formaldehyde at room temperature for 10 mins followed by quenching with 0.125M glycine (final concentration).  The cells were washed twice with ice cold PBS containing protease inhibitors (1mM phenylmethylsulfonyl fluoride (PMSF), 1 ug/ml aprotinin and 1ug/ml pepstatin A), harvested and treated with SDS lysis buffer for 10 min on ice.  Resulting lysates were sonicated to shear the DNA to fragment lengths of 200 to 500bp.
10 ng chromatin immunoprecipitated DNA was used for each library prep using Illumina Truseq Chip Library Prep Kit according to the manufacturer’s instructions

tag: chip antibody

value: histone H3K4me1 polyclonal antibody (Active Motif, cat# 39297, lot# 01714002)


title: mBcells_KMT2D_HET_input


title: mBcells_KMT2D_HET_H3K4me1


title: mBcells_KMT2D_WT_input


title: mBcells_KMT2D_HOM_input


title: mBcells_KMT2D_WT_H3K4me1


title: spleen DC of GF Rag KO mice injected with naïve CD4 T cells

city: Pohang

first: Jaeu

last: Yi

country: South Korea

institute: POSTECH

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to mouse reference transcriptome build mm10 (M10, GRCm38.p4) from GENCODE (http://www.gencodegenes.org/mouse_releases/10.html)
Fragments Per Kilobase Million (FPKM) were calculated by RSEM with default parameters.
Differentially expressed genes were identified by edgeR-3.16.5 [49] given absolute fold change > 2 and FDR < 10-3
Genome_build: mm10
Supplementary_files_format_and_content: differential gene expression comparsion with FPKM value

source_name: dendritic cells

extract_protocol:
PLN or SPL DCs were purified with flow cytometory sorting and RNA was harvested with trizol. Illumina TruSeq RNA sample prep kit was used with 1ug of total RNA for the construction of sequencing libararies.
RNA libraries were prepared for sequencing using standard Illumina protocol

tag: strain

value: spleen (SPL)


title: spleen DC of GF Rag KO mice injected with Tregs


title: Blood-G09-T26_2

value: Peripheral blood

value: Crohn’s disease (CD)

tag: age

value: Ileocolonic

value: Inflammatory

tag: gender

value: Female


title: spleen DC of un-injected GF Rag KO mice


title: PLN DC of GF Rag KO mice injected with naïve CD4 T cells

value: peripheral lymph node (PLN)


title: PLN DC of GF Rag KO mice injected with Tregs


title: PLN DC of un-injected GF Rag KO mice


title: HAS70-1

city: Los Angeles

first: Steve

last: Cole

state: CA

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

hyb_protocol: Standard Illumina hybridization protocol for cRNA target (carried out by UCLA Neuroscience Genomics Core).

scan_protocol: Standard Illumina scan protocol for gene expression profiling (carried out by UCLA Neuroscience Genomics Core).

data_processing: Raw probe intensity values and quantile-normalized gene expression values were generated by Illumina GenomeStudio software using Gene Expression module 1.1.1.  All probe and gene values are provided, with no additional filtering.

source_name: Peripheral Blood

label_protocol: Ambion TotalPrep cRNA target synthesis for gene expression profiling (carried out UCLA Neuroscience Genomics Core).

extract_protocol: Total RNA was extracted from PBMC using Qiagen Rneasy reagents on a QIACube instrument.

tag: participant

tag: time

tag: inlove

tag: illness

tag: intercourse

tag: oralsex

tag: semenexposure

value: PBMC


title: HAS70-2


title: HAS72-2


title: MIN6_Control3

city: Nagoya

first: Kunihiko

last: Araki

state: Outside the United States or Canada

address: 65 Tsurumai-cho, Showa-ku

department: Neurology

country: Japan

institute: Nagoya University

description: Mouse insulinoma cell line

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix Expresson Console Software (ThermoFisher Scientific) according to the default analysis settings.

source_name: MIN6 treated by control siRNA

label_protocol: Biotinylated cRNA were prepared using GeneChip 3'IVT PLUS Reagent Kit (Thermo Fisher Scientific) according to the standard manufacturer's protocol from 100 ng total RNA.

growth_protocol: MIN6 cells were cultured in Dulbecco’s modified Eagle’s medium containing 10% (v/v) fetal bovine serum with 5% penicillin/streptomycin and β-mercaptoethanol at 37℃ and 5% CO2.

extract_protocol: Total RNA was extracted from MIN6 cells using an RNeasy Mini Kit according to the manufacturer’s instructions.

treatment_protocol: MIN6 cells seeded at a density of 3.0 × 105 cells on a 12-well plate were electroporated with 100 pmol siRNA (Control　and TDP-43) using the NEON Transfection System (electroporation: 1200 V pulse, 20 ms width).

tag: cell line


title: HAS72-1


title: HAS74-1


title: MIN6_Control1

description: Mouse insulinoma cell line


title: MIN6_TDP2

description: Mouse insulinoma cell line

source_name: MIN6 treated by TDP siRNA


title: HAS69-2


title: HAS69-1


title: HAS70-3


title: HAS74-2


title: MIN6_TDP3

description: Mouse insulinoma cell line


title: MIN6_Control2

description: Mouse insulinoma cell line


title: MIN6_TDP1

description: Mouse insulinoma cell line


title: HAS66-2


title: HAS58-1


title: HAS68-2


title: HAS62-1


title: HAS56-2


title: HAS69-3


title: HAS59-2


title: HAS54-1


title: HAS59-1


title: HAS62-2


title: HAS68-1


title: HAS56-1


title: HAS58-2


title: HAS54-2


title: HAS66-1


title: HAS52-1


title: HAS52-2


title: HAS49-2


title: HAS50-2


title: HAS53-1


title: HAS39-2


title: HAS36-2


title: HAS50-1


title: HAS34-2


title: HAS44-1


title: HAS47-2


title: HAS45-1


title: HAS44-2

value: missing


title: HAS45-3


title: HAS43-3


title: HAS43-2


title: HAS39-1


title: HAS35-1


title: HAS45-2


title: HAS35-2


title: HAS47-1


title: HAS36-1


title: HAS34-3


title: HAS37-2


title: HAS49-1


title: HAS37-3


title: HAS43-1


title: HAS37-1


title: HAS53-2


title: HAS34-1


title: HAS30-1


title: HAS31-2


title: HAS32-1


title: HAS21-2


title: HAS22-2


title: HAS28-1


title: HAS32-2


title: HAS19-1


title: HAS21-3


title: HAS28-3


title: HAS30-3


title: HAS32-3


title: HAS24-1


title: HAS26-2


title: HAS26-1


title: HAS30-2


title: HAS27-2


title: HAS21-1


title: HAS22-1


title: HAS28-2


title: HAS29-1


title: HAS31-1


title: HAS24-2


title: HAS19-2


title: HAS18-2


title: HAS19-3


title: HAS27-1


title: HAS18-3


title: HAS18-1


title: HAS29-2


title: HAS14-2


title: HAS17-1


title: HAS11-2


title: HAS11-3


title: HAS13-1


title: HAS7-1


title: HAS3-1


title: HAS14-3


title: HAS17-2


title: HAS14-1


title: HAS10-1


title: HAS2-2


title: HAS5-3


title: HAS10-2


title: HAS11-1


title: HAS13-2


title: HAS10-3


title: HAS7-2


title: HAS3-2


title: A549 w/ TGFbeta LB9

city: Stony Brook

first: John

middle: D

last: Haley

state: NY

address: BST 9-168, SB Medical

institute: Stony Brook University

data_processing:
Illumina base calling; FASTQ
TopHat alignment
RSEM
Genome_build: hg19
Supplementary_files_format_and_content: txt, gene level

source_name: A549 lung

growth_protocol: A549 cell were grown in RPMI-1640, 10% FBS

extract_protocol:
Qiagen RNA Easy
Illumina standard protocol, polyA

treatment_protocol: 10ng/ml TGFbeta3 (~21 days)

tag: mutation

value: Kras

tag: treatment

value: 10ng/ml TGFbeta3


title: A549 Control LB13

value: control


title: A549 w/ TGFbeta LB10


title: A549 Control LB16


title: HAS1-1


title: HAS9-2


title: HAS7-3


title: HAS9-1


title: HAS5-2


title: HAS2-1


title: HAS5-1


title: HAS1-2


title: 21B_L3 H358 lung cells

data_processing:
TopHat
RSEM
Genome_build: hg19

source_name: 21B_L3 H358 lung cells

extract_protocol:
Qiagen RNA Easy
Illumina

treatment_protocol: 10ng/ml TGFbeta3

tag: time hours

value: H358 + TGFbeta

tag: growth factor


title: 180B_L3 H358 lung cells

source_name: 180B_L3 H358 lung cells


title: 72A_L3 H358 lung cells

source_name: 72A_L3 H358 lung cells


title: 8A_L3 H358 lung cells

source_name: 8A_L3 H358 lung cells


title: 24B_L3 H358 lung cells

source_name: 24B_L3 H358 lung cells


title: 24A_L3 H358 lung cells

source_name: 24A_L3 H358 lung cells


title: 6B_L3 H358 lung cells

source_name: 6B_L3 H358 lung cells


title: 21A_L3 H358 lung cells

source_name: 21A_L3 H358 lung cells


title: 7B_L3 H358 lung cells

source_name: 7B_L3 H358 lung cells


title: 8B_L3 H358 lung cells

source_name: 8B_L3 H358 lung cells


title: 6A_L3 H358 lung cells

source_name: 6A_L3 H358 lung cells


title: 16A_L3 H358 lung cells

source_name: 16A_L3 H358 lung cells


title: 72B_L3 H358 lung cells

source_name: 72B_L3 H358 lung cells


title: 16B_L3 H358 lung cells

source_name: 16B_L3 H358 lung cells


title: 4B_L3 H358 lung cells

source_name: 4B_L3 H358 lung cells


title: 4A_L3 H358 lung cells

source_name: 4A_L3 H358 lung cells


title: 2B_L3 H358 lung cells

source_name: 2B_L3 H358 lung cells


title: 0B_L3 H358 lung cells

source_name: 0B_L3 H358 lung cells


title: 0A_L3 H358 lung cells

source_name: 0A_L3 H358 lung cells


title: 1A_L3 H358 lung cells

source_name: 1A_L3 H358 lung cells


title: 180A_L3 H358 lung cells

source_name: 180A_L3 H358 lung cells


title: 1B_L3 H358 lung cells

source_name: 1B_L3 H358 lung cells


title: 2A_L3 H358 lung cells

source_name: 2A_L3 H358 lung cells


title: Input-UM-ChIPseq

city: Gothenburg

first: Subazini

last: TK

address: Medicineragatan 9A

country: Sweden

institute: Gothenburg university

description: UnMutCLL-H3K4me1_peaks.broadPeak.sorted.bam.bedgraph.gz

data_processing:
For ChIP seq, Raw reads containing adapter sequences, were removed using CutAdapt v2.2.1.
Cleaned reads were than aligned to GRCh38 reference genome, using Bowtie v1.0.0 --best -n 2 -k 1 -m 1 -t.
Aligned reads were used to call peaks with MACS v2.1.0 -f BAM --broad --broad-cutoff 0.05 -B -g hs, over corresponding inputs.
After peak calling for each sample, UCSC’s tool WigCorrelation was used on BED files, to estimate the correlation between samples.
For RNA seq, Raw reads containing adapter sequences, were removed, using CutAdapt v2.2.1. Cleaned reads were aligned using STAR v2.5.2b. Aligned reads were used for quantification, using SubRead v1.5.2 FeatureCount with Gencode v24 annotation. Normalization of read counts was performed with RPKM normalization, using an in-house script.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include counts, RPKM values

source_name: Human Peripheral Blood

extract_protocol:
For hMeDIP and MeDIP seq, genomic DNA was extracted using  DNA extraction kit, Total RNA for RNA seq was extracted using RNA extraction kit and then quality was asses using Bioanalyser. For ChIP seq chromatin was extracted, sponicated and specific antibody was used to pulldown the ChIP DNA.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: tissue

value: Human Peripheral Blood

tag: tumor type

value: Chronic lymphocytic leukemia

tag: tumor classification

value: IGHV unmutated CLL


title: Input-M-ChIPseq

description: MutCLL-H3K4me1_peaks.broadPeak.sorted.bam.bedgraph.gz

value: IGHV mutated CLL


title: UM2_ChIP_seq_Ab1

description: UM-CLL-H3K27ac_peaks.broadPeak.sorted.bam.bedgraph.gz


title: UM2_ChIP_seq_Ab2


title: UM3_ChIP_seq_Ab1


title: UM3_ChIP_seq_Ab2