title: HeLa bioreplica 1

status: Public on Dec 31 2019

type: SRA

city: Xiamen

first: Huifen

last: Cao

email: hfcao_bnu@163.com, hfcao@hqu.edu.cn

state: Fujian

address: 668 Jimei Road

department: School of Biomedical Sciences

country: China

institute: Huaqiao University

library_source: genomic

data_processing:
Library strategy: SSiNGLe-ILM
Only paired-end raw reads where read 1 started with 10G’s, read 2 started with 12T’s and each base of each read had Phred quality score >20 were selected.
Such reads were then aligned to the GRCh37/hg19 or GRCm38/mm10 assemblies of human or mouse genomes respectively using BWA-MEM (Version 0.7.12) with default settings. Only pairs of reads where both reads 1 and 2 uniquely mapped to the genome with appropriate configuration and spacing were kept.
Pairs of reads where fraction of T’s in the 20-base 5’ upstream sequence in the read 2 alignment was >40% were removed from the downstream analyses.
A single-strand break was defined as the first base after 12 T’s in the read 2.
Genome_build: hg19 for human and mm10 for mouse
Supplementary_files_format_and_content: bed.gz files containing coordinates of single-strand breaks

molecule: genomic DNA

organism: Homo sapiens

source_name: HeLa

growth_protocol: Human chronic myeloid leukemia cell line K562 was obtained from Cell Bank of Chinese Academy of Sciences. Cells were cultured in RPMI 1640 (Thermo Fisher Scientific) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (Thermo Fisher Scientific) and 1% (v/v) pen-strep (Thermo Fisher Scientific) at 37°C and 5% CO2. Mouse neuroblastoma (N2a) and human cervical carcinoma HeLa cell lines were obtained from National Infrastructure of Cell Line Resource. N2a cells were cultured in MEM/EBSS (HyClone), supplemented with 10% (v/v) heat-inactivated fetal bovine serum (Thermo Fisher Scientific) and 1% (v/v) pen-strep (Thermo Fisher Scientific) at 37°C and 5% CO2. HeLa cells were cultured following at the same condition as K562 cells.

extract_protocol:
Cells were crosslinked with formaldehyde in vivo, fragmented with MNase and used for genomic DNA extraction.
Samples were prepared according to the SSiNGLe-ILM protocol. Briefly, nuclei were isolated from cells crosslinked in vivo with formaldehyde and subjected to MNase treatment to fragment DNA to 150-500bp. The genomic DNA was then isolated after cross-link reversal and subjected to polyA-tailing using terminal transferase to tag positions of endogenous single-strand DNA breaks (products of MNase fragmentation would not be tailed under these conditions). The polyA-tailed single-strand DNA molecules were then used as templates for 2nd strand DNA synthesis with a chimeric 5’-DNA-RNA-3’ oligonucleotide followed by polyC-tailing of the 2nd strand DNA. The resulting polyA- and polyC-tailed double-strand DNA molecules were used for Illumina sequencing library construction using PCR with oligonucleotides containing appropriate adaptors at their 5’ ends.

treatment_protocol: For drug treatments, 1-2 million cells were seeded at 1 million cells per ml of medium per well in 24- (1ml media) or 6-well (2-3 ml) plates. After 16 hours, the following chemicals were added separately: 0.1% DMSO, 0.5mM H2O2, 1μM imatinib (Abmole Bioscience Inc, M3241), 0.0462µM romidepsin (Abmole Bioscience Inc, M2007), 1μM talazoparib (Abmole Bioscience Inc, M1732), 1μM SN-38 (Abmole Bioscience Inc, M3016), 40μM 10074-G5 (Sigma, 475957), 1μM YM-155 (Abmole Bioscience Inc, M2342) and 100μM etoposide (Abmole Bioscience Inc, M2326) and incubated for 6, 12, 24, 36 or 48 hours. All drugs (with exception of H2O2) were dissolved in DMSO, concentration of which was kept at 0.1% in all treatments. All treatments were done in two biological replicas for SSiNGLe-ILM. The following treatments were performed on separate batch of cells for SSiNGLe-SMS: DMSO, etoposide, SN-38, romidepsin, imatinib and talazoparib for 6, 12, 24 (with the exception of imatinib), 36 and 48 hours. For the Nt.BbvCI experiments, hydrogen peroxide treatment was done only for 6 hours and un-treated cells grown under the same conditions were used as controls.

tag: cell line

value: HeLa

tag: cell type

value: cervical cancer cell line


title: Nuclei from H2O2-treated cells digested with Nt.BbvCI and then treated with SAP bioreplica 1

value: chronic myelogenous leukemia cell line


title: HeLa bioreplica 2


title: Nuclei from H2O2-treated cells digested with Nt.BbvCI and then treated with SAP bioreplica 2


title: Nuclei from H2O2-treated cells digested with Nt.BbvCI and then treated with SAP bioreplica 3


title: Nuclei from H2O2-treated cells digested with Nt.BbvCI bioreplica 1


title: Nuclei from H2O2-treated cells digested with Nt.BbvCI bioreplica 2


title: Nuclei from H2O2-treated cells digested with Nt.BbvCI bioreplica 3


title: THP1-derived dendritic cells, Scr-3

city: shanghai

first: Niu

last: liman

address: Building No.5(West Area),No.280 South Chongqing Road

department: Shanghai Institute of Immunology,Department of Immunology and Microbiology

institute: Shanghai Jiao Tong University School of Medicine

library_source: transcriptomic

data_processing:
Illumina bcl2fastq software was used for base-calling
STAR(2.5.3a) software was used for read alignment, parameter setting as follows:—twopassMode Basic|--outSAMstrandField intronMotif|--alignSJstitchMismatchNmax 5 -1 5 5
FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) was calculated, and then normalized with TMM standard; DESeq2 software was used to filter differentially expressed genes, according to the standard that |log2(fold change)|>=1 and P value <=0.05
In processed data file, G1 refers to the mean value of Scr ctr group(2 biological repilcations) values; G2 refers to the mean value of normalized P155 group(2 biological repilcations) values;
Genome_build: hg38
Supplementary_files_format_and_content: seq_Processed data file of THP-1derived DCs -e.g. geo_submission_December 28.xlsx

molecule: total RNA

source_name: THP1-derived dendritic cells

extract_protocol:
All samples were washed twice with PBS, and total RNA was extracted with RNAiso Plus (Takara Bio) and purified with magnetic oligo (dT) beads after denaturation.  Purified mRNA samples were reverse transcribed into fragmented DNA samples and adenylated at the 3’ ends.
Adaptors were ligated to construct a library. DNA was quantified by Qubit (Invitrogen). After cBot cluster generation, DNA samples were then sequenced by an Illumina HiSeq X Ten SBS instrument from Genergy Bio (Shanghai).

treatment_protocol: THP1-derived DCs were treated with P155 or Scr for 2 h and then treated with R848 (1 µg/ml) for another 2 h.

value: THP1-derived dendritic cells

tag: development stage

value: on Day7 of differentiation  induction

tag: treatment

value: Scramble microPEP(Scr)


title: THP1-derived dendritic cells, Sample155-2


title: THP1-derived dendritic cells, Sample 155-1


title: THP1-derived dendritic cells, Scr-2


title: K562 treated with YM-155 for 48 hours bioreplica 1


title: K562 treated with YM-155 for 6 hours bioreplica 1


title: K562 treated with YM-155 for 36 hours bioreplica 2


title: Genomic DNA digested with AsiSI after Mnase fragmentation and purification_B1


title: HeLa bioreplica 3


title: K562 treated with YM-155 for 6 hours bioreplica 2


title: K562 treated with YM-155 for 48 hours bioreplica 2


title: K562 treated with YM-155 for 24 hours bioreplica 1


title: K562 treated with YM-155 for 24 hours bioreplica 2


title: K562 treated with YM-155 for 12 hours bioreplica 2


title: Genomic DNA digested with AsiSI after Mnase fragmentation and purification_B2


title: K562 treated with Talazoparib for 6 hours bioreplica 2


title: K562 treated with YM-155 for 12 hours bioreplica 1


title: K562 treated with Talazoparib for 6 hours bioreplica 1


title: K562 treated with Talazoparib for 48 hours bioreplica 1


title: K562 treated with Talazoparib for 36 hours bioreplica 1


title: K562 treated with Talazoparib for 36 hours bioreplica 2


title: K562 treated with Talazoparib for 48 hours bioreplica 2


title: K562 treated with YM-155 for 36 hours bioreplica 1


title: K562 treated with SN-38 for 6 hours bioreplica 2


title: K562 treated with Talazoparib for 24 hours bioreplica 2


title: K562 treated with Talazoparib for 12 hours bioreplica 1


title: K562 treated with SN-38 for 48 hours bioreplica 2


title: K562 treated with Talazoparib for 12 hours bioreplica 2


title: K562 treated with Talazoparib for 24 hours bioreplica 1


title: K562 treated with SN-38 for 48 hours bioreplica 1


title: K562 treated with SN-38 for 36 hours bioreplica 1


title: K562 treated with SN-38 for 36 hours bioreplica 2


title: K562 treated with SN-38 for 6 hours bioreplica 1


title: K562 treated with SN-38 for 24 hours bioreplica 1


title: K562 treated with SN-38 for 12 hours bioreplica 2


title: K562 treated with SN-38 for 24 hours bioreplica 2


title: K562 treated with Romidespin for 6 hours without formaldehyde crosslinking


title: K562 treated with SN-38 for 12 hours bioreplica 1


title: K562 treated with Romidespin for 6 hours bioreplica 1


title: K562 treated with Romidespin for 48 hours without formaldehyde crosslinking


title: K562 treated with Romidespin for 48 hours bioreplica 2


title: K562 treated with Romidespin for 6 hours bioreplica 2


title: K562 treated with Romidespin for 48 hours bioreplica 1


title: K562 treated with Romidespin for 36 hours without formaldehyde crosslinking


title: K562 treated with Romidespin for 36 hours bioreplica 2


title: K562 treated with Romidespin for 24 hours without formaldehyde crosslinking


title: K562 treated with Romidespin for 24 hours bioreplica 2


title: K562 treated with Romidespin for 12 hours without formaldehyde crosslinking


title: K562 treated with Romidespin for 24 hours bioreplica 1


title: K562 treated with Romidespin for 12 hours bioreplica 2


title: K562 treated with Romidespin for 12 hours bioreplica 1


title: K562 treated with Imatinib for 6 hours bioreplica 1


title: K562 treated with Imatinib for 6 hours bioreplica 2


title: K562 treated with Imatinib for 36 hours bioreplica 1


title: K562 treated with Imatinib for 24 hours bioreplica 1


title: K562 treated with Imatinib for 12 hours bioreplica 2


title: K562 treated with Imatinib for 24 hours bioreplica 2


title: K562 treated with Imatinib for 36 hours bioreplica 2


title: K562 treated with Imatinib for 48 hours bioreplica 1


title: K562 treated with Etoposide for 6 hours bioreplica 2


title: K562 treated with Etoposide for 6 hours without formaldehyde crosslinking


title: K562 treated with Imatinib for 48 hours bioreplica 2


title: K562 treated with Etoposide for 48 hours without formaldehyde crosslinking


title: K562 treated with Etoposide for 6 hours bioreplica 1


title: K562 treated with Etoposide for 48 hours bioreplica 2


title: K562 treated with Etoposide for 48 hours bioreplica 1


title: K562 treated with Etoposide for 36 hours without formaldehyde crosslinking


title: K562 treated with Imatinib for 12 hours bioreplica 1


title: K562 treated with Etoposide for 36 hours bioreplica 2


title: K562 treated with Romidespin for 36 hours bioreplica 1


title: K562 treated with Etoposide for 24 hours without formaldehyde crosslinking


title: K562 treated with Etoposide for 36 hours bioreplica 1


title: K562 treated with Etoposide for 24 hours bioreplica 2


title: K562 treated with Etoposide for 24 hours bioreplica 1


title: K562 treated with Etoposide for 12 hours without formaldehyde crosslinking


title: K562 treated with Etoposide for 12 hours bioreplica 2


title: K562 treated with Etoposide for 12 hours bioreplica 1


title: K562 treated with DMSO for 6 hours bioreplica 1


title: K562 treated with DMSO for 6 hours bioreplica 2


title: K562 treated with DMSO for 36 hours bioreplica 1


title: K562 treated with DMSO for 6 hours without formaldehyde crosslinking


title: K562 treated with DMSO for 48 hours without formaldehyde crosslinking


title: K562 treated with DMSO for 24 hours bioreplica 2


title: K562 treated with DMSO for 24 hours bioreplica 1


title: K562 treated with DMSO for 36 hours bioreplica 2


title: K562 treated with DMSO for 48 hours bioreplica 1


title: K562 treated with DMSO for 12 hours bioreplica 2


title: K562 treated with DMSO for 12 hours bioreplica 1


title: K562 treated with DMSO for 24 hours without formaldehyde crosslinking


title: K562 treated with DMSO for 12 hours without formaldehyde crosslinking


title: K562 treated with 10074-G5 for 6 hours bioreplica 2


title: K562 treated with 10074-G5 for 48 hours bioreplica 2


title: K562 treated with 10074-G5 for 48 hours bioreplica 1


title: K562 treated with 10074-G5 for 24 hours bioreplica 2


title: K562 treated with 10074-G5 for 36 hours bioreplica 1


title: K562 treated with 10074-G5 for 36 hours bioreplica 2


title: K562 treated with 10074-G5 for 24 hours bioreplica 1


title: K562 treated with DMSO for 48 hours bioreplica 2


title: K562 treated with 10074-G5 for 12 hours bioreplica 1


title: K562 treated with DMSO for 36 hours without formaldehyde crosslinking


title: K562 treated with 10074-G5 for 6 hours bioreplica 1


title: Caco-2 cells of OTA and B. subtilis CW14 co-treatment group-3

city: Beijing

first: Peng

last: Meng Xue

address: 17 Qinghua Donglu

institute: China Agricultural university

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw RNA-seq reads were trimmed adaptor sequences and removed low-quality reads using cutadapt (v1.10).
Reas were aligned to the hg9 reference genome using tophat2(v2.0.13).
Reads aligned to genes are counted by cufflinks (v2.2.1). The FPKMs are normalized using cuffnorm. Differentially expressed genes are calculated using cuffdiff .
Genome_build: hg19
Supplementary_files_format_and_content: Microsoft Office Excel files include FPKMs values for each sample

source_name: derived from a human colon adenocarcinoma.

growth_protocol: The cells cultured medium was DMEM containing 4.5 g/L glucose, 10% FBS, antibiotics(100 units/mL penicillin and 100 g/mL streptomycin), 10 mM HEPES buffer and 1% NEAA at 37℃ in a humidified atmosphere of 5% CO2 in air. Caco-2 cells were cultured and differentiated in 12-well transwell chambers (Corning, USA) at a density of 4×104 cells/cm2, and the medium was replaced every other day within 7 days of cell inoculation, then changed daily until 21 days.

extract_protocol:
Caco-2 cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Total RNA was extracted using RNeasy Micro Kit (QIAGEN, 74004). Extracted RNA was quantified with the Qubit RNA Assay Kit(Invitrogen).
Further mRNA library construction was performed with NEBNext Ultra RNA Library Prep Kit for Illumina(NEB, E7530) according to the Manuals. The libraries were sequenced on Illumina Hiseq X Ten instruments with 150bp pair-end reads. All clusters that passed the quality filter were exported into fastq files.

treatment_protocol: HBSS containing 10 mM HEPES was used as transport buffer. Cell monolayers were preincubated with transport buffer and maintained at 37 ℃ until required. The volume of buffer in the apical (AP) and basolateral (BL) chambers was 0.5 mL and 1.5 mL, respectively. Transport assays were performed by adding 15 μmol/L OTA and/or 1010 CFU/mL B. subtilis CW14 to the AP chamber(0.5 mL/well).

value: OTA and B. subtilis CW14

value: human intestinal epithelial cell line


title: Caco-2 cells of OTA and B. subtilis CW14 co-treatment group-2


title: Caco-2 cells of OTA and B. subtilis CW14 co-treatment group-1


title: Caco-2 cells of B. subtilis CW14 treatment group-3

value: B. subtilis CW14


title: Caco-2 cells of OTA treatment group-1

value: OTA


title: Caco-2 cells of OTA treatment group-3


title: Caco-2 cells of OTA treatment group-2


title: Caco-2 cells of B. subtilis CW14 treatment group-1


title: Caco-2 cells of no treatment group-3


title: K562 treated with 10074-G5 for 12 hours bioreplica 2


title: Brain, Dube3a Alone R2

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

country: USA

institute: UTHSC

data_processing:
QC trimming Q >= 30 using fastx-trim
Alignment with STAR using drosophila melanogaster  human transcript
Raw read counts collected
Differential Expression using DeSeq2
Genome_build: Drosophila melanogaster
Supplementary_files_format_and_content: csv file containing raw reads for each sample

organism: Drosophila melanogaster

source_name: Whole Brain

growth_protocol: Flies grown at 25deg till 3-5 days post eclosure

extract_protocol:
TRI reagent on dissected brain.
PGM library.

tag: tissue

value: Brain

tag: genotype

value: control (Background)


title: Brain, Dube3a Alone R3


title: HCC82-P

city: Shanghai

first: Yun

last: Liu

address: 130 Dong An Road

institute: Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence (30bp), and masked for low-complexity or low-quality sequence, then mapped to hg9 whole genome using osa 4.0.2.1
Raw counts were calculated using htseq-count parameters -q -s reverse
Genome_build: hg9
Supplementary_files_format_and_content: csv files include raw counts for each sample

source_name: tumor peripheral from HCC patient #82

extract_protocol:
Liver samples were extracted, homogenized and MAIT cells were sorted out using flow cytometry sorting. RNA was harvested using Trizol reagent. CloneTech SMART-Seq v4 Ultra Low Input RNA Kit (Cat #634889) was used with 2 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using CloneTech SMART-Seq v4 Ultra Low Input RNA Kit

value: liver

tag: diagnosis

value: HCC

value: MAIT cells


title: HCC77-P

source_name: tumor peripheral from HCC patient #77


title: active bear_single-end_reads

city: Berlin

first: Xintian

middle: Arthur

last: YOU

address: Robert-Roessle-str. 10

country: Germany

institute: Max-Delbrueck-Center for Molecular Medicine

description: RNA from skeleton muscle tissue from two active bears named "Star" and "Tia"

data_processing:
Basecalls performed using Illumina RTA, version 1.6.32.0
454 reads were pre-assembled using Roche Newbler version 2.3
Paired-end Illumina reads were pre-assembled using SOAPdenovo version 1.3
Final transcript set was assembled using Roche Newbler version 2.3 using pre-assembled 454 contigs and pre-assembled Illumina contigs
Single-end Illumina reads were aligned to final transcript set using SOAP2 with default parameters
Supplementary_files_format_and_content: fasta file for the final transcript set and tab-delimited file for transcript expression (measured in RPKM)

organism: Ursus arctos

extract_protocol:
Total RNA from grizzly bear muscle was isolated using the standard TRIzol protocol (Invitrogen) with an additional 70% ethanol precipitation step in the end. Poly(A) RNA was then purified by two rounds of selection using the Dynabeads mRNA Purification Kit (Invitrogen) according to the manufacturer’s instructions and quantified by Nanodrop 7500 spectrophotometer. Sample quality was assessed by Bioanalyzer (Agilent Technologies).
The construction of normalized full-length-enriched cDNA libraries for 454 sequencing requires three steps: (1) the synthesis of double strand cDNA using a modified RACE technique, (2) the subsequent removal of poly(A):T tails using the methylation sensitive type II restriction enzyme GsuI, followed by the ligation of a new DNA adaptor, and (3) the normalization of the resulting cDNA library using duplex-specific nuclease (DSN). The DSN normalization method is based on the denaturation–reassociation of double-stranded (ds) cDNA coupled with the degradation of the ds cDNA fraction formed by abundant transcripts (Shagin et al. 2002; Zhulidov et al. 2004) and requires the presence of adaptor sequences at each terminus of the cDNA to prime PCR amplification.

tag: developmental stage

value: adult (10 years)

value: gastrocnemius muscle

tag: hibernation status

value: non-hibernating (active)


title: HCC77-T

source_name: primary tumor from HCC patient #77


title: Brain, Repo>Dube3a R1

value: glial overexpression of Dube3a


title: active_hibernating_pooled_bear

description: pooled RNA from skeleton muscle tissues from both active and hibernated bears

value: pooled sample with RNA from both non-hibernating and hibernating bears


title: HCC79-P

source_name: tumor peripheral from HCC patient #79


title: CD3+ T cell control

city: St. Paul

first: Cheryl

last: Dvorak

state: MN

address: 1971 Commonwealth Avenue

department: Veterinary and Biomedical Sciences

institute: University of Minnesota

description:
CD3_control_S12
For_expression_levels_reads_per_million_reads.xlsx

data_processing:
Raw data was analyzed by the University of Minnesota Informatics Institute (UMII). Adapters were trimmed using trimmomatic and mapping was performed using bowtie2.
Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood City, CA) using raw read counts.
Genome_build: Sus Scrofa 11.1
Supplementary_files_format_and_content: Two excel files are provided. DEG's were determined using the file comparing CD21 to the 6 lymphoma samples. A comparison of gene expression levels was performed by calculating reads/million reads to normalize the expression between samples.

organism: Sus scrofa

source_name: CD3+ T cell control

growth_protocol: Lymphoma cells were manually dissociated from lymph nodes and spleen and cultured at 50,000 cells/well in complete RPMI 1640 media until proliferation was observed. Clonal populations were then obtained from samples that proliferated using limiting dilution culture for a total of 4 rounds of limiting dilutions. Four of the clones obtained from lymph node and 2 obtained from the spleen were used for sequence analysis.

extract_protocol:
RNA from the same number of cells for each sample was isolated using the Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) following manufacturer’s instructions.
Libraries were constructed and paired end sequencing run on the Illumina HiSeq 2500 at the University of Minnesota Genomics Center following manufacturer's protocols..

tag: tissue/cell type source

value: Splenocytes

value: CD3+ magnetically enriched splenocytes


title: hibernating bear_single-end_reads

description: RNA from skeleton muscle tissue from two hibernated bears named "Star" and "Tia"

value: hibernating


title: Caco-2 cells of no treatment group-2


title: Brain, elav>Dube3a R1

value: neuronal overexpression of Dube3a


title: Caco-2 cells of no treatment group-1

value: human intestinal epithelial cell line


title: HCC79-T

source_name: primary tumor from HCC patient #79


title: CD21+ B cell control

description:
CD21_control_S11
processed data file:
CD21v4LN2_Sp_DEGs.xlsx
For_expression_levels_reads_per_million_reads.xlsx

source_name: CD21+ B cell control

value: CD21+ magnetically enriched splenocytes


title: Brain, Repo>Dube3a R2


title: Brain, elav>Dube3a R3


title: HDL-29

source_name: healthy liver from individual #29

value: healthy


title: HDL-28

source_name: healthy liver from individual #28


title: Spleen_2

description:
Spleen_2_S10
processed data file:
CD21v4LN2_Sp_DEGs.xlsx
For_expression_levels_reads_per_million_reads.xlsx

source_name: lymphoma clone_spleen

value: Spleen tumor

value: cell culture lymphoma clone


title: Caco-2 cells of B. subtilis CW14 treatment group-2

value: B. subtilis CW14


title: Brain, Repo>Dube3a R3

value: Brain


title: Brain, Dube3a Alone R1

value: control (Background)


title: Brain, elav>Dube3a R2


title: Spleen_1

description:
Spleen_1_S9
processed data file:
CD21v4LN2_Sp_DEGs.xlsx
For_expression_levels_reads_per_million_reads.xlsx


title: DB-mixtures

city: Chengdu

first: Song

last: Yang

address: No.211, Huimin Road, Wenjiang District, Chengdu City, Sichuan Province, P.R.China

institute: Sichuan Agricultural University College of Animal Science and Technology

description:
domestic pig
DB-P

data_processing:
Illumina Casava1.82 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to itself assembly genome using Tophat version 2.1.0
StringTie version 1.2.2 were applied to quantify gene expression and obtain FPKM expression values.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each tissue.

source_name: Mixture of multiple tissues (heart, liver, spleen, lung, kidney, muscle, ovary)

extract_protocol:
The total RNA was extracted using the TrIzol reagent (Life Technologies, Beijing, China) according to the manufacturer’s protocols. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: 60 days old

value: Mixture of multiple tissues

tag: breed name

value: Northeast min pig


title: DB-ovary

description:
domestic pig
DB-O

source_name: Ovary

value: Ovary


title: DB-subcutaneous adipose

description:
domestic pig
DB-F

source_name: Subcutaneous adipose

value: Subcutaneous adipose


title: DB-heart

description:
domestic pig
DB-H

source_name: Heart

value: Heart


title: DB-liver

description:
domestic pig
DB-L

source_name: Liver

value: Liver


title: DB-spleen

description:
domestic pig
DB-S

source_name: Spleen

value: Spleen


title: Lymph_Node_2

description:
Lymph_Node_2_S6
processed data file:
CD21v4LN2_Sp_DEGs.xlsx
For_expression_levels_reads_per_million_reads.xlsx

source_name: lymphoma clone_lymph node

value: Lymph node tumor


title: DB-longissimus dorsi

description:
domestic pig
DB-M

source_name: Longissimus dorsi

value: Longissimus dorsi


title: Lymph_Node_3

description:
Lymph_Node_3_S7
processed data file:
CD21v4LN2_Sp_DEGs.xlsx
For_expression_levels_reads_per_million_reads.xlsx


title: NKR

city: Haikou

first: Min

last: Xu

address: No.58 Renmin Avenue,Haikou, Hainan, China

institute: Hainan University

description: NKR-VS-LKR.GeneDiffExpFilter.txt

data_processing:
Primary sequencing data that produced by Illumina HiSeqTM 2000, called as raw reads, is subjected to quality control (QC) that determine if a resequencing step is needed
After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences. QC of alignment is performed to determine if resequencing is needed. The alignment data is utilized to calculate distribution of reads on reference genes and mapping ratio. If alignment result passes QC, we will proceed with downstream analysis including gene expression and deep analysis based on gene expression(PCA/correlation/screening differentially expressed genes and so on).
Further, we also can perform deep analysis based on DEGs,including Gene Ontology (GO) enrichment analysis,Pathway enrichment analysis, cluster analysis, protein-protein interaction network analysis and finding transcriptor factor.
Genome_build: GCA_000313855.2
Supplementary_files_format_and_content: tab-delimited text files include gene ID, length, expression, FPKM values log2 ratio and soon for each Sample.

organism: Musa acuminata AAA Group

source_name: banana seedlings

growth_protocol: seedlings of uniform appearance, symptomatology, and height were selected

extract_protocol:
The improved CTAB (cetyltrimethylammonium bromide) method was used for RNA extraction (Elizabeth et al. 2008)
Total RNA samples were first treated with DNase I to degrade any possible DNA contamination. The mRNA was enriched using oligo(dT) magnetic beads. After mixing with fragmentation buffer, the mRNA was fragmented into short fragments. The first-strand cDNA was synthesized using a random hexamer primer. Buffer, dNTPs, RNase H, and DNA polymerase I were then added to synthesize the second-strand cDNA. The double-stranded cDNA was purified using magnetic beads. End repair and 3'-end single nucleotide A (adenine) addition were then performed. Finally, sequencing adaptors were ligated to the fragments and the fragments were enriched by polymerase chain reaction (PCR) amplification. During the quality control (QC) step, a 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA) and a StepOnePlus Real-Time PCR System (Applied Biosystems Inc., Foster City, CA, USA) were used to qualify and quantify sequences for the sample library

treatment_protocol: control and low-K+ groups were respectively treated with Hoagland complete culture solution and the low-K+ culture solution.

tag: tissue type

value: roots

tag: group

value: normal-potassium group (NK)

tag: cultivar

value: Cavendish

tag: processing time

value: 60 days


title: DB-kidney

description:
domestic pig
DB-K

source_name: Kidney

value: Kidney


title: Lymph_Node_4

description:
Lymph_Node_4_S8
processed data file:
CD21v4LN2_Sp_DEGs.xlsx
For_expression_levels_reads_per_million_reads.xlsx

value: cell culture lymphoma clone


title: DB-psoas major muscle

description:
domestic pig
DB-YaoJ

source_name: Psoas major muscle

value: Psoas major muscle


title: Lymph_Node_1

description:
Lymph_Node_1_S5
processed data file:
CD21v4LN2_Sp_DEGs.xlsx
For_expression_levels_reads_per_million_reads.xlsx


title: LKR

description: NKR-VS-LKR.GeneDiffExpFilter.txt

value: low potassium group (LK)


title: DB-lung

description:
domestic pig
DB-LU

source_name: Lung

value: 60 days old

value: Lung


title: NKL

description: NKL-VS-LKL.GeneDiffExpFilter.txt

value: leaves


title: LKL

description: NKL-VS-LKL.GeneDiffExpFilter.txt


title: Liver of 10-week cellulose-fed mouse, biological rep2

type: RNA

city: Urla

first: Bunyamin

last: Akgul

state: izmir

address: Gulbahcekoyu

department: Molecular Biology and Genetics

country: Turkey

institute: Izmir Institute of Technology

description: Gene expression data from liver of mice fed on cellulose for 10 weeks

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with EukGE_2v5-450 protocol.

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

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

label: biotin

organism: Mus musculus

source_name: 8-week old male C57BL/6J mouse fed on cellulose diet for 10 weeks

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (GeneChip Expression Analysis Technical Manual rev5, Affymetrix).

growth_protocol: 8-week old mice were divided into two groups and maintained at a non-barrier facility of Institute of Biomedical Sciences, Taipei, Taiwan, ROC.

extract_protocol: Total RNA was isolated from the frozen liver tissues using Qiagen RNeasy Midi Kit according to the manufacturer's instructions.

treatment_protocol: Garlic bulbs (husk free) were homogenized with a food processor, lyophilized, ground into dry powder in a mortar with pestle and stored at -20 C until use. Mice were fed (ad libitum) a diet containing 20/ vitamin free casein, 10% sucrose, 53.95% cornstarch, 7% soybean oil, 3.5% AIN93 regular mineal mix, 1% AIN93G vitamin mix, 0.25% choline bitartrate (41.1% choline), 0.3% L-cysteine with the adition of 4% cellulose (Control diet) or 4% lyophilized raw garlic powder (Garlic diet). At the end of 6 and 10-week treatment periods, mice were sacrifificed by cervical dislocation to collect livers, which were snap-frozen in liquid nitrogen for storage at -80C until use.

tag: starting age

value: 8-week old

tag: gender

value: male

tag: strain

tag: organ

tag: diet

value: 4% cellulose in a special diet (Yeh and Yeh, 1994)


title: Liver of 10-week cellulose-fed mouse, biological rep1

value: Liver


title: Liver of 6-week garlic-fed mouse, biological rep3

description: Gene expression data from liver of mice fed on raw garlic powder for 6 weeks

source_name: 8-week old male C57BL/6J mouse fed on garlic diet for 6 weeks

value: 4% lyophilized raw garlic powder in a special diet (Yeh and Yeh, 1994)


title: Liver of 6-week garlic-fed mouse, biological rep2


title: Liver of 10-week cellulose-fed mouse, biological rep3


title: Liver of 10-week garlic-fed mouse, biological rep3

description: Gene expression data from liver of mice fed on raw garlic powder for 10 weeks

source_name: 8-week old male C57BL/6J mouse fed on garlic diet for 10 weeks


title: Liver of 10-week garlic-fed mouse, biological rep2


title: Liver of 10-week garlic-fed mouse, biological rep1


title: Liver of 6-week cellulose-fed mouse, biological rep2

description: Gene expression data from liver of mice fed on cellulose for 6 weeks

source_name: 8-week old male C57BL/6J mouse fed on cellulose diet for 6 weeks


title: Liver of 6-week cellulose-fed mouse, biological rep3


title: Liver of 6-week garlic-fed mouse, biological rep1


title: mono_blood_3

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

description: Monocyte Pool 3; pooled RNA isolated from monocytes from heathly donors 11 to 15; monocytes were obtained from PBMC by CD14+ bead separation.

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: R/Bioconductor, rma normalization, default parameters.

source_name: in vitro cultured blood monocytes

label_protocol: Standard Affymetrix protocol.

growth_protocol: M1- and M2- macrophages were generated from blood monocytes in vitro, as described (Martinez et al., 2006). Briefly, monocytes were cultured in 6-well plates (Nunc) in serum-free medium (5 x 106/4 ml of AIM-V) supplemented with M-CSF (50 ng/ml; R&D Systems) over 7 days followed by 18 h treatment with IFN-γ (20 ng/ml; R&D Systems) plus LPS (100 ng/ml; Sigma-Aldrich) for M1-polarization, or IL-4 (20 ng/ml; PromoKine) for M2-polarization.

extract_protocol: RNA was prepared using RNeasy micro kit (Qiagen). RNA quantity and quality were assessed using a Nanodrop 1000 Spectrometer (Peqlab) and Agilent 2100 Bioanalyzer. RNA (30 ng of each replica pool) was amplified and converted into cDNA by a linear amplification method using WT-Ovation PicoSL System in combination with the Encore® Biotin Module (both from NuGen). cDNA was further purified using MinElute Reaction Cleanup kit (Qiagen) before hybridization to Affymetrix GeneChip® Human Gene ST 1.0 Arrays.

tag: donor group

tag: disease status

value: Healthy

tag: cell type

value: Monocytes


title: mono_blood_1

description: Monocyte Pool 1; pooled RNA isolated from monocytes from heathly donors 1 to 5; monocytes were obtained from PBMC by CD14+ bead separation.


title: MFAP5-rep1

city: Houston

first: Tsz-Lun

last: Yeung

state: TX

address: 1515 Holcombe Blvd. Unit 1362

department: Gynecologic Oncology and Reproductive Medicine

institute: University of Texas MD Anderson Cancer Center

description:
MFAP5#1
Gene expression data from MFAP5-exposed endothelial cells.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: Biotin

source_name: MFAP5-treated endothelial cells

label_protocol: Biotinylated cRNA were prepared using the MessageAmp Premier RNA Amplification Kit (Ambion) according to the manufacturer's instruction from 100ng total RNA.

growth_protocol: Matrigel plugs (with/without recombinant MFAP5) were IP implanted into the peritoneal cavity of Balb/c nude mice.

extract_protocol: Total RNA extraction was performed using the PureLink RNA mini kit (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: Endothelial cells were isolated from both control and treatment matrigel plugs.

tag: strain/background

value: Balb/c nude

value: endothelial cells

tag: treatment

value: microfibrillar-associated protein 5 (MFAP5)


title: Liver of 15-week garlic-fed mouse, biological rep1

description: Gene expression data from liver of mice fed on raw garlic powder for 15 weeks

source_name: 8-week old male C57BL/6J mouse fed on garlic diet for 15 weeks

growth_protocol: 8-week old mice were divided into two groups and maintained in the SPF facility of Institute of Biomedical Sciences, Taipei, Taiwan, ROC.

treatment_protocol: Garlic bulbs (husk free) were homogenized with a food processor, lyophilized, ground into dry powder in a mortar with pestle and stored at -20 C until use. Mice were fed (ad libitum) a diet containing 20/ vitamin free casein, 10% sucrose, 53.95% cornstarch, 7% soybean oil, 3.5% AIN93 regular mineal mix, 1% AIN93G vitamin mix, 0.25% choline bitartrate (41.1% choline), 0.3% L-cysteine with the adition of 4% cellulose (Control diet) or 4% lyophilized raw garlic powder (Garlic diet). At the end of the 15-week treatment period, mice were sacrificed by cervical dislocation to collect livers, which were snap-frozen in liquid nitrogen for storage at -80C until use.


title: Liver of 15-week cellulose-fed mouse, biological rep1

description: Gene expression data from liver of mice fed on cellulose for 15 weeks

source_name: 8-week old male C57BL/6J mouse fed on cellulose diet for 15 weeks


title: Liver of 6-week cellulose-fed mouse, biological rep1


title: Control-rep3

description:
CTL#3
Gene expression data from control endothelial cells.

source_name: Control endothelial cells

value: control


title: MFAP5-rep3

description:
MFAP5#3
Gene expression data from MFAP5-exposed endothelial cells.


title: M2-MP_in vitro_3

description: M2-macrophage (MΦ) Pool 3: pooled RNA isolated from M2 cells from healthy donors 11 to 15; M2-macrophages were generated from blood monocytes (isolated from PBMC of one healthy donor using CD14+ microbeads) by culturing them in the presence of MCSF for 7 days. Thereafter, polarization towards M2 was induced with IL-4 (described in Martinez et al., 2006).

source_name: in vitro generated M2 macrophages

value: M2 macrophages


title: mono_blood_2

description: Monocyte Pool 2; pooled RNA isolated from monocytes from heathly donors 6 to 10; monocytes were obtained from PBMC by CD14+ bead separation.


title: Liver of 15-week cellulose-fed mouse, biological rep2


title: Liver of 15-week garlic-fed mouse, biological rep3


title: Control-rep1

description:
CTL#1
Gene expression data from control endothelial cells.


title: HCC82-T

source_name: primary tumor from HCC patient #82

tag: tissue

value: liver

tag: diagnosis

value: HCC

value: MAIT cells


title: Control-rep2

description:
CTL#2
Gene expression data from control endothelial cells.


title: MFAP5-rep2

description:
MFAP5#2
Gene expression data from MFAP5-exposed endothelial cells.


title: Liver of 15-week garlic-fed mouse, biological rep2


title: M2-MP_in vitro_2

description: M2-macrophage (MΦ) Pool 2: pooled RNA isolated from M2 cells from healthy donors 6 to 10; M2-macrophages were generated from blood monocytes (isolated from PBMC of one healthy donor using CD14+ microbeads) by culturing them in the presence of MCSF for 7 days. Thereafter, polarization towards M2 was induced with IL-4 (described in Martinez et al., 2006).


title: Liver of 15-week cellulose-fed mouse, biological rep3


title: M1-MP_in vitro_1

description: M1-macrophage (MΦ) Pool 1: pooled RNA isolated from M1 cells from healthy donors 1 to 5; M1-macrophages were generated from blood monocytes (isolated from PBMC of one healthy donor using CD14+ microbeads) by culturing them in the presence of MCSF for 7 days. Thereafter, polarization towards M1 was induced with IFNgamma plus LPS (described in Martinez et al., 2006).

source_name: in vitro generated M1 macrophages

value: M1 macrophages


title: slanDC_PBMC_2

description: CD1c+ DCs FACS-sorted from PBMCs of healthy donor 2, gated as slan+ cells among live, single, CD11c+CD56-CD19-CD3- cells.

source_name: CD1c+ DCs FACS-sorted from PBMCs

extract_protocol: RNA was prepared using RNeasy micro kit (Qiagen). RNA quantity and quality were assessed using a Nanodrop 1000 Spectrometer (Peqlab) and Agilent 2100 Bioanalyzer. RNA (0.5–15 ng) was amplified and converted into cDNA by a linear amplification method using WT-Ovation PicoSL System in combination with the Encore® Biotin Module (both from NuGen). cDNA was further purified using MinElute Reaction Cleanup kit (Qiagen) before hybridization to Affymetrix GeneChip® Human Gene ST 1.0 Arrays.

tag: donor/patient

value: healthy

value: CD1c+ DCs


title: M1-MP_in vitro_2

description: M1-macrophage (MΦ) Pool 2: pooled RNA isolated from M1 cells from healthy donors 6 to 10; M1-macrophages were generated from blood monocytes (isolated from PBMC of one healthy donor using CD14+ microbeads) by culturing them in the presence of MCSF for 7 days. Thereafter, polarization towards M1 was induced with IFNgamma plus LPS (described in Martinez et al., 2006).


title: slanDC_PBMC_3

description: CD1c+ DCs FACS-sorted from PBMCs of healthy donor 3, gated as slan+ cells among live, single, CD11c+CD56-CD19-CD3- cells.


title: MP_RCC_91

description: macrophages FACS-sorted from ccRCC tissue suspension of patient 91; gated as CD209-CD14+ cells among CD45+, live, single, CD11c+ CD3- cells.

source_name: macrophages FACS-sorted from ccRCC

value: clear cell renal cell carcinoma

value: macrophages


title: BRCA1 Null - H3K27ac antibody

city: Indianapolis

first: Guanglong

last: Jiang

state: IN

department: Medical and Molecular Genetics

institute: Indiana University School of Medicine

data_processing:
ChIP-seq reads were aligned to human genome hg19 assembly with bowtie2.
Reads aligned to gene promoter regions (-2k ~ 2k corresponding to the transcription start site of each gene) were counted with bamutils command from ngsutils package.
Differential analysis for reads in the promoter region for each gene is coducted with edgeR in statistical enviroment R.
Genome_build: hg19
Supplementary_files_format_and_content: csv spreadsheet with read counts

source_name: Ovarian cancer cell line UWB1.289

growth_protocol: UWB1.289 cells were cultured at 37°C, 5% CO2 in media containing 1:1 MEBM (Lonza, Elburn, IL, Cat. No. CC-3151) and RPMI 1640 (ATCC, Cat. No. 30-2001) supplemented with 3% fetal bovine serum (FBS), 1% penicillin-streptomycin solution, and MEGM Single-Quots (Lonza, Cat. No. CC-4136).

extract_protocol:
Chromatin was prepared using a kit (#17-295, Millipore, Billerica, MA) following the manufacturer’s protocol.
DNA libraries for H3K9ac and H3K27ac ChIPseq were prepared and sequenced at the University of Chicago Genomics Facility, Knapp Center for Biomedical Discovery (Chicago, IL).

treatment_protocol: Experimental groups differed in BRCA1 mutation status and received no further treatment.

tag: mutation status

tag: antibody


title: slanDC_PBMC_1

description: CD1c+ DCs FACS-sorted from PBMCs of healthy donor 1, gated as slan+ cells among live, single, CD11c+CD56-CD19-CD3- cells.


title: BRCA1 WT - H3K9ac antibody

value: Plus BRCA1


title: BRCA1 Null - H3K9ac antibody


title: BRCA1 WT - H3K27ac antibody


title: MP_RCC_DD1

description: macrophages FACS-sorted from ccRCC tissue suspension of patient DD1; gated as CD209-CD14+ cells among CD45+, live, single, CD11c+ CD3- cells.


title: ercDC_RCC_91

description: ercDCs FACS-sorted from ccRCC tissue suspension of patient 91; gated as CD209+CD14+ cells among CD45+, live, single, CD11c+ CD3- cells.

value: ercDCs


title: M1-MP_in vitro_3

description: M1-macrophage (MΦ) Pool 3: pooled RNA isolated from M1 cells from healthy donors 11 to 15; M1-macrophages were generated from blood monocytes (isolated from PBMC of one healthy donor using CD14+ microbeads) by culturing them in the presence of MCSF for 7 days. Thereafter, polarization towards M1 was induced with IFNgamma plus LPS (described in Martinez et al., 2006).

value: Healthy


title: BRCA1 WT - Input control


title: MP_RCC_89

description: macrophages FACS-sorted from ccRCC tissue suspension of patient 89; gated as CD209-CD14+ cells among CD45+, live, single, CD11c+ CD3- cells.


title: M2-MP_in vitro_1

description: M2-macrophage (MΦ) Pool 1: pooled RNA isolated from M2 cells from healthy donors 1 to 5; M2-macrophages were generated from blood monocytes (isolated from PBMC of one healthy donor using CD14+ microbeads) by culturing them in the presence of MCSF for 7 days. Thereafter, polarization towards M2 was induced with IL-4 (described in Martinez et al., 2006).


title: ercDC_RCC_74

description: ercDCs FACS-sorted from ccRCC tissue suspension of patient 74; gated as CD209+CD14+ cells among CD45+, live, single, CD11c+ CD3- cells.


title: ercDC_RCC_89

description: ercDCs FACS-sorted from ccRCC tissue suspension of patient 89; gated as CD209+CD14+ cells among CD45+, live, single, CD11c+ CD3- cells.


title: MP_RCC_94

description: macrophages FACS-sorted from ccRCC tissue suspension of patient 94; gated as CD209-CD14+ cells among CD45+, live, single, CD11c+ CD3- cells.


title: BRCA1 Null Entinostat 2

description:
Tophat.UCSC_hg19.counts.csv
DM-8

data_processing:
RNAseq reads were aligned to the human genome hg19 with tophat.
The aligned bam files were filtered with bamutils from ngsutils with parameters "-mismatch 2 -mapped -eq NH 1"
The filtered bam file were used to count reads with ngsutils.
Genome_build: hg19
Supplementary_files_format_and_content: csv spreadsheet

extract_protocol:
Total RNA was extracted with Stat-60 Reagent and Poly(A) mRNA was isolated using a NEBNext Poly(A) mRNA Magnetic Isolation Module (#7490S, New England Biolabs Inc., Ipswich, MA) following the manufacturer’s protocols.
cDNA libraries were prepared with a NEBNext® mRNA Library Prep Master Mix Set for Illumina (#E6110S, New England Biolabs Inc.)

treatment_protocol: Cells were treated with 0.5 uM entinostat or DMSO (control) for 24 hours.

tag: brca1 mutation

value: 0,5 uM entinostat


title: CD1c_DC_PBMC_1

description: CD1c+ DCs FACS-sorted from PBMCs of healthy donor 1, gated as CD1c+ cells among live, single, CD11c+CD56-CD19-CD3- cells.


title: ercDC_RCC_66

description: ercDCs FACS-sorted from ccRCC tissue suspension of patient 66; gated as CD209+CD14+ cells among CD45+, live, single, CD11c+ CD3- cells.


title: MP_RCC_DD2

description: macrophages FACS-sorted from ccRCC tissue suspension of patient DD2; gated as CD209-CD14+ cells among CD45+, live, single, CD11c+ CD3- cells.


title: ercDC_RCC_94

description: ercDCs FACS-sorted from ccRCC tissue suspension of patient 94; gated as CD209+CD14+ cells among CD45+, live, single, CD11c+ CD3- cells.


title: BRCA1 Null Control 2

description:
Tophat.UCSC_hg19.counts.csv
DM-7

value: DMSO


title: CD1c_DC_PBMC_3

description: CD1c+ DCs FACS-sorted from PBMCs of healthy donor 3, gated as CD1c+ cells among live, single, CD11c+CD56-CD19-CD3- cells.


title: MP_RCC_66

description: macrophages FACS-sorted from ccRCC tissue suspension of patient 66; gated as CD209-CD14+ cells among CD45+, live, single, CD11c+ CD3- cells.


title: ercDC_RCC_DD2

description: ercDCs FACS-sorted from ccRCC tissue suspension of patient DD2; gated as CD209+CD14+ cells among CD45+, live, single, CD11c+ CD3- cells.


title: CD1c_DC_PBMC_2

description: CD1c+ DCs FACS-sorted from PBMCs of healthy donor 2, gated as CD1c+ cells among live, single, CD11c+CD56-CD19-CD3- cells.


title: BRCA1 Null Control 1

description:
Tophat.UCSC_hg19.counts.csv
DM-3


title: BRCA1 WT Control 2

description:
Tophat.UCSC_hg19.counts.csv
DM-5


title: BRCA1 Null Entinostat 1

description:
Tophat.UCSC_hg19.counts.csv
DM-4


title: BRCA1 WT Entinostat 1

description:
Tophat.UCSC_hg19.counts.csv
DM-2


title: BRCA1 WT Entinostat 2

description:
Tophat.UCSC_hg19.counts.csv
DM-6


title: BRCA1 WT Control 1

description:
Tophat.UCSC_hg19.counts.csv
DM-1


title: S4_2

city: Baltimore

first: Xin

last: Chen

state: MD

address: 3400 North Charles Street

department: Biology

institute: JHU

data_processing:
Bowtie 0.12.7 was used for alignment against drosophila genome (Flybase dmel_r5.43) with parameter: -a --phred33-quals -n 2 -e 70 -l 28 -m 1 --best –strata
data filtering: only uniquely mapped one with at most two mismatches were used
Assign read to gene: gene exon genomic region were created by merging the annotation of protein, ribosomal RNA etc. An in-house perl script to search and assign the read to the gene. If a read belongs to more than one gene exon region, it will split its count equally into each gene it mapped to.
EdgeR was used to quantitatively measure the level of transcripts normalized across different samples which is termed Corrected Read per Kilobase of gene model per Million mapped reads (cRPKM). This value is used to compare gene expression level among different group of samples (according to their development stage and profile of clustering (which is only for LC stage)
Genome_build: drosophila melanogaster dmel_r5.43
Supplementary_files_format_and_content: Table of Corrected Read per Kilobase of gene model per Million mapped reads (cRPKM) for all genes within each differentiation stages

source_name: 4-cell Spermatogonia

extract_protocol:
Immediately after isolation, the cysts were treated with mild detergent to permeabilize the plasma membrane while keeping the nucleus intact.
Permeabilization allowed mRNA to be reverse transcribed using poly-dT attached to one universal primer sequence. Poly A was added to the single strand DNA 3’ end using terminal transferase. Second strand DNA was synthesized using poly-dT attached to another universal primer sequence. Finally, the resulting library was amplified using both universal primers.

treatment_protocol: Testes were dissected in S2 insect media.Two Tungsten micro-needles were used to tear the muscle sheath layer, resulting in spilled germ cell cysts into the media.The cysts were viewed using inverted microscope and were picked using glass needle

value: testes

value: germline stem cell (GSC)

tag: Stage

value: 4-cell Spermatogonia


title: S16

source_name: 16-cell Spermatogonia

value: 16-cell Spermatogonia


title: S8_1

source_name: 8-cell Spermatogonia

value: 8-cell Spermatogonia


title: S8_2


title: GB1

source_name: Gonialblast

value: Gonialblast


title: S4_1


title: aly2

source_name: arrested spermatocyte cyst from always early (aly)


title: aly1

value: arrested spermatocyte cyst from always early (aly)


title: GB2


title: MCs_placenta2_2

city: marseille

first: Amira

last: Ben Amara

address: 27  Boulevard Leï Roue

country: France

institute: IHU-CRCM

description: Purified cells

hyb_protocol: RNA was analyzed using microarray chips including 45,000 probes (4x44K Whole Human Genome, Agilent Technologies) and One-color Microarray Based Gene Expression Analysis. Hybridization was performed at 65°C using the in situ Hybridization Plus kit (Agilent Technologies) for 17 hours.

scan_protocol: Arrays were scanned with a pixel size of 5 µm with the DNA Microarray Scanner  G2505C. Image analysis and correction of intra-array signals were performed with the Feature Extraction Software10.7.3.1 (Agilent Technologies).

data_processing: Microarray data analysis was performed using the GeneSpring software. Raw data were filtered and normalized, unsupervised and supervised analyses were done using hierarchical clustering, principal composant analysis (PCA) and the signicantly modulated genes using GeneSpring Software (Agilent Technologies). Genes were considered to be differentially expressed when fold change (FC) was  FC ≥ 2 with p-value (p) was p < 0.001 in at least one of the 3 pair combinations. Gene Ontology (GO) annotations attributed to biological processes and corrected p ≤ 0.001 (Bonferroni correction) allow us to identify the biological functions that were modulated,

label_protocol: In brief, 300 ng RNA were labeled with cyanine-3-CTP using the Low RNA Input Fluorescent Amplification Kit from Agilent Technologies.

growth_protocol: For MCs; placental cells were collected following an enzymatic digestion and deposited on a 25-60% Percoll cushions and centrifuged at 1000 x g for 20 min. Placental MCs were isolated following a double positive selection using anti-CD117 (Miltenyi Biotec) and anti-FcRI antibodies (Bühlmann).HMC-1.2 were cultured in Iscove's Modified Dulbecco's Medium (IMDM, Life Technologies) supplemented with 10% fetal bovine serum (FBS, Life Technologies), 100 IU/ml penicillin and 50 µg/ml streptomycin (Life Technologies) at 37°C

extract_protocol: RNA was extracted using an RNeasy Mini kit (Qiagen, Courtaboeuf, France). The quantity and quality of total RNA were assessed using the Nanodrop (Thermo Scientific, Illkirch, France) and a 2100 Bioanalyzer (Agilent Technologies, Massy, France). The RNA was eluted in 30 µl of water and stored at -80°C.

treatment_protocol: cells were cultured at 37°C for 24 hours before processing RNAs extraction.

value: Primary Placenta Mast Cell

value: placenta


title: HMC-1.2_3

description: Purified cells

source_name: cell line MHC-1.2

value: cell line

tag: cell line


title: MCs_placenta2_1

description: Purified cells


title: BRCA1 Null - Input control


title: MCs_placenta1_2

description: Purified cells


title: HMC-1.2_1

description: Purified cells


title: MCs_placenta1_1

description: Purified cells


title: Donor 3: M1 MФ

city: Regensburg

first: James

middle: Alexander

last: Hutchinson

state: Bavaria

department: General Surgery

institute: University Hospital Regensburg

description: Isolated monocytes were cultured for 6 days at a density of 1x10^5 cells/cm^2 in Cell+ coated plates with RPMI medium containing 20% FCS, 100 ng/ml rhM-CSF, P/S and 2mM GlutaMax. The cells were then stimulated with IFN-g at 25 ng/ml and 100 ng/ml LPS for a further 24 hours.

hyb_protocol: Samples were hybridized according to the manufacture's instruction. 1.65 µg labeled cRNA was supplemented with 11 µl Agilent 10x blocking agent, 2.2 µl Agilent 25x fragmentation buffer and nuclease-free water up to 55 µl final volumen. The sample was incubated at 60°C for 30 minutes, supplemented with 55 µl 2x hybridisation buffer and 100 µl of the mix was hybridisized for 16h at 65°C using an SureHyb chamber and an Agilent hybridization oven. Arrays were disassembled and washed for 1 minute in Agilent gene Expression (GE)  wash buffer 1 followed by washing 1 minute in prewarmed (37°C) GE wash buffer 2.

scan_protocol: Images were scanned immediately after washing using a DNA microarray scanner (Agilent) at 5 µm resolution.

data_processing: Data was processed using Feature Extraction Software (Agilent) and further analyzed using GeneSpring GX software version 10. Raw data was normalized by a 75 percentile shift, log2-transformed and shifted to the median of all samples.

source_name: Human CD14(+) monocyte-derived macrophages

label_protocol: Labeling and hybridization were performed using the Agilent Gene Expression system according to the manufacturer’s instructions. In brief, 500 ng to 1000 ng of high-quality RNA were amplified and Cyanine 3-CTP labeled with the One Color Low RNA Input Linear Amplification Kit (Agilent). Labeling efficiency was controlled using the NanoDrop spectrophotometer.

growth_protocol: As described in Sample Characteristics

extract_protocol: Total cellular RNA of the different cell types was isolated using the RNeasy Plus Kit (Qiagen). RNA concentration was measured with a ND-1000 Spectrophotometer (NanoDrop, Thermo Fisher Scientific) and quality was controlled on agarose gels or using the Agilent Bioanalyzer.

treatment_protocol: As described in Sample Characteristics

tag: gender

value: male

tag: individual

value: Donor 3

tag: origin

value: CD14(+) monocyte-derived macrophages

value: M1 MФ


title: HMC-1.2_2

description: Purified cells


title: Donor 3: M2a MФ

description: Isolated monocytes were cultured for 6 days at a density of 1x10^5 cells/cm^2 in Cell+ coated plates with RPMI medium containing 10% FCS, 100 ng/ml rhM-CSF, P/S and 2mM GlutaMax. The cells were then stimulated with IL-4 at 20 ng/ml for a further 24 hours in medium containing 5% FCS and no M-CSF.

value: M2a MФ


title: Donor 2: M2b MФ

description: Isolated monocytes were cultured for 7 days at a density of 1x10^5 cells/cm^2 in Cell+ plates coated with human IVIG. The RPMI-based culture medium contained 10% FCS, 100 ng/ml rhM-CSF, P/S and 2mM GlutaMax.

value: Donor 2

value: M2b MФ


title: HMC-1.2_4

description: Purified cells


title: Donor 3: M reg

description: Isolated monocytes were cultured for 6 days at a density of 1x10^5 cells/cm^2 in Cell+ coated plates with RPMI medium containing 10% HABS, 5 ng/ml rhM-CSF, P/S and 2mM GlutaMax. The cells were further stimulated with IFN-g at 25 ng/ml for 24 hours.

value: M reg


title: Donor 3: M reg + LPS

description: Isolated monocytes were cultured for 6 days at a density of 1x10^5 cells/cm^2 in Cell+ coated plates with RPMI medium containing 10% HABS, 5 ng/ml rhM-CSF, P/S and 2mM GlutaMax. The cells were then stimulated with IFN-g at 25 ng/ml for 24 hours, after which the cells were exposed to 100 ng/ml LPS for a further 24 hours.

value: M reg + LPS


title: Donor 2: M2a MФ


title: Donor 2: M1 MФ


title: Donor 2: M2c MФ

description: Isolated monocytes were cultured for 6 days at a density of 1x10^5 cells/cm^2 in Cell+ coated plates with RPMI medium containing 20% FCS, 100 ng/ml rhM-CSF, P/S and 2mM GlutaMax. The cells were then stimulated with dexamethasone at 10(-7) M for a further 24 hours in medium containing 5% FCS in medium containing 5% FCS.

value: M2c MФ


title: Donor 3: M2c MФ


title: Donor 2: M0 MФ

description: Isolated monocytes were cultured for 6 days at a density of 1x10^5 cells/cm^2 in Cell+ coated plates with RPMI medium containing 20% FCS, 100 ng/ml rhM-CSF, P/S and 2mM GlutaMax. The cells were then grown for a further 24 hours in medium containing 5% FCS and no M-CSF.

value: M0 MФ


title: Donor 3: IFN-g MФ

description: Isolated monocytes were cultured for 6 days at a density of 1x10^5 cells/cm^2 in Cell+ coated plates with RPMI medium containing 10% FCS, 100 ng/ml rhM-CSF, P/S and 2mM GlutaMax. The cells were then stimulated with IFN-g at 25 ng/ml for a further 24 hours.

value: IFN-g MФ


title: Donor 2: M reg + LPS


title: Donor 3: M0 MФ


title: Donor 3: M reg w/o IFN-g

description: Isolated monocytes were cultured for 7 days at a density of 1x10^5 cells/cm^2 in Cell+ coated plates with RPMI medium containing 10% HABS, 5 ng/ml rhM-CSF, P/S and 2mM GlutaMax.

value: M reg w/o IFN-g


title: Donor 1: M2a MФ

value: Donor 1


title: Donor 2: M reg


title: Donor 2: M reg w/o IFN-g


title: Donor 2: IFN-g MФ


title: Donor 1: M0 MФ


title: WT_Input_16h

city: New York

first: Mahesh

last: Bachu

email: bmahesh07@gmail.com, bachum@hss.edu

state: New York

address: 535 E 70th St 6th Floor

institute: Hospital For Special Surgery

data_processing:
deepTools(2.4.3-1)
Bamcoverage
bamCoverage --bam ${j}.bam -of bigwig -o ${j}.SeqDepthNorm.bw --binSize 10 --normalizeTo1x 2150570000 --ignoreForNormalization chrX --extendReads 150 --centerReads --smoothLength 30
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

source_name: Murine embryonic fibroblasts (MEFs)

growth_protocol: MEFs were grown in Dulbucco’s minimal essential medium (DMEM) containing 10% donor bovine serum at 37°C.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min and nuclei were pelleted after sequential wash and resuspended in sonication buffer (0.1% SDS, 1mM EDTA, 10mM Tris (pH8.1)) and sonicated in a Covaris to shear the chromatin into 200-300 bp fragments. 50ug of chromatin was immunoprecipitated using anti-H3K36me3 antibody (Abcam), anti-HA antibody (Abcam) and anti-ZMYND11 antibody (Millipore). Immunoprecipitated chromatin was de-crosslinked and DNA purified.
ChIP-seq libraries were constructed using a NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs). DNA sequence was performed by NextSeq system (Illumina).

treatment_protocol: WT MEFs and NSD2 KO MEFs were treated with mouse recombinant IFNβ (100 units/ml, PBL Interferon Source) for 16h.

tag: genotype/variation

value: WT

tag: strain

tag: time point

tag: agent

value: IFN-Beta


title: KO_Input_0h

value: NSD2 KO


title: WT_0h_H3K36me2

value: Anti-Histone H3 (di methyl K36) antibody - ChIP Grade (ab9049)


title: KO_Input_16h


title: NSD2 KO_0h_H3K36me2


title: NSD2 KO_16h_ZMYND11

value: Anti-ZMYND11 Antibody-ABE1889


title: WT_16h_ZMYND11


title: NSD2 KO_0h_ZMYND11


title: Donor 1: M2c MФ

value: male

value: CD14(+) monocyte-derived macrophages

tag: cell type


title: Donor 1: IFN-g MФ


title: Donor 1: M reg + LPS


title: Donor 1: M1 MФ

value: M1 MФ


title: Donor 1: M reg


title: Donor 1: M2b MФ


title: Donor 1: M reg w/o IFN-g


title: WT_16h_H3K36me3

value: Anti-Histone H3 (tri methyl K36) antibody - ChIP Grade (ab9050)


title: SNU-668

city: Stanford

first: Hanlee

last: Ji

state: CA

address: 269 Campus Drive

department: Division of Oncology

institute: Stanford University

data_processing:
Data was processed with the cellranger package as provided freely by 10X Genomics
Reads were aligned to 10X Genomics' GRCh38 reference
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix mtx and tsv files

source_name: gastric cancer cell line

growth_protocol: Cells were grown in standard conditions as recommended by the suppliers (eg. RPMI with 10% FBS) at 37C

extract_protocol:
Cells were dissociated with trypsin and filtered with a FlowMi device to generate single cell suspensions
Cells were processed with the 10X Genomics single cell transcriptomics platform (3' v2)
Illumina single cell RNA-Seq


title: SNU-16 replicate 2


title: SNU-601


title: SNU-16 replicate 1


title: NSD2 KO_16h_H3K36me3


title: MKN-45


title: NUGC-4


title: NSD2 KO_0h_H3K36me3


title: KATOIII

value: KATOIII


title: WT_0h_H3K36me3


title: NCI-N87


title: HGC-27 repicate 2


title: NSD2 KO_16h_H3.3

value: Anti-HA tag antibody - ChIP Grade (ab9110)


title: WT_Input_0h


title: HGC-27 replicate 1


title: WT_0h_ZMYND11


title: NSD2 KO_0h_H3.3


title: SNU-638


title: BICR78F

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

data_processing:
Sequence reads were aligned to hg19 reference sequence using subread aligner.
RefGene exon coordiatates were obtained from UCSC table browser.
Mapped sequencing reads were assigned to hg19 refGene using featureCounts.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Entrez gene IDs and counts (number of mapped reads per gene) for each Sample

source_name: CAFs from genetically unstable oral cancers

growth_protocol: All cells cultured in DMEM plus 10% FBS.

extract_protocol:
Total RNA extracted using RNEasy kits (Qiagen)
Library prepared using standard illumina protocols.
Paired-end RNAseq of read length 100bp


title: WT_0h_H3.3


title: BICR3F

value: CAFs from genetically unstable oral cancers


title: BICR63F


title: BICR69F

source_name: CAFs from genetically stable oral cancers


title: BICR73F

value: CAFs from genetically stable oral cancers


title: WT_16h_H3.3


title: AS_E6_82_(miRNA-1_0_2Xgain)

city: Sydney

first: Alen

last: Faiz

state: NSW

address: 431 Glebe Point Rd

country: Australia

institute: Woolcock Institute of Medical Research

hyb_protocol: The hybridized samples were washed and stained using Affymetrix fluidics station 450.

scan_protocol: Microarrays were scanned using Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: The data were normalized with R using the affy package RMA() function

source_name: Bronchial biopsy

label_protocol: Total RNA was labelled using the FlashTag™ Biotin HSR RNA Labeling Kit

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Patients included in this study were treated with 1) Placebo twice daily for 30 months; 2) fluticasone 500µg twice daily with or without salmeterol 50µg twice daily for 30 months.

tag: time

value: 6 months

tag: treatment

value: Fluticasone + Salmeterol

tag: smoking status

value: smoker

tag: copd severity

value: GOLD Stage II

value: Bronchial biopsy


title: AS_E5_81_(miRNA-1_0_2Xgain)

value: 0 months

tag: tissue


title: AS_E7_83_(miRNA-1_0_2Xgain)

value: 30 months

value: ex-smoker


title: BICR66F


title: BICR59F


title: AS_E3_100_(miRNA-1_0_2Xgain)


title: AS_E3_78_(miRNA-1_0_2Xgain)


title: AS_E2_IG85_(miRNA-1_0_2Xgain)

value: Fluticasone


title: AS_E2_99_(miRNA-1_0_2Xgain)


title: AS_E1_98_(miRNA-1_0_2Xgain)


title: NHOF7

source_name: normal human oral fibroblasts

value: normal human oral fibroblasts


title: AS_E1_IG84_(miRNA-1_0_2Xgain)


title: AS_E1_93_(miRNA-1_0_2Xgain)

value: Placebo


title: AS_E2_1095-11_(miRNA-1_0_2Xgain)


title: AS_E2_77_(miRNA-1_0_2Xgain)


title: AS_E3_IG97_(miRNA-1_0_2Xgain)


title: AS_E1_76_(miRNA-1_0_2Xgain)


title: BICR31F


title: AS_E4_79_(miRNA-1_0_2Xgain)


title: AS_D8_IG75_(miRNA-1_0_2Xgain)


title: AS_D7_71_(miRNA-1_0_2Xgain)


title: AS_D8_73_(miRNA-1_0_2Xgain)


title: NHOF1


title: AS_D7_IG72_(miRNA-1_0_2Xgain)


title: AS_D7_67_(miRNA-1_0_2Xgain)


title: AS_D8_88_ReHyb(miRNA-1_0_2Xgain)


title: AS_D8_80_(miRNA-1_0_2Xgain)


title: PDC12

city: Barcelona

first: Anna

last: Esteve-Codina

address: Carrer Baldiri Reixac 4-8

country: Spain

institute: CNAG-CRG

description:
AE1195
COUNTS_genes_LUNGCANCER_13

data_processing:
mapping with STAR version 2.5.3a
quantification with RSEM version 1.3.0
Genome_build: Homo sapiens gencode version 27
Supplementary_files_format_and_content: matrix of counts (text)

source_name: NSCLC patient derived cells

growth_protocol: PDC cells were cultured in ACL-4 medium (base medium RPMI-1640 (Gibco) supplemented with 5% fetal bovine serum) and maintained at 37ºC and 5% CO2. The tumor cells were passaged once or twice a week and plated into a new flask. In general, tumor cultures were free of stromal cells within 4–6 passages.

extract_protocol: Total RNA was extracted using a PureLink RNA Mini Kit (Invitrogen).

value: lung; derived from metastatic site:pleural effusion

tag: histopathology

value: LuAD

value: former smoker

tag: treatment history

value: treatment-naive


title: AS_D6_IG68_(miRNA-1_0_2Xgain)


title: PDC13

description:
AE1198
COUNTS_genes_LUNGCANCER_13

value: LuSCC

value: current smoker

value: ND (non determined)


title: PDC10

description:
AE1196
COUNTS_genes_LUNGCANCER_13


title: NHOF2


title: PDC8

description:
AE1193
COUNTS_genes_LUNGCANCER_13

value: never smoker


title: PDC9

description:
AE1194
COUNTS_genes_LUNGCANCER_13


title: PDC11

description:
AE1199
COUNTS_genes_LUNGCANCER_13


title: AS_D6_66_(miRNA-1_0_2Xgain)

value: 6 months

value: Fluticasone + Salmeterol

value: smoker


title: AS_D5_27_ReHyb(miRNA-1_0_2Xgain)

value: 0 months

value: GOLD Stage II

value: Bronchial biopsy


title: AS_D6_58_ReHyb(miRNA-1_0_2Xgain)

value: Fluticasone


title: AS_D5_65_(miRNA-1_0_2Xgain)


title: AS_D4_24_ReHyb(miRNA-1_0_2Xgain)

value: 30 months


title: PDC7

description:
AE1192
COUNTS_genes_LUNGCANCER_11

value: Chemotherapy


title: AS_D6_70_(miRNA-1_0_2Xgain)

value: ex-smoker


title: AS_D4_55_(miRNA-1_0_2Xgain)


title: AS_D4_64_(miRNA-1_0_2Xgain)


title: AS_D4_92_(miRNA-1_0_2Xgain)


title: PDC6

description:
AE1191
COUNTS_genes_LUNGCANCER_11

value: lung; derived from metastatic site:pleural effusion

value: LuAD

value: Chemotherapy, immunotherapy


title: PDC5.2

description:
TKI-resistant
AE1189
COUNTS_genes_LUNGCANCER_11

value: LuAD transdifferentiation into SCLC/LuSCC

value: TKI-resistant


title: AS_D5_IG61_(miRNA-1_0_2Xgain)


title: AS_D6_95_(miRNA-1_0_2Xgain)


title: PDC5

description:
pre-treatment
AE1188
COUNTS_genes_LUNGCANCER_11

value: TKI treatment before resistance


title: AS_D3_63_(miRNA-1_0_2Xgain)


title: AS_D3_91_(miRNA-1_0_2Xgain)


title: AS_D4_IG54_(miRNA-1_0_2Xgain)


title: AS_D3_23_ReHyb(miRNA-1_0_2Xgain)


title: AS_D3_17_(miRNA-1_0_2Xgain)

value: Placebo


title: PDC4.2

description:
TKI-resistant
AE1187
COUNTS_genes_LUNGCANCER_11

value: never smoker


title: AS_D2_IG52_(miRNA-1_0_2Xgain)

value: Fluticasone + Salmeterol


title: AS_D2_90_(miRNA-1_0_2Xgain)

value: smoker


title: PDC4

description:
pre-treatment
AE1186
COUNTS_genes_LUNGCANCER_11

value: treatment-naive


title: AS_D5_69_(miRNA-1_0_2Xgain)

value: 0 months

value: GOLD Stage II


title: AS_D3_IG53_(miRNA-1_0_2Xgain)

value: Bronchial biopsy


title: PDC3

description:
AE1183
COUNTS_genes_LUNGCANCER_11


title: AS_D2_22_ReHyb(miRNA-1_0_2Xgain)


title: PDC1

description:
AE1181
COUNTS_genes_LUNGCANCER_11


title: AS_D2_62_(miRNA-1_0_2Xgain)


title: PDC2

description:
AE1182
COUNTS_genes_LUNGCANCER_11


title: AS_C8_87_(miRNA-1_0_2Xgain)

value: 6 months


title: AS_D1_21_ReHyb(miRNA-1_0_2Xgain)

value: Fluticasone


title: AS_C8_IG50_(miRNA-1_0_2Xgain)

value: ex-smoker


title: AS_D2_16_(miRNA-1_0_2Xgain)


title: AS_D1_89_(miRNA-1_0_2Xgain)


title: AS_C7_86_(miRNA-1_0_2Xgain)


title: AS_C8_57_(miRNA-1_0_2Xgain)


title: AS_C7_56_(miRNA-1_0_2Xgain)


title: AS_C7_IG45_(miRNA-1_0_2Xgain)

value: 30 months

value: GOLD Stage III


title: AS_C8_2101-11_(miRNA-1_0_2Xgain)


title: HT-29-shMLKL-TBZ5h-2

city: Seoul

first: Jae whan

last: Song

address: Yonsei-ro 50

department: Department of Biochemistry

country: South Korea

institute: College of Life Science and Biotechnology

description: TNFa + BV6 + zVAD-fmk (TBZ) - 5h

data_processing:
Preprocessed reads were matched to reference genome sequence using TopHat program (version 2.0.13) and then aligned reads were generated.
Cufflinks program (version 2.2.1) was used for transcript assambly
Expression levels were normalized with length of transcript and depth of coverage.
Expression profile data was exported by normalized FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values.
Differentially expressed transcripts included in the groups were selected through statistical verification.
In case that the genomic information was known, functional annotation and gene-set enrichment analysis were performed on the basis of GO and KEGG database.
Using STAR 2.4.0f1, GATK 2015.1-3.4.0-1-ga5ca3fc, variant calling was performed.
Fusion genes were predicted using defuse program (version deFuse 0.6.2).
Genome_build: UCSC hg19
Supplementary_files_format_and_content: HT29_shGFPvsshMLKL_DMSOvsTBZ.txt

growth_protocol: HT-29 cells were maintained in RPMI in 5% CO2 at 37°C

extract_protocol:
HT-29 cells were lysed with ice cooled trizol reagent and total RNAs were isolated.
In order to construct cDNA libraries with the TruSeq Stranded mRNA LT Sample Prep Kit, 1ug of total RNA was used. The protocol consisted of polyA-selected RNA extraction, RNA fragmentation, random hexamer primed reverse transcription and 100nt paired-end sequencing by Illumina HiSeq2000. The libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide and qualified using an Agilent Technologies 2100 Bioanalyzer

treatment_protocol: Sample 3,4,7 and 8 were treated with 20 ng/mL TNFa + 2 µM BV6 + 30 µM zVAD-fmk (TBZ)

value: human colorectal adenocarcinoma

tag: gene knockdown

value: MLKL knockdown using lentivirus

value: TNFalpha + BV6 + zVAD-fmk (TBZ)


title: HT-29-shMLKL-TBZ5h-1

description: TNFa + BV6 + zVAD-fmk (TBZ) - 5h

tag: cell line


title: HT-29-shMLKL-DMSO1

description: DMSO

value: DMSO


title: HT-29-shMLKL-DMSO2

description: DMSO


title: HT-29-shGFP-TBZ5h-2

description: TNFa + BV6 + zVAD-fmk (TBZ) - 5h


title: HT-29-shGFP-TBZ5h-1

description: TNFa + BV6 + zVAD-fmk (TBZ) - 5h


title: HT-29-shGFP-DMSO2

description: DMSO


title: AS_C7_2101-3_(miRNA-1_0_2Xgain)


title: AS_C7_18_ReHyb(miRNA-1_0_2Xgain)


title: AS_C6_IG44_(miRNA-1_0_2Xgain)


title: AS_C6_74_(miRNA-1_0_2Xgain)

value: Placebo


title: AS_C6_25_(miRNA-1_0_2Xgain)


title: AS_C6_14_ReHyb(miRNA-1_0_2Xgain)


title: AS_C5_IG43_(miRNA-1_0_2Xgain)


title: AS_C6_2101-1_(miRNA-1_0_2Xgain)


title: AS_C5_2100-11_(miRNA-1_0_2Xgain)


title: AS_C5_49_(miRNA-1_0_2Xgain)


title: AS_C5_2098-1-2_(miRNA-1_0_2Xgain)


title: neg_2

city: Hangzhou

first: Lili

last: Xia

address: No.1 Xueshi Road

institute: Zhejiang University

data_processing:
Downstream analysis was performed using a combination of programs including Bowtie2, Tophat2, HTseq, Cufflink and our wrapped scripts.
Alignments were parsed using Tophat program and differential expressions were determined through DESeq/DEGseq.
Gene fusion and difference of alternative splicing event were detected by MISO and TopHatfusion software
Reference genome and gene model annotation files were downloaded from genome website, browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome were TopHat v2.0.9. Bowtie uses a BWT(Burrows-Wheeler Transformer) algorithm for mapping built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using reads to the genome and Tophat can generate a database of splice junctions based on the gene model annotation file and thus achieve a better mapping result than other non-splice mapping tools.
Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using the DESeq  R package (1.10.1). DESeq provide statistical routines for determining differential expression  in digital gene expression data using a model based on the negative binomial distribution.  The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for  controlling the False Discovery Rate(FDR). Genes with an adjusted P-value <0.05 found by  DESeq were assigned as differentially expressed.
Genome_build: TopHat v2.0.9
Supplementary_files_format_and_content: Excel files containg information of all 6 samples

growth_protocol: The human SiHa cell lines were purchased from ATCC. SiHa cells were cultured in DMEM Medium with 10% fetal bovine serum and incubated in a 37 °C humidified incubator with 5% CO2.

extract_protocol:
SiHa cells were transfected with si-CNN3 or si-NC for 24h. And then, the medium containing transfection reagents was replaced by fresh medium. 48h post transcription, RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
si-NC sense: UUCUCCGAACGUGUCACGUTT
si-CNN3#1 sense: GCAGAUGGGAACCAACAAATT

tag: tissue source

value: cervix

value: SiHa (ATCC)

value: transfected with si-NC


title: neg_1


title: AS_C4_IG39_(miRNA-1_0_2Xgain)

value: Fluticasone + Salmeterol

value: smoker


title: AS_C5_13_ReHyb(miRNA-1_0_2Xgain)

value: GOLD Stage II


title: AS_D1_IG51_(miRNA-1_0_2Xgain)

value: Bronchial biopsy


title: AS_C3_IG38_(miRNA-1_0_2Xgain)

value: 6 months


title: HT-29-shGFP-DMSO1

description: DMSO


title: AS_C4_12_ReHyb(miRNA-1_0_2Xgain)


title: cnn3_2

value: transfected with si-CNN3


title: cnn3_3


title: neg_3


title: AS_C4_2100-3_(miRNA-1_0_2Xgain)

value: Fluticasone

value: ex-smoker


title: cnn3_1


title: AS_C3_2073-3_(miRNA-1_0_2Xgain)


title: AS_C4_48_(miRNA-1_0_2Xgain)

value: 30 months


title: AS_C3_47_(miRNA-1_0_2Xgain)


title: AS_C3_11_ReHyb(miRNA-1_0_2Xgain)


title: AS_C2_2097-11_(miRNA-1_0_2Xgain)


title: AS_C2_46_(miRNA-1_0_2Xgain)

value: 0 months


title: AS_C3_2100-1_(miRNA-1_0_2Xgain)

value: GOLD Stage III


title: AS_C2_2073-1_(miRNA-1_0_2Xgain)


title: AS_C2_2088-11_ReHyb(miRNA-1_0_2Xgain)


title: AS_C2_IG37_(miRNA-1_0_2Xgain)


title: AS_C4_2078-1_(miRNA-1_0_2Xgain)


title: AS_C1_IG35_(miRNA-1_0_2Xgain)


title: AS_C1_2097-3_(miRNA-1_0_2Xgain)


title: AS_C1_42_(miRNA-1_0_2Xgain)


title: AS_C1_2088-1_(miRNA-1_0_2Xgain)


title: AS_C1_2034-3_(miRNA-1_0_2Xgain)


title: AS_B8_41_(miRNA-1_0_2Xgain)


title: AS_B8_IG34_(miRNA-1_0_2Xgain)


title: AS_B7_40_(miRNA-1_0_2Xgain)


title: AS_B6_2108-11_(miRNA-1_0_2Xgain)


title: AS_B7_IG20_(miRNA-1_0_2Xgain)


title: AS_B7_2085-11_(miRNA-1_0_2Xgain)


title: AS_B6_36_(miRNA-1_0_2Xgain)


title: AS_B7_2018-1_(miRNA-1_0_2Xgain)


title: AS_B8_2097-1_(miRNA-1_0_2Xgain)


title: AS_B8_2018-11_(miRNA-1_0_2Xgain)


title: AS_B8_2034-1_(miRNA-1_0_2Xgain)


title: AS_B6_2085-3_(miRNA-1_0_2Xgain)


title: AS_B5_2108-1_(miRNA-1_0_2Xgain)


title: AS_B5_33_(miRNA-1_0_2Xgain)


title: AS_B6_2017-11_(miRNA-1_0_2Xgain)


title: AS_B6_2026-3_(miRNA-1_0_2Xgain)


title: AS_B3_31_(miRNA-1_0_2Xgain)


title: AS_B7_2026-11_(miRNA-1_0_2Xgain)


title: AS_B3_2052-3_(miRNA-1_0_2Xgain)


title: AS_B4_2083-11_(miRNA-1_0_2Xgain)


title: AS_B4_32_(miRNA-1_0_2Xgain)


title: AS_B4_1101-11_(miRNA-1_0_2Xgain)


title: AS_B4_2011-11_(miRNA-1_0_2Xgain)


title: AS_B5_2085-1_(miRNA-1_0_2Xgain)


title: AS_B3_1101-1_(miRNA-1_0_2Xgain)


title: AS_B4_2052-11_(miRNA-1_0_2Xgain)


title: AS_B2_2011-1_(miRNA-1_0_2Xgain)


title: AS_B3_2069-11_(miRNA-1_0_2Xgain)


title: AS_B5_2017-1_(miRNA-1_0_2Xgain)


title: AS_B5_2026-1_(miRNA-1_0_2Xgain)


title: AS_B2_2052-1_(miRNA-1_0_2Xgain)


title: AS_A7_26_(miRNA-1_0_2Xgain)


title: AS_B2_2069-1_(miRNA-1_0_2Xgain)


title: AS_A8_2047-3_(miRNA-1_0_2Xgain)


title: AS_A8_1092-11_(miRNA-1_0_2Xgain)


title: AS_B3_2011-3_(miRNA-1_0_2Xgain)


title: AS_B2_30_(miRNA-1_0_2Xgain)


title: AS_A8_2062-1_(miRNA-1_0_2Xgain)


title: AS_B1_1100-1_(miRNA-1_0_2Xgain)


title: SK-HI-SETDB1_KD_H3K4me1

city: Heidelberg

first: Jochen

last: Utikal

address: Im Neuenheimer Feld 280

department: Clinical Cooperation Unit Dermato-Oncology

institute: German Cancer Research Center

description: SKmel28 subclone with SETDB1 extra gene copies.

data_processing:
Sequence reads were aligned against the human reference genome (hg19) using BWA version 0.5.9-r16.
Call peaks alignment analysis was conducted with MACS2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.bedGraph: Input-subtracted, whole-genome coverage tracks (bigWig files) of aligned reads were generated.

source_name: melanoma cells

growth_protocol: Human melanoma cells were maintained in RPMI 1640  medium (100 U/ml penicillin, 100 µg/ml streptomycin) and supplemented with 10% FBS (Biochrom) in 5% CO2 at 37°C. All experiments were performed with cells at 50-80% confluence.

extract_protocol:
Cells were crosslinked and then collected. Cell pellets were lysated and nuclei were sonicated. Sonicated DNA was immunoprecipitated against H3K9me 3 or H3K4me1 antibodies.
ChIP-Seq DNA libraries preparation was performed with NEB Next Ultra DNA Library Kit, according to the manufacturer’s protocol.

value: melanoma cell line

tag: variation

value: SETDB1 knockdown

tag: chip antibody

value: H3K4me1 (Abcam, ab8895)


title: SK-HI-SETDB1_NT_H3K4me1

value: control


title: AS_A8_28_(miRNA-1_0_2Xgain)

value: Placebo


title: AS_D1_15_(miRNA-1_0_2Xgain)


title: AS_A8_1096-11_(miRNA-1_0_2Xgain)


title: C32_OE_H3K4me1

value: SETDB1 overexpression


title: AS_B1_29_(miRNA-1_0_2Xgain)


title: C32_EV_H3K4me1


title: AS_A7_1096-3_(miRNA-1_0_2Xgain)


title: AS_A7_2047-1_(miRNA-1_0_2Xgain)


title: AS_A7_1092-1_(miRNA-1_0_2Xgain)


title: AS_B1_2047-11_(miRNA-1_0_2Xgain)


title: SK-HI-SETDB1_KD_H3K9me3

value: H3K9me3 (Abcam, ab8898)


title: AS_A7_2060-11_(miRNA-1_0_2Xgain)

value: smoker


title: AS_A5_1079-1_(miRNA-1_0_2Xgain)

value: GOLD Stage II


title: SK-HI-SETDB1_NT_H3K9me3


title: AS_B1_2062-11_(miRNA-1_0_2Xgain)

value: Bronchial biopsy


title: AS_A5_1095-3_(miRNA-1_0_2Xgain)

value: 6 months


title: C32_OE_H3K9me3


title: AS_A5_102_(miRNA-1_0_2Xgain)


title: AS_A4_2037-1_(miRNA-1_0_2Xgain)


title: NICD4_3

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

data_processing:
RNA-seq library from 15 cell lines were sequenced in Illumina HiSeq Machines, Base-calling perfromed using RTA software and demultiplexed to obtain individual Fastq files.
The samples were sequenced 51 bp on the HiSeq 2000. The reads were aligned against the human genome build 37 using Tophat version 2.0.6. Tophat was supplied with a known set of gene-models using a GTF file (Ensembl version 66). HTSeq-count was then used to generate a list of the total number of uniquely mapped reads for each gene and sample. The resulting dataset contained 31,352 gene entries with mRNA transcript counts.
Genome_build: GRCh37 (Ensembl version 66 for GTF)
Supplementary_files_format_and_content: text file contains counts (generated by HTSeq-count) for all the analysed samples (15 samples, 3 replicates in each group for 5 groups, making it total 15 samples)

source_name: Doxycyclin induced NICD4 expressing HCT116

extract_protocol:
Total RNA was extracted using TRIzol reagent (15596-018, Ambion life technologies) according to the manufactures protocol.  2,5 mL of TRIzol reagent was used . The cells were lysed and homogenized in 15 mL tube(s) (Falcon). 0.2 vol. of chloroform (Chloroform stab./Amylene, Biosolve) was added to the homogenate and the tube(s) were shaken vigorously for 20 seconds. The tube(s)  were incubated for 2-3 minutes at room temperature and centrifuged  (Hettich, rotanta 46 RS) for 1 hour at 4 C . Approximately 70% of the upper aqueous phase was transferred to a clean 15 mL tube and 0.5x volume of isopropanol  (33539, Sigma-Aldrich, ) was added. The tube(s) were incubated overnight at -20 C and centrifuged for 30 minutes at 4 C. The supernatant was removed and the pellet was washed twice with 80% ethanol  (32221-2.5L, Sigma-Aldrich). The total RNA pellet was air-dried for 10 minutes and dissolved  in nuclease free water (AM9937, Ambion life technologies). Quality and quantity of the total RNA was assessed by the 2100 Bioanalyzer (Agilent) using a Nano chip (Agilent).
Sequencing libraries were generated using the TruSeq RNA Sample Preparation v2 Guide (Illumina Part # 15026495 Rev. F) according to the manufacturer's instructions. Briefly, polyadenylated RNA from intact total RNA was purified using oligo-dT beads. Following purification the RNA was fragmented, random primed and reverse transcribed using SuperScript II Reverse Transcriptase (Invitrogen, part # 18064-014). Second strand synthesis was performed using Polymerase I and RNaseH. The resulting cDNA was converted to blunt end fragments using an end repair mix (Illumina), followed by 3' end adenylation and ligated to Illumina Paired-end sequencing adapters and subsequently amplified by 16 cycles of PCR. The libraries were analyzed on a 2100 Bioanalyzer (Agilent) using a 7500 chip(Agilent) and diluted to 10nM.

value: human colorectal cell line

tag: genotype/variation

value: Doxycyclin induced NICD4 expression


title: AS_A5_2037-3_(miRNA-1_0_2Xgain)

value: ex-smoker


title: AS_B2_1100-11_(miRNA-1_0_2Xgain)

value: 30 months

value: Fluticasone


title: AS_A4_2023-1_(miRNA-1_0_2Xgain)

value: 0 months


title: AS_A5_2023-11_(miRNA-1_0_2Xgain)


title: AS_A6_103_(miRNA-1_0_2Xgain)


title: C32_EV_H3K9me3

value: melanoma cell line


title: NICD4_1

source_name: Doxycyclin induced NICD3 expressing HCT116

value: Doxycyclin induced NICD3 expression


title: NICD4_2


title: AS_A6_1079-11_(miRNA-1_0_2Xgain)


title: NICD3_3


title: NICD3_2


title: AS_A4_1076-11_(miRNA-1_0_2Xgain)

value: GOLD Stage III


title: NICD3_1

value: Doxycyclin induced NICD23expression


title: AS_A4_1095-1_(miRNA-1_0_2Xgain)


title: NICD2_3

source_name: Doxycyclin induced NICD2 expressing HCT116

value: Doxycyclin induced NICD2 expression


title: NICD2_1


title: NICD2_2


title: AS_A6_2060-1_(miRNA-1_0_2Xgain)


title: AS_A2_2102_11_(miRNA-1_0_2Xgain)


title: AS_B1_1102-1_(miRNA-1_0_2Xgain)


title: AS_A6_1096-1_(miRNA-1_0_2Xgain)

value: Placebo


title: AS_A3_1076-1_(miRNA-1_0_2Xgain)


title: NICD1_3

source_name: Doxycyclin induced NICD1 expressing HCT116

value: Doxycyclin induced NICD1 expression


title: AS_A6_2037-11_(miRNA-1_0_2Xgain)


title: AS_A3_2102_3_(miRNA-1_0_2Xgain)


title: NICD1_2


title: AS_A2_1106-1_(miRNA-1_0_2Xgain)

value: smoker


title: AS_A3_2025-11_(miRNA-1_0_2Xgain)

value: GOLD Stage II


title: Negative Control siRNA, replicate 1

city: Oslo

first: Leonardo

middle: A.

last: Meza-Zepeda

address: Ullernchausseen 70

department: Department of Tumor Biology

country: Norway

institute: Oslo University Hospital

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Raw data was exported from GenomeStudio (Illumina) and quantile normalised in J-Express.

source_name: ATCC® HTB-26™

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

growth_protocol: Cells were maintained in RPMI1640 (Lonza, Basel, Switzerland) supplemented with 10% foetal calf serum (PAA Laboratories GmbH, Pasching, Austria), and GlutaMAX (Invitrogen, California, USA) at 37°C with 5 % CO2.

extract_protocol: RNA was isolated using the standard TRIzol procedure (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: Cells were transfected using Interferin and 15nM siRNA, following the manufacturer's protocol (Polyplus), and cells were harvested 4 days after transfection.

value: Triple-negative breast cancer

tag: sample origin

value: Pleural effusion

tag: gender

value: Female

tag: sirna

value: Negative Control siRNA


title: HMGA2 siRNA, replicate 1

tag: cell type

value: HMGA2 siRNA


title: MDA-MB-231 not transfected replicate 1


title: AS_A2_2025-3_(miRNA-1_0_2Xgain)

tag: time

value: 6 months

value: ex-smoker

value: Bronchial biopsy


title: NICD1_1

value: human colorectal cell line


title: AS_A3_1080-11_(miRNA-1_0_2Xgain)

value: 30 months

tag: treatment

value: Fluticasone


title: AS_A2_1080-3_(miRNA-1_0_2Xgain)

tag: smoking status


title: EV_1

source_name: Isogenic empty vector control HCT116

value: Isogenic empty vector control


title: Negative Control siRNA, replicate 2


title: AS_A3_1106.11_(miRNA-1_0_2Xgain)

tag: copd severity


title: EV_3


title: EV_2


title: AS_A4_101_(miRNA-1_0_2Xgain)

value: 0 months

tag: tissue


title: HMGA2 siRNA, replicate 2


title: MDA-MB-231 not transfected, replicate 2


title: MCF-7 input Ethanol

city: Rennes

first: Raphaël

last: Métivier

address: Campus de Beaulieu

institute: CNRS UMR 6290

description: Input

data_processing:
Basecalls were performed using CASAVA (v1.8. or v1.8.2) to produce fastq files. The multiple files generated were the catenated into a single one.
Reads were aligned to the hg19 reference genome assembly using bowtie (Langmead et al., Genome Biol., 2009) with parameters allowing at most two mismatches and selected for unique mapping onto the genome.
Extracted reads were  converted to .wig signal files using samtools (Li et al., Bioinformatics, 2009) and MACS (Zhang et al., Genome Biol, 2008) with default parameters, incluing a normalization step towards the input sequences.
MACS (Zhang et al., Genome Biol, 2008) with default parameters, incluing a normalization step towards the input sequences
MACS 2.1.1.2016 (Feng et al., 2012) was then used for peak calling using low/up mfold bound adjusted to 5 and 50 respectively and at different P-valuep-values cutoff. Input control file was used as reference for these peak-callings.
Genome_build: hg19
Supplementary_files_format_and_content: .wig files containing MACS (v1.4) signals

source_name: breast cancer cell line

growth_protocol: Cells were maintained  in DMEM (Gibco, Invitrogen)/10% FCS (BioWest) supplemented or not with selection antibiotics for integrated vectors ( 5 µg/ml blasticidin, 75 µg/ml Zeocin ).

extract_protocol:
Cells were and lysed for 10 min in ice in 300 µl of lysis buffer [10 mM EDTA, 50 mM Tris-HCl (pH 8.0), 0.1% SDS, 0.5% Empigen BB (Sigma)]. Crosslinked chromatin was sheared to an average size of 400 bp by sonication for 15 min with 30secs on/off cycles at full power in a BioRuptor apparatus (Diagenode). Following 10 minutes of centrifugation at 10,000 x g, 30 µl were kept as input fraction and the remainder diluted 5 fold in IP buffer (2 mM EDTA, 100 mM NaCl, 20 mM Tris-HCl [pH 8.1], and 0.5%Triton X-100) before proceeding to immunoprecipitation overnight at 4°C under rocking using 2 µg of antibodies and 5 µg of yeast tRNAs. Complexes were recovered after 3 hr incubation at 4°C with 5 µg of yeast tRNAs and 100 µl of a 50% protein A or protein G-Sepharose beads slurry (Amersham Pharmacia Biosciences). Precipitates were then serially washed, using 500 µl of Washing Buffers (WB) I [2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 0.1% SDS, 1% Triton X-100, 150 mM NaCl], WB II [2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 0.1% SDS, 1% Triton X-100, 500 mM NaCl], WB III [1 mM EDTA, 10 mM Tris-HCl (pH 8.1), 1% NP-40, 1% Deoxycholate, 0.25 M LiCl] and then twice with 1 mM EDTA, 10 mM Tris-HCl (pH 8.1). Precipitated complexes were removed from the beads through two sequential incubations of 10 min with 50 µl of 1% SDS, 0.1 M NaHCO3. Crosslink was reversed by an overnight incubation at 65°C with 50 µg of Proteinase K (Sigma). Following a subsequent incubation of the samples with 2.5 µg RNAse (Sigma) for 1h at 37°C, the DNA was then purified on NucleoSpin™ columns (Macherey-Nagel) using NTB buffer and eluted in 40 µl of elution buffer. Efficiency of the ChIP assay was evaluated using qPCR positive and negative controls before proceeding to subsequent steps. For each ChIP conditions, from 18 to 20 individually prepared samples were pooled and submitted for library preparation.
Libraries were prepared according to Illumina's instructions by IGBMC sequencing facility (Strasbourg, France)

treatment_protocol: 15.10E6 MCF-7 control or MCF-7 MKL1ΔN200 cells were cultivated for 48h in DMEM/10% serum followed by 3 days of culture in DMEM/2.5% charcoal-stripped serum (BioWest).  Expression of the MKL1 ΔN200 transgene in MCF-7 MKL1D200 cells was induced 48h before the E2 treatment by adding Tetracycline (Sigma) at a final concentration of 1 microg/ml. Cells were treated for 50 minutes with 10-8M final estradiol and fixed for 10 min at room temperature in a PBS solution containing 1.5% formaldehyde (ACROS). After a 5 min quenching with 0.125M glycine, cells were washed twice in ice-cold PBS and collected in 1 ml of cold buffer (100 mM Tris-HCl [pH 9.4] and 100 mM DTT).

tag: integrated vectors

value: pcDNA6/TR and pcDNA4/TO, Invitrogen

tag: hormone treatment

value: Ethanol (0.01% final)


title: MCF-7 MKL1D200 ChIP ER E2

description: Chipped

value: pcDNA6/TR and pcDNA4/TO -MKL1 deltaN200, Invitrogen

value: 10-8M Estradiol (Sigma)

value: HC-20, sc-543, Santa Cruz Biotechnology


title: AS_A1_2025-1_(miRNA-1_0_2Xgain)

value: Placebo

value: GOLD Stage II


title: AS_A2_1030-11_(miRNA-1_0_2Xgain)

value: smoker


title: MCF-7 input E2

description: Input


title: MCF-7 MKL1D200 ChIP ER Ethanol

description: Chipped


title: MCF-7 Control ChIP ER E2

description: Chipped


title: AS_A1_1080-1_(miRNA-1_0_2Xgain)


title: MCF-7 Control ChIP ER Ethanol

description: Chipped


title: RS411 BCL6

city: San Francisco

first: Huimin

last: Geng

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

data_processing:
Counts: Raw image data were converted into base calls via the Illumina pipeline CASAVA version 1.8 with default parameters. All 51-bp-long paired-end reads were mapped to the reference human genome sequence, hg18, using BWA aligner (Li H. and Durbin R. (2009) Bioinformatics, 25:1754-60) with the default parameters. Only reads mapping uniquely to the genome with not more than 2 mismatches were retained for downstream analysis.
Peaks: Peak detection was performed with the ChIPseeqer program (Giannopoulou and Elemento, BMC Bioinformatics 2011, 12:277) and annotated to genes and/or promoters based on hg18 refseq genes downloaded from the UCSC Genome Browser
Genome_build: human hg18 build
Supplementary_files_format_and_content: bigwig and bigbed formats
Genome Build:
RS411_BCL6.bigWIG: hg18
RS411_BCL6_target_1.bigBED: hg18

source_name: RS411 cells

growth_protocol: The human RS4;11 ALL cells were maintained in Roswell Park Memorial Institute medium (RPMI-1640, Invitrogen, CA) with 10% fetal bovine serum (FBS), 100 IU/ml penicillin and 100 μg/ml streptomycin.

extract_protocol: Genomic DNA-fragment libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufacture’s instructions (Illumina, CA). Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs into phosphorylated blunt ends with the use of T4 DNA polymerase and E. coli DNA polymerase I Klenow fragment. Illumina single-end adapters were ligated to the ends of the DNA fragments. Ligation products were purified on a 2% agarose gel with a size selection of 200-300bp. Fifteen PCR cycles were performed with Illumina genomic DNA primers that anneal to the ends of the adapters. The purified PCR-amplified fragment libraries were quantified with the use of the PicoGreen dsDNA Quantitation Assay with the Qubit Fluorometer (Invitrogen, CA). The size range of libraries was validated on the Agilent Technologies 2100 Bioanalyzer with the High Sensitivity DNA Kit (Agilent, CA).

treatment_protocol: RS411 cells were fixed with 1% formaldehyde, lysed and sonicated to generate fragments less than 500bp. Sonicated lysates were incubated with antibodies overnight and after increasing stringency washes immunocomplexes were recovered and DNA was isolated.

value: MLL-AF4 pre-B acute lymphomablastic leukemia

tag: chip antibody host, amount, catelog number and provider

value: Rabbit, 2ug, 4242, Cell Signaling


title: AS_A1_1030-1_(miRNA-1_0_2Xgain)


title: input

data_processing:
Counts: Raw image data were converted into base calls via the Illumina pipeline CASAVA version 1.8 with default parameters. All 51-bp-long paired-end reads were mapped to the reference human genome sequence, hg18, using BWA aligner (Li H. and Durbin R. (2009) Bioinformatics, 25:1754-60) with the default parameters. Only reads mapping uniquely to the genome with not more than 2 mismatches were retained for downstream analysis.
Peaks: Peak detection was performed with the ChIPseeqer program (Giannopoulou and Elemento, BMC Bioinformatics 2011, 12:277) and annotated to genes and/or promoters based on hg18 refseq genes downloaded from the UCSC Genome Browser
Genome_build: human hg18 build
Supplementary_files_format_and_content: bigwig and bigbed formats
Genome Build:
RS411_input.bigWIG: hg18

value: Rabbit, 2ug, 2729, Cell Signaling


title: AS_A1_1041-1_(miRNA-1_0_2Xgain)

value: Bronchial biopsy


title: Mouse Control3

city: Seville

first: Alejandro

last: Martin-Montalvo

address: Av/ Américo Vespucio 24

institute: CABIMER

description: Gene expression data from human pancreatic islets isolated from healthy donors

hyb_protocol: Following fragmentation, 3.8 µg of single-stranded cDNA were hybridized for 16 hr at 45ºC on GeneChip® Human Gene 2,0 ST Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G

data_processing: The .CEL files were generated using Affymetrix AGCC software and further processed into expression values using Robust Multiarray Average (RMA) method by Irrizarry et al. The following statistical data analysis (ANOVA unpaired one-way) were performed using the TAC software (Transcriptome Analysis Console) developed by Affymetrix.

source_name: Mouse Control3 pancreatic islets from healthy donor

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 2ng total RNA Labeling Protocol (Manual Target Preparation for GeneChip® Whole Transcript (WT) Expression ArraysWT Pico Reagent Kit, ©2015 Affymetrix Inc.)

growth_protocol: Pancreatic iselts from healthy donors were isolated, cultured and processed

extract_protocol: Total RNA was extracted using the RNAeasy plus micro kit (Qiagen) following the instructions of the manufacturer.

treatment_protocol: Islet preparations were washed, handpicked and subsequently maintained in CMRL-1066 (Gibco) containing 5.6 mM glucose supplemented with 10% FCS, 100 Units/ml penicillin, 100 μg/ml streptomycin and 100 μg/ml gentamycin. At 16 hours upon reception islets  were invected with a control P SIN Dual-GFP lentiviral vector. Islets were processed for RNA exptraction at 96 hours post infection.

value: Murine pancreatic islets

tag: lentivirus

value: control


title: Mouse PAX8 3

source_name: Mouse PAX8 3 pancreatic islets from healthy donor

value: over-expression of the PAX8 gene


title: Mouse Control2

source_name: Mouse Control2 pancreatic islets from healthy donor