title: PBMC9_24h_Mock

city: Singapore

first: Siti Naqiah

last: Amrun

address: 8A Biomedical Grove, Immunos

country: Singapore

institute: Singapore Immunology Network

description: total number of reads: 29008404

data_processing:
Base calling and de-multiplexing of indexed reads were performed by CASAVA version 1.8.2 (Illumina)
The raw fastq files were trimmed to remove Illumina adapter sequences using Cutadapt version 1.2.1 (60). The option “-O 3” was set, so that the 3' end of any reads which matched the adapter sequence over at least 3 bp was removed
reads were further trimmed to remove low quality bases, using Sickle version 1.200 with a minimum window quality score of 20. After trimming, reads shorter than 50 bp were removed.
If both reads from a pair passed this filter, each was included in the R1 (forward reads) or R2 (reverse reads) file. If only one of a read pair passed this filter, it was included in the R0 (unpaired reads) file
Genome_build: reference genome used for alignment was the human reference genome assembly GRCh38
Supplementary_files_format_and_content: xlsx files containing log2(fold change) values, p-value, q-value and signficance

source_name: peripheral blood mononuclear cells (PBMCs)

extract_protocol:
Cell pellet were extracted using Trizol-chloroform method and Qiagen Micro RNA kit
ScriptSeq v2 RNA-Seq Library Preparation protocol

tag: donor

tag: timepoint (hpi)

tag: infection

value: Mock-infected


title: PBMC9_24h_5

status: Public on Mar 16 2020

type: SRA

description: total number of reads: 33467108

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

value: peripheral blood mononuclear cells (PBMCs)

value: Severe EV71


title: 5792

type: RNA

city: Oklahoma City

first: Judith

middle: A.

last: James

state: Oklahoma

address: 825 NE 13th Street

department: Arthritis and Clinical Immunology

country: USA

institute: Oklahoma Medical Research Foundation

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The data were normalized in R using bgAdjust background correction, vst variance stabilizing transformation, and rank invariant normalization.
6 samples were determined to be outliers and were dropped prior to normalization: 200319680117_E 200308380073_J 200308380073_K 200308380073_L 200308380104_E 200667730029_E

label: biotin

source_name: Whole Blood

label_protocol: RNA was amplified, in vitro transcribed, and labeled using the Illumina Bead-Expression Kit for Illumina Human HT-12 v4·0 whole genome expression chip.

extract_protocol: Total cellular RNA was isolated and purified from PAXgene tubes (PAXgene Blood RNA kit, Qiagen Inc, Valencia, CA). RNA quality and quantity were determined using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Globin mRNA and ribosomal RNAs (Globin-Zero Gold kit, Illumina, San Diego, CA, USA) were depleted.

tag: subject id

tag: case/control

value: SLE Case

tag: study group

value: High/Low

tag: sledai group

value: High


title: PBMC9_24h_3

description: total number of reads: 31635143

value: Moderate EV71


title: PBMC9_24h_1

description: total number of reads: 35385798

value: Mild EV71


title: 5485


title: PBMC9_12h_HI

description: total number of reads: 29682411

value: Heat-inactivated EV71


title: 3599

value: Low


title: G4 Rep1

city: Beijing

first: Jiayang

last: Li

address: Beichen West Road

country: China

institute: Institute of Genetics and Developmental Biology, CAS

data_processing:
The paired end clean reads of RNA-seq were aligned using STAR with default parameter.
Then fragment quantifications were computed with featureCounts in the paired-end mode, whose features are exons with default parameters.
Expression differentiation analyses were conducted by R package DESeq with three biological replicates, and genes with P-value less than 0.05 were selected for further analysis.
Genome_build: Arabidopsis reference genome TAIR10
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each sample.

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: Arabidopsis seeds were surface sterilized, vernalized at 4 ºC for 2-4 days, germinated and grown on the 0.5× Murashige and Skoog (MS) medium containing 1.0% sucrose and 0.7% agar under a long day photoperiod (16-h light, 8-h dark cycle) with a light intensity of 60-80 μE m−2 sec−1 at 21 ºC

extract_protocol:
Seedlings were frozen and ground into powder in liquid nitrogen, and RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Whole seedlings grown for 10 days on MS plates were collected and balanced in 0.5× MS liquid medium for 2h, then treated with 5 μM GR244DO in the greenhouse for 2h or 4 h.

tag: ecotype

value: Col

tag: genotype

value: wild-type

value: seedling

tag: developmental stage

tag: treatment

tag: time

value: 4 hours


title: PBMC9_12h_Mock

description: total number of reads: 35686669


title: PBMC9_24h_HI

description: total number of reads: 37124747


title: 5661


title: 3427


title: 4374

value: High Only


title: 533071

value: Control

value: no val


title: 4407


title: PBMC9_12h_5

description: total number of reads: 31943354


title: PBMC9_12h_3

description: total number of reads: 26388896


title: PBMC9_6h_5

description: total number of reads: 26988125


title: PBMC9_6h_HI

description: total number of reads: 26094023


title: PBMC9_12h_1

description: total number of reads: 23320254


title: 541728


title: PBMC9_6h_Mock

description: total number of reads: 35229224

value: Mock-infected


title: 4369

value: Low Only


title: PBMC9_6h_3

description: total number of reads: 36477087

value: peripheral blood mononuclear cells (PBMCs)


title: 6830

value: SLE Case


title: PBMC9_6h_1

description: total number of reads: 31336649


title: PBMC9_0h_HI

description: total number of reads: 31238913


title: 4139

value: High/Low


title: PBMC9_0h_5

description: total number of reads: 24534583

value: Severe EV71


title: PBMC9_0h_Mock

description: total number of reads: 28744685


title: 4296

value: High


title: PBMC9_0h_1

description: total number of reads: 24844294

value: Mild EV71


title: 6098


title: 5924


title: 3761


title: 5133


title: 6620


title: PBMC9_0h_3

description: total number of reads: 36170888

value: Moderate EV71


title: 6746


title: 5945


title: 6246

value: Low


title: PBMC8_24h_Mock

description: total number of reads: 32225133


title: PBMC8_24h_HI

description: total number of reads: 32863815

value: Heat-inactivated EV71


title: PBMC8_24h_5

description: total number of reads: 41071957


title: PBMC8_24h_3

description: total number of reads: 32034945


title: 4156


title: PBMC8_24h_1

description: total number of reads: 35168633


title: 6144


title: PBMC8_12h_HI

description: total number of reads: 35814571


title: 3314


title: 6521


title: 4150


title: PBMC8_12h_Mock

description: total number of reads: 30031154


title: 5971


title: PBMC8_12h_5

description: total number of reads: 31319958


title: 5706


title: PBMC8_12h_1

description: total number of reads: 30771140


title: 598207


title: 4551


title: PBMC8_12h_3

description: total number of reads: 31975548


title: PBMC8_6h_HI

description: total number of reads: 31567420


title: 4798


title: PBMC8_6h_5

description: total number of reads: 33946793


title: PBMC8_6h_Mock

description: total number of reads: 37763861


title: PBMC8_6h_3

description: total number of reads: 32231194


title: PBMC8_0h_HI

description: total number of reads: 24785875


title: PBMC8_6h_1

description: total number of reads: 27160809


title: 6342


title: PBMC8_0h_5

description: total number of reads: 27260641


title: PBMC8_0h_Mock

description: total number of reads: 27979447


title: 3641


title: PBMC8_0h_3

description: total number of reads: 27762235


title: 4375


title: 4973


title: 5051


title: 4903


title: 4278


title: 4301


title: 6014


title: 6651


title: PBMC8_0h_1

description: total number of reads: 19889106


title: PBMC7_24h_Mock

description: total number of reads: 37665514


title: PBMC7_24h_5

description: total number of reads: 35773597


title: PBMC7_24h_HI

description: total number of reads: 32426029


title: 6429


title: PBMC7_24h_3

description: total number of reads: 36858180


title: 6291


title: PBMC7_12h_HI

description: total number of reads: 31662488


title: PBMC7_24h_1

description: total number of reads: 41667212


title: PBMC7_12h_Mock

description: total number of reads: 30097479


title: 6052


title: PBMC7_12h_5

description: total number of reads: 36617277


title: PBMC7_12h_1

description: total number of reads: 29115691


title: PBMC7_6h_HI

description: total number of reads: 30843792


title: PBMC7_6h_Mock

description: total number of reads: 29742560


title: PBMC7_6h_5

description: total number of reads: 29182869


title: 7268


title: 7025


title: 6307


title: PBMC7_6h_3

description: total number of reads: 26235350


title: 3576


title: 6418


title: PBMC7_6h_1

description: total number of reads: 38802308


title: 6504


title: 5510


title: 4824


title: 6405


title: PBMC7_12h_3

description: total number of reads: 30194400


title: PBMC7_0h_HI

description: total number of reads: 35172089


title: PBMC7_0h_5

description: total number of reads: 29080381


title: 3684


title: 6180


title: PBMC7_0h_3

description: total number of reads: 29659805


title: 3280


title: PBMC7_0h_Mock

description: total number of reads: 28256777


title: 590058


title: 5695


title: 6303


title: PBMC7_0h_1

description: total number of reads: 25651110


title: PBMC6_24h_Mock

description: total number of reads: 24045099


title: 6281


title: 4543


title: 4477


title: PBMC6_24h_1

description: total number of reads: 44450081


title: PBMC6_24h_3

description: total number of reads: 32810260


title: PBMC6_12h_HI

description: total number of reads: 42316784


title: PBMC6_12h_Mock

description: total number of reads: 33678428


title: 6051


title: PBMC6_12h_5

description: total number of reads: 31693970


title: PBMC6_12h_3

description: total number of reads: 36921489


title: PBMC6_12h_1

description: total number of reads: 29715956


title: 6788


title: 4282


title: PBMC6_24h_HI

description: total number of reads: 32076639


title: PBMC6_24h_5

description: total number of reads: 32285247


title: PBMC6_6h_Mock

description: total number of reads: 26327550


title: 6987


title: PBMC6_6h_5

description: total number of reads: 24816995


title: 560024


title: 3807


title: 3503


title: 3966


title: 3501


title: 3556


title: PBMC6_6h_1

description: total number of reads: 29384039


title: 5697


title: PBMC6_6h_3

description: total number of reads: 28503010


title: PBMC6_0h_HI

description: total number of reads: 27308198


title: 7184


title: 6337


title: 6060


title: PBMC6_0h_Mock

description: total number of reads: 22394557


title: 3975


title: PBMC6_0h_5

description: total number of reads: 26660536


title: PBMC6_0h_1

description: total number of reads: 25949468


title: PBMC6_0h_3

description: total number of reads: 28355115


title: 3775


title: 3940


title: 10x_CAF_030386_Control-CAF_S1

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

description: CAF, 10x Chromium

data_processing:
FastQC v.0.11.3 was used to observe read quality
FastX v. 0.0.14 was used to trim data
Fluidigm data: Tophat2 v 2.1.0 was used to align reads to the genome with max-intron-length set to 560, min-intron-length set to 60,  and strandedness set to "fr-firststrand".
Fluidigm data:HTSeq Count v. 0.6.1  was used to count reads aligning to genes, feature was set to "exon" and attribute was set to "gene id", stranded was set to "reverse" and intersection-nonempty was used
Chromium data:  Cellranger was used to do initial quality control, alignment, and counting
Fluidigm and chromium proceesed data: Seurat was used to normalize and perform DE analysis. The number of reads for the control and experimental groups were then compared to identify differentially expressed genes
Genome_build: Ensembl Genome Reference Consortium Human Build 38 (GRCh38.p3)
Supplementary_files_format_and_content: FASTQ files

source_name: whole cell

growth_protocol: prostate CAF cells were selected, for Fluidigm data cells were processed in two batches.  Fastq files or samples with "-1" after the name are in batch 2.

extract_protocol:
followed the C1 Fluidigm and 10x Chromium preparation protocols
Capture sites containing 0 or >1 cell were excluded, and cells with positive ethidium homodimer-1 staining were also excluded.  Cell lysis, reverse transcription, and cDNA amplification of single cells were conducted following the protocol for mRNA sequencing (Fluidigm) or 10x Chromium.

tag: cell type

value: CAF cells


title: C1_CAF_023253_E12

description:
CAF, C1 Fluidigm platform
GeneCounts_caf_c1.csv

tag: column in countmatrix


title: 7172


title: 6513


title: 6871


title: 7330


title: C1_CAF_023254_F12


title: C1_CAF_023255_H12

description: CAF, C1 Fluidigm platform


title: 6226


title: 541578


title: C1_CAF_023250_B12


title: 7687


title: C1_CAF_023252_D12


title: C1_CAF_023248_H11


title: C1_CAF_023247_G11


title: 6674


title: C1_CAF_023246_E11


title: C1_CAF_023251_C12


title: C1_CAF_023245_D11


title: C1_CAF_023244_C11


title: C1_CAF_023241_H10


title: C1_CAF_023242_A11


title: C1_CAF_023239_E10


title: 500161


title: C1_CAF_023237_C10


title: C1_CAF_023238_D10


title: 5484


title: 6065


title: 3261


title: 5955


title: C1_CAF_023236_B10


title: 4862


title: C1_CAF_023235_A10


title: 4334


title: 4193


title: 6000


title: 6477


title: 6713


title: 5227


title: C1_CAF_023240_G10


title: C1_CAF_023232_F9


title: C1_CAF_023233_G9


title: C1_CAF_023234_H9


title: C1_CAF_023231_D9


title: 560050


title: C1_CAF_023230_C9


title: 5602


title: 3836


title: 5995


title: 3796


title: 6538


title: 7609


title: 4328


title: 4956


title: POSH2

city: Shanghai

first: Guohong

last: Hu

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health

data_processing:
Read quality were performed for all samples by using FastQC (version 0.11.2) (Andrews.2010) software with the default parameters.
Skewer (v0.2.2) (Bolger AM, el at. 2014) software was used to remove the adapter sequence of raw data(Fastq) and the reads whose length is longer than 75bp were selected after adapters were removed. Then the selected reads, named as Clean reads, were used for downstream analysis.
The alignment analysis can basically be divided into two steps: 1)genemeGenerate Build an index; 2) Sequence alignment. In this project, clean reads of each sample were align to reference genome by using STAR software with default parameters.
Expression estimation of gene and transcript was performed by using RSEM, TMM and CPM normalized read counts of genes were applied to compare between two samples in the downstream analysis.
Genes whose CPM and TMM value is greater than 1 in at least one sample were selected. The criteria for significantly differentially expressed genes was:  |FC| >= 2.
Genome_build: hg19
Supplementary_files_format_and_content: raw count matrix on gene level; CPM_TMM normalized data

growth_protocol: 500ml DMEM/F12 (1:1) + 10ug/ml Insulin + 20ng/ml EFG + 0.5ug/ml Hydrocortizone +25ml Horse Serum + 5ml Pen/strep

extract_protocol:
Trizol reagent was used to extract RNA, then total RNA was subjected to Hiseq PE150 RNA-Seq.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: no treatment.

value: epithelial-like

tag: genotype/variation

value: POSH2 overexpressed

tag: cell line


title: 6806


title: C1_CAF_023229_B9


title: C1_CAF_023228_A9


title: control

value: control


title: C1_CAF_023227_H8


title: C1_CAF_023226_G8


title: CD44LS

data_processing:
Read quality were performed for all samples by using FastQC (version 0.11.2) (Andrews.2010) software with the default parameters.
Skewer (v0.2.2) (Bolger AM, el at. 2014) software was used to remove the adapter sequence of raw data(Fastq) and the reads whose length is longer than 75bp were selected after adapters were removed. Then the selected reads, named as Clean reads, were used for downstream analysis.
The alignment analysis can basically be divided into two steps: 1)genemeGenerate Build an index; 2) Sequence alignment. In this project, clean reads of each sample were align to reference genome by using STAR software with default parameters.
Expression estimation of gene and transcript was performed by using RSEM, TMM and CPM normalized read counts of genes were applied to compare between two samples in the downstream analysis.
Genes whose CPM and TMM value is greater than 5 in at least one sample were selected. The criteria for significantly differentially expressed genes was: |FC| >= 2.
Genome_build: hg19
Supplementary_files_format_and_content: raw count matrix on gene level
gene_FPKM_mat - FPKM matrix on gene level
gene_TPM_mat - TPM matrix on gene level
gene_CPM_TMM_anno - edgeR normalized expression matrix on gene level

source_name: HMLER

growth_protocol: MEGM

extract_protocol:
Trizol reagent was used to extract RNA, then total RNA was subjected to Hiseq PE150 RNA-Seq.
Rribosomal-RNA was removed and the rest was used for library construction. RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: subpopulation

value: breast cancer stem cell-like

tag: sphere-derived

value: YES

value: HMLER


title: 6575


title: 3571

value: High Only


title: 4207


title: CD44L-3

value: non-breast cancer stem cell-like

value: NO


title: 5287

value: SLE Case

value: High/Low


title: 541980

value: Control

value: no val


title: C1_CAF_023225_F8


title: 6567

value: High


title: 4561


title: C1_CAF_023224_D8


title: CD44H-3

value: mesenchymal-like


title: CD44L-2


title: 4183

value: Low Only

value: Low


title: C1_CAF_023223_C8

value: CAF cells


title: PBMC6_6h_HI

description: total number of reads: 25618024

value: peripheral blood mononuclear cells (PBMCs)

tag: donor

tag: timepoint (hpi)

tag: infection

value: Heat-inactivated EV71


title: 5594

tag: subject id

tag: case/control


title: CD44H-1

value: breast cancer stem cell-like


title: C1_CAF_023220_F7


title: 4004

tag: study group

tag: sledai group


title: 6407


title: 6602


title: 6309


title: 6233


title: CD44L-1

value: epithelial-like


title: 3977


title: 6772


title: PTX3

value: HMLER


title: 6928


title: 500016


title: C1_CAF_023222_A8


title: C1_CAF_023219_E7


title: control3

value: control


title: C1_CAF_023218_D7


title: CD44H-2


title: C1_CAF_023221_H7


title: C1_CAF_023249_A12


title: 5944


title: ChIPseq_INPUT_SH4

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

description: ChIP-seq experiment

library_source: genomic

data_processing:
ChIP-seq analysis: Alignment: Sequence reads of the samples without spike-in were mapped to the human genome (hg19) using BOWTIE (PubMed ID 19261174) with the option -m 1. Sequence of the reads of hte samples with spike-in were mapped to a synthetic genome containing the human and the fruit fly chromosomes (hg19+dm3).
ChIP-seq analysis: Peak detection was performed with MACS (PubMed ID: 18798982). Peaks were reported in BED format. ChIP-seq genome-wide profiles without spike-in were normalized by the total number of reads of each sample. ChIP-seq genome-wide profiles with spike-in were normalized by the total number of fly reads of each sample.
ChIP-seq analysis: Differential peak calling between peaks reported for each pair of replicates in two conditions was performed using DiffBind (PubMed ID 22217937) with P value < 0.05 and FDR < 1
Genome_build: hg19
Supplementary_files_format_and_content: *.bdg.gz (BedGraph, genome-wide ChIP-seq/RNA-seq); *.bed (BED, ChIP-seq signal enriched regions); peaks.txt: DiffBind, ChIP-seq differential peak calling

molecule: genomic DNA

growth_protocol: DU145 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) (Gibco), 1x L-glutamine (Gibco) and 1x Pen/Strep (Gibco).

extract_protocol:
Chromatin preparation and ChIP experiments were performed with the ChIP-IT High Sensitivity Kit from Active Motif (#53040) according to the manufacturer’s instructions.
Libraries were prepared according to Illumina instructions.

value: Human prostate cancer cell line

tag: chip antibody

value: none (input)


title: ChIPseq_INPUT_from_MTF2_SH4_R2

description: ChIP-seq experiment


title: 4268

value: SLE Case

value: High Only


title: C1_CAF_023216_G6


title: ChIPseq_INPUT_from_MTF2_CTR_R2

description: ChIP-seq experiment


title: 4211


title: C1_CAF_023214_E6


title: ChIPseq_MTF2_SH4_R2

description: ChIP-seq experiment

value: MTF2 (Proteintech 16208-1-AP) / Drosophila H2Av (Active Motif #61686).


title: C1_CAF_023215_F6


title: 3896


title: 3799

value: High/Low


title: ChIPseq_MTF2_CTR_R2

description: ChIP-seq experiment


title: 3986


title: 7065

value: Control

value: no val


title: 5965

value: High


title: C1_CAF_023217_C7


title: 4329

value: Low


title: ChIPseq_INPUT_SH4_R2

description: ChIP-seq experiment


title: C1_CAF_023212_B6

value: CAF cells


title: ChIPseq_INPUT_CTR_R2

description: ChIP-seq experiment


title: 6660


title: C1_CAF_023213_D6


title: 4898


title: 3633


title: 4804

value: Low Only


title: ChIPseq_H3K27me3_SH4_R2

description: ChIP-seq experiment

value: H3K27me3 (Millipore #07-449) / Drosophila H2Av (Active Motif #61686).


title: 3644


title: 5950


title: 4293


title: 6169


title: ChIPseq_H3K27me3_CTR_R2

description: ChIP-seq experiment


title: C1_CAF_023209_G5


title: C1_CAF_023208_F5


title: C1_CAF_023211_A6


title: C1_CAF_023207_E5


title: 3791


title: C1_CAF_023210_H5


title: 5753


title: 500110


title: 6213


title: ChIPseq_SUZ12_CTR_R2

description: ChIP-seq experiment

value: SUZ12 (Abcam #ab12073)


title: ChIPseq_EZH2_SH4_R2

description: ChIP-seq experiment

value: EZH2 (Cell Signaling #5246)


title: ChIPseq_SUZ12_SH4_R2

description: ChIP-seq experiment


title: C1_CAF_023205_C5


title: 7181


title: C1_CAF_023206_D5


title: ChIPseq_PHF19_SH4_R2

description: ChIP-seq experiment

value: PHF19 (Cell Signaling #77271) / Drosophila H2Av (Active Motif #61686).


title: ChIPseq_EZH2_CTR_R2

description: ChIP-seq experiment


title: 3665


title: 3407


title: 5267


title: ChIPseq_PHF19_CTR_R2

description: ChIP-seq experiment


title: C1_CAF_023203_A5


title: 6603


title: C1_CAF_023202_H4


title: 7068


title: C1_CAF_023200_E4


title: 5696


title: 258

city: Cuernavaca

first: Fernanda

last: Cornejo

address: Av Universidad 2001

country: Mexico

institute: Instituto de Biotecnología UNAM

data_processing:
Quality filtering with Trimmomatic, remotion of adapters and ambiguous bases.
rRNA depletion with Ribopicker.
Alignment to the human genome and transcriptome (GRCh_snp_tran) with HISAT2
Non-human sequences were assembled using Trinity
Abundance of expression was determined by  FPKM was used for the normalization of sequencing depth and transcripts length, considerating only the transctipts with FPKM>1
Supplementary_files_format_and_content: normalized abundance measurements RSEM

source_name: fecal sample

extract_protocol:
Total RNA was extractedfrom fecal samples using the ZR Soil/Fecal RNA MicroPrep (Zymo Research) and RNeasy Mini Kit (Qiagen).
Libraries were prepared following the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs)

tag: phenotype

value: obese-metabolic syndrome


title: 146


title: 153


title: 090

value: obese


title: 7054


title: 4520


title: C1_CAF_023199_D4


title: 3733


title: 6354


title: 6525


title: 6077


title: 074


title: C1_CAF_023201_G4


title: 5639


title: C1_CAF_023198_B4


title: 024


title: 4776


title: 5984


title: C1_CAF_023197_G3


title: C1_CAF_023196_F3


title: 164

value: normal weight


title: 6785

value: SLE Case


title: 3887

value: High Only


title: C1_CAF_023194_D3


title: C1_CAF_023195_E3


title: RNAseq_PHF19S_SH168_Replicate1

description: RNA-seq experiment

data_processing:
RNA-seq analysis: Alignment: Sequence reads were mapped against the hg19 human genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1.
processed data files format and content: Files *.bdg.gz (BedGraph, genome-wide ChIP-seq/RNA-seq)
Genome_build: hg19

source_name: Human prostate cancer cell line

growth_protocol: DU145 cells were cultured in Dulbecco´s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) (Gibco), 1x L-glutamine (Gibco) and 1x Pen/Strep (Gibco).

extract_protocol:
(RNA-seq) RNA was extracted with the RNeasy kit (Qiagen) following manufacturer's instruction
Libraries were prepared according to Illumina instructions.

tag: tissue

value: Human prostate cancer cell line


title: 4943

value: High/Low


title: RNAseq_PHF19S_CTR_Replicate1

description: RNA-seq experiment


title: 6865


title: 4169


title: C1_CAF_023193_B3


title: C1_CAF_023192_H2


title: 015


title: 4146


title: RNAseq_PHF19L_CTR_Replicate3

description: RNA-seq experiment


title: 6426


title: RNAseq_PHF19L_SH4_Replicate3

description: RNA-seq experiment


title: RNAseq_PHF19L_SH4_Replicate2

description: RNA-seq experiment


title: C1_CAF_023190_F2


title: C1_CAF_023191_G2


title: C1_CAF_023189_E2


title: RNAseq_PHF19L_CTR_Replicate2

description: RNA-seq experiment


title: 6372


title: 4490


title: RNAseq_PHF19L_SH4_Replicate1

description: RNA-seq experiment


title: 4486


title: 541938

value: Control


title: C1_CAF_023204_B5


title: 3895


title: RNAseq_PHF19L_CTR_Replicate1

description: RNA-seq experiment


title: C1_CAF_023187_C2


title: 7540


title: 6503


title: ChIPseq_IGG_CTR

description: ChIP-seq experiment

data_processing:
ChIP-seq analysis: Alignment: Sequence reads of the samples without spike-in were mapped to the human genome (hg19) using BOWTIE (PubMed ID 19261174) with the option -m 1. Sequence of the reads of hte samples with spike-in were mapped to a synthetic genome containing the human and the fruit fly chromosomes (hg19+dm3).
ChIP-seq analysis: Peak detection was performed with MACS (PubMed ID: 18798982). Peaks were reported in BED format. ChIP-seq genome-wide profiles without spike-in were normalized by the total number of reads of each sample. ChIP-seq genome-wide profiles with spike-in were normalized by the total number of fly reads of each sample.
processed data files format and content: Files *.bdg.gz (BedGraph, genome-wide ChIP-seq/RNA-seq)
processed data files format and content: Files .bed (BED, ChIP-seq signal enriched regions)
Genome_build: hg19

extract_protocol:
(ChIP-seq) Chromatin preparation and ChIP experiments were performed with the ChIP-IT High Sensitivity Kit from Active Motif (#53040) according to the manufacturer’s instructions.
Libraries were prepared according to Illumina instructions.

value: IGG (Abcam #ab172730)


title: C1_CAF_023186_B2


title: Dim fraction of patient P40489 (ME)

type: genomic

city: Bronx

first: Boris

last: Bartholdy

state: NY

address: 1300 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
P40489-Dim

hyb_protocol: We used the EZ DNA Methylation kit (Zymo Research) for bisulfite conversion of 500 ng of genomic DNA obtained from at least 0.5 x 10e6 cells of each fractionated CLL sample. Further sample processing and hybridization was carried out according to Illumina's suggested guidelines.

scan_protocol: Arrays were imaged using iScan using standard manufacturer recommended scanner settings.

data_processing: The intensities of the images were extracted using GenomeStudio Methylation module software and processed in R/Bioconductor using the ‘ChAMP’ package and custom scripts. Briefly, we used default settings to filter out probes by detection p < 0.01 using the minfi method, discarded probes with < 3 beads in at least 5% of samples, performed BMIQ normalization to adjust for technical bias, followed by batch correction between slides using comBat from the ‘sva’ package, which resulted in improved correlation and tighter clustering of replicate samples. In addition, probes near SNPs and cross-hybridizing probes were removed using the rmSNPandCH function from the ‘DMRcate’ package. Only samples having Dim, Int, Br and Tot fractions and matching gene expression were used in the linked publication, the other samples were included in the normalization procedure, and the duplicate samples were used to assess performance of batch correction. We used limma to identify differentially methylated CpGs (DMC) using the M-values (logit-transformed beta-values) of the normalized, filtered methylation data.

label: Cy5 and Cy3

source_name: sorted CLL PBMCs

label_protocol: Methylation high-density profiling was carried out by using the Illumina Infinium HD Human Methylation 450K BeadChip according to manufacturer’s instructions.

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were separated by Ficoll-Paque density gradient centrifugation from heparinized venous blood obtained 3 months before, during or 3 months after the 6 week 2H2O labeling period, and cryopreserved. Before sorting, CLL PBMCs were thawed and incubated with murine anti-human monoclonal antibodies CD5-PECy7, CXCR4-PE, and CD19-Pacific Blue (BD Biosciences). After gating on CD19+CD5+ cells, equal numbers of viable cells falling into proliferative (“Dim”; CXCR4DimCD5Bright), intermediate (“Int”, CXCR4IntCD5Int, IF), resting (“Br”; CXCR4BrightCD5Dim), or Dbr (CXCR4BrightCD5Bright) based on reciprocal densities of CXCR4 and CD5 (~5% of the clone for each fraction) were sorted with a BD FACSAria. After sorting, cells were washed, pelleted, and stored at -80º until DNA extraction was performed.

tag: patient

tag: fraction

value: Dim

tag: ighv

value: M

tag: Sex

tag: birthrate (% cells/day)

value: sorted CLL PBMCs


title: C1_CAF_023188_D2

tag: cell type

value: CAF cells

tag: column in countmatrix


title: Br fraction of patient P40489 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
P40489-Br

extract_protocol: We used the EZ DNA Methylation kit (Zymo Research) for bisulfite conversion of 500 ng of genomic DNA obtained from at least 0.5 x 10e6 cells of each fractionated CLL sample.

value: Br


title: 3719

value: High


title: 5986


title: Tot fraction of patient P40489 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
P40489-Tot

value: Tot


title: 3778

value: Low Only

value: Low


title: 5035


title: C1_CAF_023185_A2


title: Int fraction of patient P40489 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
P40489-Int

value: Int


title: C1_CAF_023184_H1


title: ChIPseq_MTF2_SH4

description: ChIP-seq experiment

tag: cell line

value: MTF2 (Proteintech 16208-1-AP) / Drosophila H2Av (Active Motif #61686).


title: C1_CAF_023182_A1


title: ChIPseq_MTF2_CTR

description: ChIP-seq experiment


title: ChIPseq_INPUT_CTR

description: ChIP-seq experiment


title: Tot fraction of patient P40344 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
P40344-Tot


title: Br fraction of patient P40344 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
P40344-Br


title: ChIPseq_H3K27me3_SH4

description: ChIP-seq experiment

value: H3K27me3 (Millipore #07-449) / Drosophila H2Av (Active Motif #61686).


title: DBr fraction of patient P40344 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
P40344-DBr

value: DBr


title: 6292

value: SLE Case


title: Int fraction of patient P40344 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
P40344-Int


title: ChIPseq_H3K27me3_CTR

description: ChIP-seq experiment

value: Human prostate cancer cell line


title: 6537

value: High/Low


title: ChIPseq_INPUT_from_MTF2_CTR

description: ChIP-seq experiment


title: C1_CAF_023179_B11-1


title: Pellet fraction from D2R cells from the dorsal striatum (DS) (replicate 3)

city: Montpellier

first: Emmanuel

last: Valjent

address: 141, rue de la cardonille

department: Neurobiology

country: France

institute: INSERM

data_processing:
Illumina Base-calling (RTA 2.7.7)
Illumina demultiplexing ( no mismatches ) and fastq generation (bcl2fastq 1.8.4)
mapping against Mus musculus (GRCm38) with gem-split-mapper
gene quantification with gemtools (v1.7) and gencode annotation (v.M8)
Genome_build: GRCm38
Supplementary_files_format_and_content: txt (gene raw counts)

organism: Mus musculus

source_name: D2R-expressing neurons

extract_protocol:
Tagged ribosome-bound mRNAs were isolated by HA immunoprecipitation as described (Puighermanal et al 2016 ) and the RNA was extracted using RNeasy Microkit (Qiagen)
TruSeq®Stranded mRNA LT Sample Prep Kit (Illumina Inc., Rev.E, October 2013)

tag: genotype

tag: age

value: 2-4 months old

value: brain

tag: tissue region

value: dorsal striatum (DS)

value: D2R-expressing neurons

tag: rip antibody

value: anti-HA

value: Ribosome-bound RNA


title: Int fraction of patient P40323 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
P40323-Int

value: M

value: F

value: sorted CLL PBMCs


title: C1_CAF_023178_A11-1

value: CAF cells


title: ChIPseq_SUZ12_SH4

description: ChIP-seq experiment

value: SUZ12 (Abcam #ab12073) / Drosophila H2Av (Active Motif #61686).


title: Melanoma cell line subclone 2 MCM1D

city: Wien

first: David

last: Schörghofer

address: Währingerstraße 10

department: Department for Pathobiochemistry and Genetics

country: Austria

institute: Medical University of Vienna

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented,  labeled, and hybridized to each array as per manufacturer`s instructions (Affymetrix).

scan_protocol: The arrays were scanned using the appropriate Gene Chip Scanner.

data_processing:
CEL files were processed via the genotyping console 4.2.0 using default parameters. CHP files were generated via the genotyping console 4.2.0 using default parameters. Normalization was performed using the birdseed v2 algorithm.
primary data description: Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

source_name: Melanoma cell line MCM1D

label_protocol: According to the manufacturer`s protocol (Affymetrix)

growth_protocol: Melanoma cells were cultured in MIM medium supplemented with 2 % FCS containing: 80 % MCDB153, 20 % Leibovitz`s l15, 5 µg/ml Insuline, bovine, 0.5 ng/ml Epidermal Growth Factor (EGF), 1.68 mM CaCl2, 100 IU/ml Penicillin, 100 µg/ml Streptomycin and 2 µg/ml Ciprofloxacin at 37°C at 5% CO2

extract_protocol: DNA was isolated by using the All Prep DNA Kit (Qiagen, Hilden, Germany) according to the manufacturer`s protocol.

value: melanoma

tag: origin

value: Melanoma cell line MCM1D derived from MCM1

tag: cell malignancy

value: tumor forming and metastasizing to lymph nodes after injection into SCID mice

tag: gender

value: male


title: Tot fraction of patient P40323 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
P40323-Tot

value: Tot


title: Br fraction of patient P40323 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
P40323-Br

value: Br


title: ChIPseq_SUZ12_CTR

description: ChIP-seq experiment

value: Human prostate cancer cell line

tag: chip antibody


title: 5117

tag: subject id

tag: case/control

value: SLE Case

tag: study group

value: High/Low

tag: sledai group

value: High


title: Pellet fraction from D2R cells from the dorsal striatum (DS) (replicate 2)

value: 2-4 months old

tag: tissue

value: brain

value: dorsal striatum (DS)

value: D2R-expressing neurons

value: anti-HA

tag: fraction


title: Melanoma cell line subclone 3 MCM1DLN

source_name: Melanoma cell line MCM1DLN

tag: cell type

value: Melanoma cell line MCM1DLN derived from MCM1D

value: tumor forming and metastasizing to lymph nodes and lung after injection into SCID mice


title: C1_CAF_023181_A12-1

value: CAF cells

tag: column in countmatrix


title: Pellet fraction from D2R cells from the dorsal striatum (DS) (replicate 1)

value: Ribosome-bound RNA


title: Tot fraction of patient P39242 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
P39242-Tot

tag: patient

tag: ighv

value: M

tag: Sex

value: F

tag: birthrate (% cells/day)

value: sorted CLL PBMCs


title: C1_CAF_023177_B10-1


title: ChIPseq_EZH2_SH4

description: ChIP-seq experiment

tag: cell line

value: EZH2 (Cell Signaling #5246) / Drosophila H2Av (Active Motif #61686).


title: ChIPseq_EZH2_CTR

description: ChIP-seq experiment

value: Human prostate cancer cell line


title: C1_CAF_023175_F9-1


title: C1_CAF_023176_G9-1


title: 5549

value: SLE Case

value: Low


title: Dim fraction of patient P40344 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
P40344-Dim

value: Dim


title: Pellet fraction from Wfs1 cells from the nucleus accumbens (Acb) (replicate 2)

source_name: Wfs1-expressing neurons

tag: genotype

tag: age

value: 2-4 months old

tag: tissue region

value: nucleus accumbens (Acb)

value: Wfs1-expressing neurons

tag: rip antibody


title: C1_CAF_023174_E9-1


title: Melanoma cell line MCM1

source_name: Melanoma cell line MCM1

value: melanoma

tag: origin

value: Melanoma cell line MCM1 derived from a melanoma patient

tag: cell malignancy

value: tumor forming, but non-metastatic after injection into SCID mice

tag: gender

value: male


title: Br fraction of patient 994 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL994-Br

value: Br


title: Int fraction of patient P39242 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
P39242-Int

value: Int


title: Pellet fraction from Wfs1 cells from the nucleus accumbens (Acb) (replicate 1)

value: brain

value: anti-HA

value: Ribosome-bound RNA


title: ChIPseq_PHF19_CTR

description: ChIP-seq experiment

tag: chip antibody

value: PHF19 (Cell Signaling #77271)


title: Melanoma cell line subclone 1 MCM1G

source_name: Melanoma cell line MCM1G

value: Melanoma cell line MCM1G derived from MCM1


title: Dim fraction of patient P39242 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
P39242-Dim

value: M

value: F

value: sorted CLL PBMCs


title: Dim fraction of patient P40323 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
P40323-Dim

value: Dim


title: Pellet fraction from D2R cells from the nucleus accumbens (Acb) (replicate 3)

value: 2-4 months old

tag: tissue

value: nucleus accumbens (Acb)

value: D2R-expressing neurons


title: C1_CAF_023173_C9-1

description:
CAF, C1 Fluidigm platform
GeneCounts_caf_c1.csv

value: CAF cells


title: Pellet fraction from D2R cells from the nucleus accumbens (Acb) (replicate 2)

tag: fraction


title: C1_CAF_023172_B9-1

tag: cell type


title: Dim fraction of patient 994 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL994-Dim


title: lncap_wt_shFF_rep6_T14

city: Vancouver

first: Nathan

middle: Allan

last: Lack

state: British Columbia

address: 2660 Oak Street

department: Vancouver Prostate Centre

country: Canada

institute: University of British Columbia

data_processing:
Pre-Process: Removal of adapters and low quaility reads were applied with TrimGalore-0.4.5(default settings)
Mapping: hisat2-2.1.0 were used with default settings.
Read counting was conducted by htseq 0.11.1 (-q -f bam -m intersection-nonempty -i gene_id -r pos)
Count data was analysed by DeSeq2 package version 1.20.0.
Genome_build: hg19  and gencode.v29lift37.basic.annotation.gtf (Counting)
Supplementary_files_format_and_content: count

source_name: prostate cancer cell line

extract_protocol:
Total RNA was extracted from cells using Nucleospin® RNA kit (Macherey Nagel, Cat# 740955)
For sequencing, RNA libraries were prepared using standard Illumina protocols. Total RNA sample is digested by DNaseІ (NEB), and purified by oligo-dT beads (Dynabeads  mRNA purification kit, Invitrogen), then poly (A)-containing mRNA were fragmented into 130bp  with First Strand buffer. First-strand cDNA is generated by N6 primer, First Strand Master Mix and  Super Script II reverse transcription(Invitrogen) (Reaction condition：25℃ for 10 min；42℃ for 40  min；70℃for 15 min). Then add Second Strand Master Mix to synthesize the second-strand cDNA  (16℃ for 1h). Purified the cDNA with Ampure XP Beads (AGENCOURT), then combine with End  Repair Mix, incubate at 20℃for 30min. Purified and add A-Tailing Mix, incubate at 37℃ for 30  min. Then combine the Adenylate 3'Ends DNA, Adapter and Ligation Mix, incubate the ligate  reaction at 20℃for 20 min. Several rounds of PCR amplification with PCR Primer Cocktail and  PCR Master Mix were performed to enrich the cDNA fragments. Then the PCR products are  purified with Ampure XP Beads (AGENCOURT).

value: LNCaP

tag: ar dependence

value: Androgen-dependent

tag: shRNA treatment

value: shFF

tag: collection time (days)


title: C1_CAF_023171_D8-1

tag: column in countmatrix


title: Pellet fraction from D2R cells from the nucleus accumbens (Acb) (replicate 1)


title: lncap_wt_shFF_rep2_T14


title: C1_CAF_023180_C11-1


title: C1_CAF_023170_C8-1


title: lncap_wt_shFF_rep5_T14


title: Input of the dorsal striatum (DS) from D2R-Cre:RiboTag mice (replicate 3)

source_name: all cell types

value: dorsal striatum (DS)

value: all cell types

value: RNA


title: Int fraction of patient 994 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL994-Int

tag: patient

value: Int

tag: ighv

tag: Sex

tag: birthrate (% cells/day)


title: C1_CAF_023169_B8-1


title: lncap_wt_sh114_rep6_T14

tag: cell line


title: lncap_wt_sh114_rep5_T14


title: C1_CAF_023168_A8-1


title: Input of the dorsal striatum (DS) from D2R-Cre:RiboTag mice (replicate 1)

tag: genotype

tag: age

value: brain

tag: tissue region

tag: rip antibody


title: lncap_wt_sh114_rep2_T14


title: Pellet fraction from Wfs1 cells from the nucleus accumbens (Acb) (replicate 3)

value: Wfs1-expressing neurons

value: anti-HA

value: Ribosome-bound RNA


title: lncap_wt_sh113_rep6_T14


title: DBr fraction of patient 934 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL934-DBr

value: DBr

value: U

value: F

value: sorted CLL PBMCs


title: Input of the dorsal striatum (DS) from D2R-Cre:RiboTag mice (replicate 2)

value: 2-4 months old


title: Input of the nucleus accumbens (Acb) from Wfs1-CreERT2:RiboTag mice (replicate 2)

value: nucleus accumbens (Acb)


title: lncap_wt_sh113_rep5_T14

value: LNCaP


title: Int fraction of patient 934 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL934-Int


title: C1_CAF_023165_E7-1

value: CAF cells


title: ChIPseq_PHF19_SH4

description: ChIP-seq experiment

value: Human prostate cancer cell line

tag: chip antibody

value: PHF19 (Cell Signaling #77271)


title: lncap_wt_sh113_rep2_T14

value: Androgen-dependent


title: Input of the nucleus accumbens (Acb) from Wfs1-CreERT2:RiboTag mice (replicate 1)

tag: tissue

value: all cell types

value: RNA


title: Input of the nucleus accumbens (Acb) from Wfs1-CreERT2:RiboTag mice (replicate 3)

value: brain

tag: fraction


title: C1_CAF_023167_G7-1

tag: cell type


title: Br fraction of patient 934 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL934-Br

value: Br


title: C1_CAF_023164_D7-1


title: Input of the nucleus accumbens (Acb) from D2R-Cre:RiboTag mice (replicate 3)


title: abl_shFF_rep6_T14

value: LNCaP-abl

tag: ar dependence

value: Androgen-independent

value: shFF


title: Tot fraction of patient 994 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL994-Tot

value: Tot

value: M


title: Tot fraction of patient 934 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL934-Tot

value: U

value: F

value: sorted CLL PBMCs


title: Input of the nucleus accumbens (Acb) from D2R-Cre:RiboTag mice (replicate 2)

value: 2-4 months old

value: nucleus accumbens (Acb)


title: abl_shFF_rep5_T14

tag: shRNA treatment


title: C1_CAF_023163_C7-1

value: CAF cells


title: C1_CAF_023162_B7-1


title: Input of the nucleus accumbens (Acb) from D2R-Cre:RiboTag mice (replicate 1)


title: abl_shFF_rep2_T14

tag: collection time (days)


title: WT-T3-Dam-14

city: New York

first: Patrizia

last: Casaccia

address: 85 St Nicholas Terrace

department: Neuroscience

institute: ASRC-CUNY

data_processing:
Library strategy: DamID-seq
Illumina HiSeq2000
FASTQs filtered for reads containing DamID primer sequence using cutadapt v1.9.1
Trimmed reads aligned to mm10 reference with BWA-MEM v0.7.17
Counts were cpm normalized; Log2 ratio of tethered Dam-ID to untethered Dam calculated and smoothed in 400bp non-adjacent windows
Differential analysis between T3 and PF samples were done with student T tests and Benjamini-Hochberg corrected
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited data table - mean scores depict DNA to laminB association in sample; bigwig files

source_name: Oligodendrocyte

growth_protocol: Mouse OPCs isolated from brain cortex of C57BL/6 mice postnatal day 7

extract_protocol:
genomic DNA amplified with methylation specific PCR and purified using Qiaquick columns
TruSeq DNA HT Sample Prep Kit

treatment_protocol: Transduced with lentiviral vectors expressing either tethered Dam-LMNB1 or untethered Dam for 1 day. Grown for 72 hours in OPC proliferationg media (PF) or OL differentiating media (T3)

value: Mouse Primary OPCs

tag: strain


title: C1_CAF_023161_A6-1

tag: column in countmatrix


title: abl_sh114_rep2_T14


title: Tot fraction of patient 753 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL753-Tot

tag: patient

tag: ighv


title: Dim fraction of patient 934 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL934-Dim

value: Dim

tag: Sex

tag: birthrate (% cells/day)


title: C1_CAF_023160_D4-1


title: C1_CAF_023159_C4-1


title: C1_CAF_023166_F7-1


title: WT-T3-Dam-12


title: Int fraction of patient 753 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL753-Int

value: Int


title: abl_sh114_rep6_T14

tag: cell line


title: Dim fraction of patient 753 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL753-Dim


title: abl_sh113_rep5_T14


title: WT-T3-Dam-13


title: C1_CAF_023157_G3-1


title: abl_sh113_rep2_T14


title: DBr fraction of patient 753 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL753-DBr

value: DBr


title: C1_CAF_023156_D3-1


title: abl_sh113_rep4_T7


title: WT-T3-Dam-Lmnb1-18


title: Br fraction of patient 753 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL753-Br


title: WT-T3-Dam-Lmnb1-20


title: WT-PF-Dam-4

source_name: Oligodendrocyte Precursor Cell


title: Br fraction of patient 678 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL678-Br


title: abl_sh113_rep3_T7


title: C1_CAF_023154_E2-1


title: DBr-2 fraction of patient 934 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL934-DBr-2


title: Tot fraction of patient 678 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL678-Tot


title: abl_sh113_rep2_T7


title: abl_sh113_rep1_T7


title: WT-PF-Dam-Lmnb1-10


title: C1_CAF_023152_C2-1

description:
CAF, C1 Fluidigm platform
GeneCounts_caf_c1.csv


title: C1_CAF_023153_D2-1


title: Int fraction of patient 678 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL678-Int


title: WT-T3-Dam-Lmnb1-19


title: abl_shFF_rep4_T7


title: C1_CAF_023155_B3-1


title: WT-PF-Dam-Lmnb1-9


title: Tot fraction of patient 650 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL650-Tot


title: C1_CAF_023151_B2-1


title: C1_CAF_023158_B4-1


title: abl_shFF_rep3_T7


title: Int fraction of patient 650 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL650-Int


title: KO6

city: Heidelberg

first: Guoliang

last: Cui

address: Im Neuenheimer Feld 280

country: Germany

institute: German cancer research center (DKFZ)

data_processing:
base calling bcl2fastq 2.19.0.316
low quality bases were removed with Fastq_quality_filter from the FASTX Toolkit 0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/index.html) with 90% of the read needing a quality phred score > 20. Homertools 4.7 33 were used for PolyA-tail trimming, and reads with a length < 17 were removed.
With STAR 2.3 34, the filtered reads were mapped against mouse genome 38 (mm10) using default parameters
Count data were generated using featureCounts 35(parameters --minReadOverlap 3 -T 3 -M -O) for the genes annotated in the gencode.vM16.gtf file.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts for all samples in a tab-separated text file annotated with Ensembl-Ids from gencode.vM16.gtf

source_name: Mouse T cells

extract_protocol:
We extracted RNA using the QIAGEN RNeasy Mini Kit and removed genomic DNA using the QIAGEN RNase-Free DNase Set
SmarTer Ultra Low Input RNA and Illumina Trueseq Stranded RNA-Kit was used for library construction. libraries were pooled with five samples in each lane and sequenced (Illumina HiSeq 2000 v4 Single-Read 50 bp)

treatment_protocol: Mice receiving Tcf7-deficient and -sufficient TCR transgenic P14 CD8+ T cells were infected with influenza A X31-33. Eight days after infection, the mice were injected with PE-conjugated anti-CD8beta to intravascularly label circulating CD8+ T cells. Lung-infiltrating T cells were stained with CD8a and CD103. CD103high Tcf7-deficient and -sufficient P14 CD8+ T cells were FACS-sorted on day 8 after X31 infection for RNA extraction and RNA sequencing (RNA-seq) analysis.

value: lung infiltrating

value: CD8+ T cells

tag: age

tag: genotype

value: Tcf7 knockout


title: Dim fraction of patient 678 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL678-Dim


title: Br fraction of patient 650 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL650-Br

value: Br


title: abl_shFF_rep2_T7

value: LNCaP-abl

value: Androgen-independent

value: shFF


title: C1_CAF_023150_E1-1


title: DBr fraction of patient 650 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL650-DBr

value: U

value: M


title: C1_CAF_023149_D1-1


title: WT-PF-Dam-Lmnb1-8


title: abl_sh113_rep6_T14


title: KO3


title: abl_shFF_rep1_T7


title: C1_CAF_023148_C1-1


title: Dim fraction of patient 650 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL650-Dim

value: sorted CLL PBMCs


title: Arcuate nucleus, Phf6_Input_Fasted_condition

first: Qian

address: 280 South Chongqing Road, Building No.5, Room 408

department: Department of Anatomy and Physiology

institute: Shanghai Jiao Tong University School of Medicine

description: Phf6_ChIPSeq_Fasted_condition_FoldEnrichment.bw

data_processing:
ChIPseq reads were mapped to the mouse reference genome (GRCm38/mm10, downloaded from UCSC, http://genome.ucsc.edu/) using Bowtie 2 (version 2.2.9) with the following parameters: --local –X 2000.
Significant peaks were called using MACS2 (version 2.1.1.20160309) with “-f BAMPE” option and default threshold of q value (BH-adjusted p value) cutoff at 0.05.
The bedgrap file containing the signal ratio of ChIP to Input samples was acquired using MACS2 WITH “bdgcmp -m FE” option.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig file containing the signal ratio of ChIP to input.

source_name: Arcuate nucleus

growth_protocol: Enriched ARC tissue dissected within 3 hours from 100 fed and 100 fasted wild-type mice (6-7 weeks old)

extract_protocol:
Lysates were clarified from sonicated nuclei and PHF6-chromatin complexes were isolated with PHF6 antibody.
Libraries were prepared following the NEB/NEBNext® Library Quant Kit for Illumina®(E7630S). Amplified libraries were size-selected using a 2% gel to capture fragments between 200 bp and 500 bp.

value: 6-7 weeks

value: wild type

tag: feeding condition

value: Fasted

value: Arcuate nucleus


title: DBr fraction of patient 638 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL638-Dbri


title: C1_CAF_023147_B1-1

source_name: whole cell

value: CAF cells


title: WT6

value: Tcf7 wildtype


title: WT3


title: Arcuate nucleus, Phf6_Input_Fed_condition

description: Phf6_ChIPSeq_Fed_condition_FoldEnrichment.bw

value: Fed

tag: chip antibody


title: Arcuate nucleus, Phf6_ChIP_Fed_condition

tag: tissue

value: Phf6 (Sigma Aldrich, HPA001023)


title: Arcuate nucleus, Phf6_ChIP_Fasted_condition


title: WT-PF-Dam-2

value: Mouse Primary OPCs


title: WT2

value: lung infiltrating

value: CD8+ T cells


title: Tot fraction of patient 638 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL638-Tot

tag: fraction

value: Tot


title: Wild-type Rep4

city: Houston

first: Laura

last: Lavery

state: TX

address: 1250 Moursund St., Suite 1350

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: Total RNA-seq from inhibitory neruons sorted from the striatum of a male wild-type mouse

data_processing:
Illumina HiSeq 2500
Raw reads were mapped to reference genome GRCm38 (GENCODE vM15 Primary assembly) using STAR aligner67 (version 2.5.3a) .
The number of reads aligned within the gene body (from TSS to TES) of each gene was tabulated using FeatureCount68 (v1.5.3) . This read counts obtained are analogous to the expression level of the gene.
Using the obtained read counts, differential gene analyses were carried out using the DESeq2(v1.6.2) package in the R environment.
Genome_build: GRCm38 (GENCODE vM15 Primary assembly)
Supplementary_files_format_and_content: Text files inclue read counts value for each gene; individual file for each sample.

source_name: Wild-type mouse #4

growth_protocol: standard animal house conditions

extract_protocol:
Single Cell RNA Purification Kit (Norgen Biotek corp.)
NuGEN Ovation RNA-Seq v2 & Rubicon ThruPlex DNA-Seq

value: whole striatum


title: Dim fraction of patient 638 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL638-Dim

value: Dim

tag: cell type


title: DBr fraction of patient 678 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL678-DBr

value: DBr

value: F


title: Int fraction of patient 638 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL638-Int

value: Int

value: M

value: sorted CLL PBMCs


title: KO2

value: Tcf7 knockout


title: C1_CAF_023146_A1-1


title: 121516 Het GK1.5-4

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from heterotypic immune, CD4+ cell deficient C57BL/6 mice.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray mogene20stmmentrezgcdf R package (version 17.0.0).

source_name: C57BL/6 mice

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: Pneumococci were grown on Blood agar (BA) plates for 14 hours at 37C 5% CO2. Sp19F was restreaked on BA plates for 4 hours at 37C 5% CO2 before infections.

extract_protocol: Single cell suspensions were generated by digestion with elastase, as previously described. Cells were isolated using a FACS Aria II after antibody staining for CD45, EpCAM, and 7AAD (viability dye).  RNA was prepared using TRIzol via the manufacturer’s recommendation. Isolated RNA was purified and DNase I treated using the RNAeasy column method (Qiagen).

treatment_protocol: Heterotypic protection was generated as previously described. Mice were infected intratracheally (i.t.) with 1-5x10^6 CFU of serotype 19F pneumococcus (Strain EF3030) or saline. A week later, mice were exposed again to either saline or Sp19F and then allowed to recover for 28-35 days. After recovery, mice were challenged i.t. with 1x10^6 CFU of serotype 3 pneumococcus (Strain ATCC6303). CD4+ cells were depleted using 500μg and 100μg of GK1.5 [BioXcell, West Lebanon, NH] i.p. and i.n. respectively, both 72 and 24 hours prior to the i.t. Sp3 challenge.

value: lung

value: lung epithelial cells

tag: cell markers

tag: exposure

tag: antibody

value: anti-CD4 GK1.5

tag: experiment date


title: WT1

tag: strain

value: Tcf7 wildtype


title: 121516 Het GK1.5-3


title: DBr fraction of patient 625 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL625-DBr

tag: patient

value: U


title: Wild-type Rep3

source_name: Wild-type mouse #3


title: Tot fraction of patient 625 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL625-Tot

source_name: sorted CLL PBMCs

tag: ighv


title: MaIL1_2_MS-RAP

city: Marburg

first: Leon

middle: Nicolas

last: Schulte

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

institute: Philipps-Universität Marburg

description: MaIL1 MS-RAP, replicate 2

data_processing:
RTA version 1.18.66.4 was used for basecalling
bcl2fastq version 1.8.4. was used for demultiplexing
Reads were mapped using the CLC genomics workbench version 10.01 and the GRCh38 human genome annotation with standard settings: mismatch cost = 2; insertion cost = 3; deletion cost = 3; length fraction = 0.8; similarity fraction = 0.8.
RPKMs were calculated based on uniqely mapped read numbers reported by the CLC genomics worbench version 10.01
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text-files including ENSEMBL gene ID, gene alias, chromosome, genomic position, unique gene reads, RPKM (samples Gradient_f1-f22: spike-in normalized RPKMs)

molecule: polyA RNA

source_name: Peripheral blood leukocytes

growth_protocol: peripheral blood derived CD14+ monocytes (MACS enrichement) were differentiated in cell culture plastic multi-well plates (4*10e5 cell per 12-well, 1 ml of medium per well) using X-Vivo-15 medium supplemented with 5 % FCS and 20 ng / ml of recombinant human GM-CSF for 8 days

extract_protocol:
Cells were washed once with PBS and RNA was extracted with Trizol. For subcellular fractionation cells were lysed with mild detergent buffer and nuclei and cytosol were seperated by centrifugation at low speed. Cytosol was cleared from remaining nuclei by high speed centrifugation and nuclear fraction was carefully washed twice with mild detergent buffer before RNA-Extraction with Trizol.
Libraries were prepared using the Illumina TruSeq Stranded mRNA kit according to the manufacturer's protocol or an in-house total RNA strand-specific library protocol from Vertis Biotech AG (Freising, Germany)

treatment_protocol: cells were stimulated with Escherichia coli LPS at a concentration of 100 ng / ml for 8 h. Samples 1-8: Cells were pre-incubated with DMSO or inhibitors for 2 h prior to LPS-stimulation

value: D8 GM-CSF macrophage

tag: precursor

value: CD14+ monocyte

tag: donor

value: healthy, caucasian

tag: agent

value: MaIL1 MS-RAP


title: Wild-type Rep2

source_name: Wild-type mouse #2

value: whole striatum


title: MaIL1_1_MS-RAP

description: MaIL1 MS-RAP, replicate 1


title: Wild-type Rep1

source_name: Wild-type mouse #1


title: Br fraction of patient 638 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL638-Br

value: Br

tag: Sex

tag: birthrate (% cells/day)


title: Dnmt3a cKO Rep4

description: Total RNA-seq from inhibitory neruons sorted from the striatum of a male Dnmt3a cKO mouse

source_name: Dnmt3a cKO mouse #4

tag: genotype


title: C2_MS-RAP

description: control MS-RAP, replicate 2

value: control MS-RAP


title: 120816 Het GK1.5-2


title: KO1

value: lung infiltrating

value: CD8+ T cells

tag: age


title: 120816 Het GK1.5-1

tag: tissue


title: 121516 Het IgG-4

description: Gene expression data from heterotypic immune, CD4+ cell sufficient C57BL/6 mice.

value: IgG


title: Dnmt3a cKO Rep3

source_name: Dnmt3a cKO mouse #3


title: Dnmt3a cKO Rep2

source_name: Dnmt3a cKO mouse #2


title: 120816 Het IgG-2


title: C1_MS-RAP

description: control MS-RAP, replicate 1


title: siMaIL1+LPS_2

description: MaIL1 siRNA2, LPS, replicate 2

value: MaIL1 siRNA2, LPS


title: siMaIL1+LPS_1

description: MaiL1 siRNA1, LPS, replicate 1

value: MaiL1 siRNA1, LPS


title: Dnmt3a cKO Rep1

source_name: Dnmt3a cKO mouse #1


title: Dim fraction of patient 625 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL625-Dim

tag: fraction

value: Dim

value: M

value: sorted CLL PBMCs


title: siCTR+LPS t_2

description: control siRNA, LPS, replicate 2

tag: cell type

value: control siRNA, LPS


title: MeCP2 cKO Rep4

description: Total RNA-seq from inhibitory neruons sorted from the striatum of a male MeCP2 cKO mouse

source_name: MeCP2 cKO mouse #4


title: 121516 Het IgG-3

value: lung

value: lung epithelial cells

tag: cell markers


title: 121516 Saline IgG-4

description: Gene expression data from naïve, CD4+ cell sufficient C57BL/6 mice.

tag: exposure

value: saline


title: 120816 Het IgG-1

tag: antibody


title: 121516 Saline IgG-3

tag: experiment date


title: siCTR+LPS_1

description: control siRNA, LPS, replicate 1

value: D8 GM-CSF macrophage

value: CD14+ monocyte

value: healthy, caucasian


title: MeCP2 cKO Rep3

source_name: MeCP2 cKO mouse #3

tag: strain

value: whole striatum


title: MeCP2 cKO Rep2

source_name: MeCP2 cKO mouse #2


title: DBr fraction of patient 609 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL609-DBr

tag: patient

value: DBr

value: U


title: siCTR2

description: control siRNA, mock, replicate 2

value: control siRNA, mock


title: Int fraction of patient 625 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL625-Int

value: Int

tag: ighv


title: siCTR1

description: control siRNA, mock, replicate 1

tag: precursor


title: Int fraction of patient 609 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL609-Int


title: 177I

city: San Francisco

first: Tatsuya

last: Tsukui

state: CA

address: 555 Mission Bay Blvd South, 282

department: Medicine

institute: UCSF

data_processing:
Demultiplex and basecall to fastq with cellranger mkfastq
Trimming of Read 2 for TSO and poly(A) with cutadapt
filtering, alligning, and barcode collapsing with zUMIs 2.0 (STAR 2.6.0 for alignment)
Cells filtered with > 12% of transcriptome from intron-spanning reads; < 20% mitochondrial origin; at least 1000 unique genes
ensembl gene IDs translated to HGNC only when a 1:1 translation was feasible using the R package biomaRt with the "Oct 2018" ensembl archive
All cells were removed that belonged to immune (PTPRC+), epithelial (EPCAM+) and entothelial populations (PECAM1+). Only collagen expressing mesenchymal cell populations remain
Genome_build: GRCh38 Release 91
Supplementary_files_format_and_content: RawCounts_triples.txt: Gene expression UMI counts of all intron and exon spanning transcripts. Data is a tab delimited text file in triples format. Three columns: "row" is the gene, "col" is the cell barcode, and "UMI_Counts" is the associated non-zero raw UMI count
Supplementary_files_format_and_content: Cell_MetaData.txt: MetaData to describe all 6,607 cells; including subject and  disease status. Each row represents a different cell barcode, columns are metadata including subject, library and disease status

source_name: Whole Lung Dissociate; Collagen expressing mesenchymal cells only

extract_protocol:
Thawed Cells were rinsed with 10% FBS; passed through 40 uM strainer
10X Genomics 3 prime v2

treatment_protocol: Enzymatic and Mechanical Digestion; Cryopreservation in 10% DMSO

tag: disease

value: IPF


title: MeCP2 cKO Rep1

source_name: MeCP2 cKO mouse #1


title: 158I


title: Br fraction of patient 625 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL625-Br

value: Br


title: Br fraction of patient 609 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL609-Br


title: 123I


title: 034I


title: LPS_3

description: LPS replicate 3

tag: donor

tag: agent

value: LPS


title: Tot fraction of patient 606 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL606-Tot

value: Tot

value: M

tag: Sex

tag: birthrate (% cells/day)


title: LPS_Cytosol_2

description: LPS, cytosol, replicate 2

data_processing:
RTA version 1.18.66.4 was used for basecalling
bcl2fastq version 1.8.4. was used for demultiplexing
Reads were mapped using the CLC genomics workbench version 10.01 and the GRCh37 human genome annotation with standard settings: mismatch cost = 2; insertion cost = 3; deletion cost = 3; length fraction = 0.8; similarity fraction = 0.8.
RPKMs were calculated for genes using the CLC genomics worbench version 10.01
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text-files including ENSEMBL gene ID, gene alias, chromosome, genomic position, unique gene reads, RPKM (samples Gradient_f1-f22: spike-in normalized RPKMs)

extract_protocol:
Cells were washed once with PBS and RNA was extracted with Trizol. For subcellular fractionation cells were lysed with mild detergent buffer and nuclei and cytosol were seperated by centrifugation at low speed. Cytosol was cleared from remaining nuclei by high speed centrifugation and nuclear fraction was carefully washed twice with mild detergent buffer before RNA-Extraction with Trizol.
Libraries were prepared using the Illumina TruSeq Stranded mRNA kit according to the manufacturer's protocol

treatment_protocol: cells were stimulated with Salmonella typhimurium LPS at a concentration of 100 ng / ml for 4 h. Samples 1-8: Cells were pre-incubated with DMSO or inhibitors for 2 h prior to LPS-stimulation

value: Peripheral blood leukocytes


title: mock_3

description: Mock control replicate 3

value: Mock control


title: 063I

tag: age


title: LPS_Nucleus_2

description: LPS, nucleus, replicate 2

tag: tissue


title: 59I

value: F


title: Br fraction of patient 606 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL606-Br

tag: fraction

value: sorted CLL PBMCs


title: Ctrl_Cytosol_2

description: Mock, cytosol, replicate 2

tag: cell type

value: D8 GM-CSF macrophage


title: Tot fraction of patient 609 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL609-Tot


title: Dim fraction of patient 609 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL609-Dim

value: Dim


title: 053I


title: 49I


title: DBr fraction of patient 606 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL606-DBr


title: LPS_Cytosol_1

description: LPS, cytosol, replicate 1

value: CD14+ monocyte

value: healthy, caucasian


title: Int fraction of patient 606 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL606-Int


title: Dim fraction of patient 606 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL606-Dim


title: LPS_Nucleus_1

description: LPS, nucleus, replicate 1


title: Ctrl_Nucleus_2

description: Mock, nucleus, replicate 2


title: 040I


title: Ctrl_Cytosol_1

description: Mock, cytosol, replicate 1


title: 120816 Saline IgG-2

value: lung

value: lung epithelial cells

tag: cell markers

value: saline

value: IgG


title: 041I

value: IPF


title: DBr-2 fraction of patient 584 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL584-DBr-2

value: DBr


title: Ctrl_Nucleus_1

description: Mock, nucleus, replicate 1


title: 022I


title: LPS_DMSO_2

description: LPS + DMSO control replicate 2


title: Br fraction of patient 584 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL584-Br

value: Br


title: 120816 Saline IgG-1

tag: exposure


title: DBr fraction of patient 584 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL584-DBr


title: 021I


title: 010I


title: DMSO_2

description: DMSO control replicate 2


title: DBr fraction of patient 569 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL569-Dbr

value: U


title: Tot fraction of patient 584 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL584-Tot

value: Tot

value: M


title: DMSO_1

description: DMSO control replicate 1

value: Peripheral blood leukocytes


title: LPS_DMSO_1

description: LPS + DMSO control replicate 1


title: 051I


title: osnrpd1ab_base_mRNA180209_rep3

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

institute: Tsinghua University

data_processing:
For whole-genome bisulfite sequencing, reads were mapped and analyzed with BRAT-BW (Harris et al., 2012). For small RNA sequencing, reads were mapped with Bowtie and analyzed by in-house PERL scripts. For RNA sequencing, reads were mapped with Tophat and differentially expressed genes were identified with DESeq2.
Genome_build: RGAP7
Supplementary_files_format_and_content: bigwig for whole-genome bisulfite sequencing; expression matrix for RNA sequencing; raw read counts for small RNA sequencing

organism: Oryza sativa Japonica Group

source_name: shoot base of seedling

growth_protocol: Seedlings of WT and transgenic lines were grown in the green chambers at 70% humidity, under conditions with daily cycles of 12 h of light at 30 °C and 12 h of dark at 25 °C.

extract_protocol:
For whole-genome bisulfite sequencing, genomic DNA was purified from the shoot base of 4-week-old seedlings using the DNeasy Plant Mini Kit (QIAGEN, 69104). For RNA sequencing, total RNA was purified from the shoot base of 4-week-old seedlings using the RNeasy Plant Mini Kit (QIAGEN, 74904). For small RNA sequencing, total RNA was purified from the shoot base of 4-week-old seedlings using TRIzol reagent (Invitrogen, 15596026). Large RNAs were selectively precipitated using 5% PEG8000 (Sigma, P5413) and 0.5 M NaCl (Sigma, S3014). Small RNAs were recovered from the supernatant by ethanol precipitation and then separated by electrophoresis using a 15% denaturing PAGE gel.
Paired-end bisulfite sequencing libraries were generated using the NEXTflex Bisulfite-Seq kit (BIOO SCIENTIFIC, NOVA-511911). Briefly, genomic DNA was sonicated to ~300 bp, end repaired and 3’ adenylated. The products were ligated with methylated adapters and then subject to size selection using Ampure XP purification beads (Beckman, A63881). Bisulfite treatment was carried out using the EZ DNA Methylation-Gold kit (ZYMO Research, D5005) according to the manufacturer’s instructions. Bisulfite-converted DNA products were amplified by PCR for 15 cycles using EX Taq DNA polymerase (Takara, RR001C). The PCR products were cleaned up using Ampure XP purification beads (Beckman, A63881). The constructed libraries were validated using the Agilent 2100 Bioanalyzer and paired-end sequenced in 150-bp on an Illumina X-Ten platform. Libraries for RNA sequencing were generated using NEXTflex RNA-Seq Kit (Bioo Scientific) according to the manufacturer’s instructions. Libraries for small RNA sequencing were generated using NEBNext Small RNA Library Prep Set for Illumina (NEB).

value: shoot base

tag: treatment

tag: substrate

value: nutrient soil


title: TN2

city: Curitiba

first: Patricia Midori

last: Murobushi Ozawa

state: PR

address: Av. Cel. Francisco H. dos Santos, 100

department: Genetics

country: Brazil

institute: Federal University of Parana

description:
Extracellular-vesicle derived miRNA
6G

data_processing:
The data alignment and mapping were performed on MiRMaster platform
DE miRNAs observed in the RNA-seq analysis were identified using the package DESeq2, on R studio.
The Benjamini and Hochberg method was used for multiple comparisons, with adjusted p<0.05 considered significant
Genome_build: hg38
Supplementary_files_format_and_content: Raw data used for analysis in txt. Excel files with ID and corresponding names, as well with processed results.

source_name: Serum

extract_protocol:
Approximatelly 1 mL of serum was used to isolate extracellular vesicles, using the kit Total Exosome Isolation Reagent from Serum (Invitrogen, CA, USA), according to manufacturer’s instructions. MiRNAs-derived from extracellular vesicles were extracted using miRVana™ miRNA Isolation Kit (Ambion, CA, USA), modified with addition of Trizol (Invitrogen, CA, USA) in substitution to phenol. All samples were ressuspended at 20µL final volume and then mixed to form the pools. Each pool was comprised of a mix of sample as follow: (CT1 (n=5), CT2 (n=5), LA1 (n=5), LA2 (n=5), TNBC1 (n=4) and TNBC2 (n=4). All pools had were composed of individuals with matching ages.
The libraries were constructed through Ion Total-RNA Seq Kit v2 (Life Technologies, CA, USA), according to manufacturer’s instructions.

value: Pools of 5 breast cancer patients

tag: group

value: Triple Negative

value: female


title: 29I


title: Dim fraction of patient 584 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL584-Dim

tag: patient

value: Dim

value: sorted CLL PBMCs


title: Int fraction of patient 584 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL584-Int

value: Int

tag: ighv


title: 025I


title: 228I


title: Br fraction of patient 569 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL569-Br


title: LA2

description:
Extracellular-vesicle derived miRNA
4G

value: Luminal A


title: LA1

description:
Extracellular-vesicle derived miRNA
3G


title: 225I

value: F


title: DBr fraction of patient 499 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL499-DBr


title: 222I

value: IPF


title: Tot fraction of patient 569 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL569-Tot


title: osnrpd1ab_base_BSseq180209_rep2


title: CT2

description:
Extracellular-vesicle derived miRNA
2G

value: Pools of 5 healthy control

value: Healthy control


title: Dim fraction of patient 569 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL569-Dim

value: U


title: Int fraction of patient 569 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL569-Int


title: 221I


title: osnrpd1ab_base_mRNA180209_rep2


title: osnrpd1ab_base_mRNA180209_rep1


title: Int fraction of patient 499 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL499-Int


title: Br fraction of patient 499 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL499-Br

value: Br


title: osnrpd1ab_base_BSseq180209_rep1


title: osnrpd1ab_base_BSseq180209_rep3


title: CT1

description:
Extracellular-vesicle derived miRNA
1G


title: 214I

value: M


title: TN1

description:
Extracellular-vesicle derived miRNA
5G


title: 212I


title: Tot fraction of patient 493 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL493-Tot

value: Tot


title: At_mut1b_DNA-seq

city: Brno

first: Vivek

middle: Kumar

last: Raxwal

address: building A26, Kamenice 753/5

department: Plant Molecular Biology

country: Czech Republic

institute: Central European Institute of Technology

description: Whole Genome DNA library

data_processing:
Library strategy: DNA-seq, 100bp single read HiSeq
quality filteration of reads using Trim Galore version 0.4.1
alignment to TAIR10 genome with BWA  version 0.7.17-r1188
sorting, removing of duplicates  and variant calling with Samtools version version 1.9
subtraction of snps with Bedtools version 2.27.1
Genome_build: TAIR10
Supplementary_files_format_and_content: vcf file showing coordinates of snps

source_name: whole seedling

growth_protocol: Seedlings  were germinated on 1/2MS media supplemented with 1% sucrose and grown vertically in a controlled environment (21°C, 16 h/8 h light/dark) for 5 days.

extract_protocol:
DNA from rosette leaves of approx. 3 weeks old mutant candidates was extracted with CTAB method.
DNA Library Prep Kit for Illumina | NEB

treatment_protocol: 5-d-old seedlings expressing PIN1:PIN1-GFP were co-treated with 10 μM NAA and 25 μM BFA for 1 hour and screened under the fluorescent microscope for individuals with PIN1- GFP signal accumulated in BFA bodies.

tag: ecotype

value: Columbia-0 (Col-0)

tag: genotype

value: 5-day-old seedlings

value: whole seedling


title: WT_base_mRNA180209_rep2

value: shoot base

value: nutrient soil


title: 47I

tag: disease


title: At_mut1c_DNA-seq

description: Whole Genome DNA library


title: At_mut1a_DNA-seq

description: Whole Genome DNA library


title: WT_base_BSseq180209_rep3


title: Int fraction of patient 493 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL493-Int


title: At_Control_DNA-seq

description: Whole Genome DNA library

value: control


title: Tot fraction of patient 499 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL499-Tot

value: sorted CLL PBMCs


title: 209I


title: 179I


title: WT_base_BSseq180209_rep2


title: Br fraction of patient 493 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL493-Br


title: agtcl20ab_5

city: Planegg

first: Tatjana

last: Kleine

address: Großhaderner Straße 2

department: Biologie I, Botanik

institute: Ludwig-Maximilians-Universität München

data_processing:
Galaxy platform
adaptors were removed with Trimmomatic (Bolger et al., 2014)
sequencing quality was accessed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were mapped to the Arabidopsis genome (TAIR10) with the gapped-read mapper TopHat 2.1.1 (Kim et al., 2013) set for Forward Read (FR) unstranded libraries and adjusting the maximum intron length to 5000 bp.
Reads were counted with featureCounts (Liao et al., 2014) with the help of the gene annotation in Araport11 (www.araport.org/data/araport11).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited file includes read count values for each sample

source_name: whole plant

growth_protocol: Plants were grown on potting soil (A210, Stender) under controlled greenhouse conditions (70-90 µE m-2 s-1, 16/8 h light/dark cycles).

extract_protocol:
the RNeasy Mini Kit (Qiagen). RNA quality was tested by agarose gel electrophoresis. Additional quality checks, RNA-Seq library preparation and long non-coding RNA sequencing (lncRNA-Seq) were performed at Novogene Biotech (Beijing, China) using standard protocols.
Illumina Tru-Seq
lncRNA-Seq

treatment_protocol: Total RNA was extracted from four-week-old wild-type and five-week-old atcgl20ab plants


title: WT_base_mRNA180209_rep3


title: WT_base_mRNA180209_rep1


title: atcgl20ab_4


title: Tot-2 fraction of patient 493 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL493-Tot-2

source_name: sorted CLL PBMCs


title: DBr-2 fraction of patient 452 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL452-DBr-2

value: DBr


title: 157I


title: 166I


title: WT_base_BSseq180209_rep1


title: 145I


title: DBr fraction of patient 452 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL452-DBr


title: Col_0_4


title: 138I


title: UIFN_8hr_Rep3

first: Stephanie

middle: Sarah

last: Pavlovich

state: Massachusetts

address: 700 Albany St, W508D

department: Microbiology

institute: Boston University School of Medicine

data_processing:
Sequencing, base-calling, and de-multiplexing was done by Tufts Genomics Center
5’ adapter sequences were trimmed using cutadapt v1.5. Reads shorter than 50 bp were discarded
Trimmed reads were mapped to the Raegyp2.0 genome with hisat2 v2.1.0
Count tables of uniquely mapped reads were tabulated with HTSeq v0.6.1p1
Count tables were used for pairwise differential expression analysis with edgeR (v3.20.9) within the R environment (R version 3.4.3)
Genome_build: Raegyp2.0 genome (RefSeq accession: GCF_001466805.2)
Supplementary_files_format_and_content: tab-delimited text file with counts for each gene

organism: Rousettus aegyptiacus

source_name: kidney

extract_protocol:
RNA was harvested in RNAzol RT and frozen at -80°C prior to extraction by pelleting out of DNA and proteins and then precipitation with isopropanol.
RNA libraries were prepared with the Illumina TruSeq® Stranded mRNA Library Prep kit. Pooled libraries underwent pippin size selection.

value: kidney fibroblasts

tag: cell line

value: RoNi/7.1 cells

value: kidney

value: Universal interferon for 8 hrs


title: UIFN_8hr_Rep2


title: Tot fraction of patient 452 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL452-Tot

data_processing: The intensities of the images were extracted using GenomeStudio Methylation module software and processed in R/Bioconductor using the ‘ChAMP’ package and custom scripts. Briefly, we used default settings to filter out probes by detection p < 0.01 using the minfi method, discarded probes with < 3 beads in at least 5% of samples, performed BMIQ normalization to adjust for technical bias, followed by batch correction between slides using comBat from the ‘sva’ package, which resulted in improved correlation and tighter clustering of replicate samples. In addition, probes near SNPs and cross-hybridizing probes were removed using the rmSNPandCH function from the ‘DMRcate’ package. Only samples having Dim, Int, Br and Tot fractions and matching gene expression were used in the linked publication, the other samples were included in the normalization procedure, and the duplicate samples were used to assess performance of batch correction. We used limma to identify differentially methylated CpGs (DMC) using the M-values (logit-transformed beta-values) of the normalized, filtered methylation data.

extract_protocol: We used the EZ DNA Methylation kit (Zymo Research) for bisulfite conversion of 500 ng of genomic DNA obtained from at least 0.5 x 10e6 cells of each fractionated CLL sample.

tag: Sex


title: UIFN_8hr_Rep1


title: Dim fraction of patient 493 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL493-Dim

value: Dim

tag: birthrate (% cells/day)


title: Br fraction of patient 452 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL452-Br

value: U


title: Col_0_2


title: D1_100_8hr_Rep2

value: recombinant D1 peptide 100ng/mL for 8 hrs


title: D1_100_8hr_Rep3


title: 135I

value: IPF

value: M

tag: age


title: 210I


title: Col_0_1


title: Int fraction of patient 452 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL452-Int

value: Int


title: D1_100_8hr_Rep1

tag: tissue


title: 137C

value: Control


title: 084C


title: Dim fraction of patient 499 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL499-Dim

tag: fraction


title: Dim fraction of patient 452 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL452-Dim

tag: cell type


title: M6: metastatic gastric cancer 6

city: Cheongju

first: Seung-Myoung

last: Son

state: Chungbuk

address: 1, Chungdae-ro, Seowon-gu

country: South Korea

institute: Chungbuk National University College of Medicin

description: metastatic gastric cancer tissue from gastric cancer patient 6

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

source_name: formalin-fixed paraffin embedded tissue

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

value: metastatic gastric cancer

tag: disease state

value: gastric cancer


title: M7: metastatic gastric cancer 7

description: metastatic gastric cancer tissue from gastric cancer patient 7


title: D1_1_8hr_Rep3

value: recombinant D1 peptide 1ng/mL for 8 hrs


title: D1_1_8hr_Rep2


title: M4: metastatic gastric cancer 4

description: metastatic gastric cancer tissue from gastric cancer patient 4


title: 484C


title: DBr fraction of patient 373 (ME)

first: Boris

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL373-Dbr

value: F


title: 081C


title: M5: metastatic gastric cancer 5

description: metastatic gastric cancer tissue from gastric cancer patient 5


title: Tot fraction of patient 373 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL373-Tot

value: Tot

value: sorted CLL PBMCs


title: 174I


title: M3: metastatic gastric cancer 3

description: metastatic gastric cancer tissue from gastric cancer patient 3


title: 253C


title: D1_0.01_8hr_Rep3

value: kidney fibroblasts

value: recombinant D1 peptide 0.01ng/mL for 8 hrs


title: M2: metastatic gastric cancer 2

description: metastatic gastric cancer tissue from gastric cancer patient 2


title: M1: metastatic gastric cancer 1

description: metastatic gastric cancer tissue from gastric cancer patient 1


title: D1_0.01_8hr_Rep2

value: RoNi/7.1 cells

value: kidney


title: 454C


title: P7: primary gastric cancer tissue 7

description: primary gastric cancer tissue from gastric cancer patient 7

value: primary gastric cancer


title: D1_0.01_8hr_Rep1


title: 001C


title: Br fraction of patient 373 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL373-Br

value: Br


title: Dim fraction of patient 373 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL373-Dim

value: Dim


title: DBr fraction of patient 331 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL331-Dbri

value: DBr


title: P6: primary gastric cancer tissue 6

description: primary gastric cancer tissue from gastric cancer patient 6


title: 003C


title: W9_100_8hr_Rep3

value: recombinant interferon omega9 100ng/mL for 8 hrs


title: atcgl20ab_2


title: 483C

value: M


title: Int fraction of patient 373 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL373-Int

value: Int


title: P5: primary gastric cancer tissue 5

description: primary gastric cancer tissue from gastric cancer patient 5


title: 192C

value: Control


title: W9_100_8hr_Rep2


title: W9_100_8hr_Rep1


title: P4: primary gastric cancer tissue 4

description: primary gastric cancer tissue from gastric cancer patient 4

value: gastric cancer


title: Int fraction of patient 331 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL331-Int


title: Tot fraction of patient 331 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL331-Tot


title: Dim fraction of patient 331 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL331-Dim


title: P3: primary gastric cancer tissue 3

description: primary gastric cancer tissue from gastric cancer patient 3


title: 065C


title: W9_1_8hr_Rep2

value: recombinant interferon omega9 1ng/mL for 8 hrs


title: P2: primary gastric cancer tissue 2

description: primary gastric cancer tissue from gastric cancer patient 2


title: Br fraction of patient 331 (ME)

description:
Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
CLL331-Br


title: W9_1_8hr_Rep3


title: W9_1_8hr_Rep1


title: 160C


title: P1: primary gastric cancer tissue 1

description: primary gastric cancer tissue from gastric cancer patient 1


title: 439C

value: F