title: Kidney_fresh_tissue_donor_83

source_name: fresh kidney tissue endothelial cells donor 83 (M, 102 d)

value: Kidney


title: Heart_fresh_tissue_donor_83

status: Public on Oct 23 2018

type: SRA

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

country: USA

institute: University of Washington

library_source: transcriptomic

data_processing:
To process sequences, Illumina RTA-generated BCL files were converted to FASTQ files and sequence read and base quality were checked using the FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) and FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Sequences were aligned to hg19 using Tophat (26). Lane level bam data files were merged using the Picard MergeSamFiles tool and suspected PCR duplicates were marked, not removed, in the alignment files using the Picard MarkDuplicates tool (http://broadinstitute.github.io/picard/). Local realignment was performed around indels, and base quality score recalibration was run using GATK tools. Fragment counts were generated using the featureCounts function in the Bioconductor Rsubread package.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data consist of tab-delimited counts per gene for each sample. The first column contains the NCBI Gene ID, and the remaining columns are counts for each gene per sample.

molecule: total RNA

organism: Homo sapiens

source_name: fresh heart tissue endothelial cells donor 83 (M, 102 d)

growth_protocol: For cultured endothelial cells, the cell suspension was plated on gelatin coated T-75 flasks in EBM-2 medium supplemented with antibiotic/antimycotic (Invitrogen), 10% FBS (Invitrogen), 100 μg/ml ECGS (Millipore), 50 μg/ml Heparin (Invitrogen), and 40 ng/ml VEGF (R&D Systems). For kidney and lung samples, epithelial cells were removed from the cell suspension before plating using EpCAM microbeads (Miltenyi Biotec) to prevent epithelial cell overgrowth. Cells were cultured at 5% O2 until confluent and then endothelial cells as the CD144 positive and CD45 negative population were sorted on BD FACSAria II at the UW SLU Flow Cytometry Facility. After sorting, organ specific endothelial cells were cultured in EBM-2 supplemented with antibiotic/antimycotic, 10% FBS, 100 μg/ml ECGS, 50 μg/ml Heparin, and 20 ng/mL VEGF, on gelatin-coated plates and used for further experiments between passages 1-3.

extract_protocol:
Total RNA from cultured and freshly isolated organ specific endothelial cells was purified using the RNAeasy Mini Kit (Qiagen) and residual DNA was removed by on-column DNase digestion. RNA quality was assessed with the Agilent RNA 6000 Nano Kit using the Agilent 2100 Bioanalyzer (Agilent Technologies). Only samples with RNA integrity number higher than 8 were kept for further analysis. RNA sequencing was performed on poly-A-enriched samples using Illumina TruSeq.
Each library was barcoded using the Illumina adapters, and amplified with 13 cycles of PCR. Library concentrations were quantified using the Quant-it dsDNA Assay (Life Technologies, Carlsbad, CA). Libraries were normalized and pooled based on Agilent 2100 Bioanalyzer results (Agilent Technologies, Santa Clara, CA), and the pools were sequenced on an Illumina HiSeq 2500.

treatment_protocol: Normal human fetal organs were obtained upon informed consent from abortion material (age 16-20 weeks) and the same donor tissues (kidney, lung, liver, and heart) were used to isolate organ specific endothelial cells. Tissues were minced finely in serum-free EBM-2 endothelial growth medium (Lonza) supplemented with 0.2 mg/ml Liberase and 100 U/ml DNase (Roche) and incubated for 30 min at 37 0C in a water bath with shaking. The resulting tissue homogenate was filtered twice through a 40 μm cell strainer to remove tissue debris and large vessels. For the isolation of fresh endothelial cells, EpCAM-positive cells were depleted first from the cell suspension using EpCAM microbeads (Miltenyi Biotec), followed by the depletion of CD45-positive cells using CD45 MicroBeads (Miltenyi Biotec). Then the CD144 positive cells were magnetically separated using CD144 MicroBeads (Miltenyi Biotec) on 2 different columns.

tag: tissue

value: Heart

tag: cell type

value: Fresh


title: Breast Cancer BC1350

type: RNA

city: Kanagawa

first: Satoko

last: Takizawa

address: kamakurashi

country: Japan

institute: Toray industries inc

description:
Breast Cancer
SH4YL58_Cell4

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).

data_processing: The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetEsophageal Cancerted) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale.

source_name: Serum

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

tag: tumor stage (figo)

tag: age

value: uncertain


title: Liver_fresh_tissue_donor_83

source_name: fresh liver tissue endothelial cells donor 83 (M, 102 d)

value: Liver


title: Lung_fresh_tissue_donor_83

source_name: fresh lung tissue endothelial cells donor 83 (M, 102 d)

value: Lung


title: Lung_fresh_tissue_donor_85

source_name: fresh lung tissue endothelial cells donor 85 (M, 122 d)


title: Breast Cancer BC1351

description:
Breast Cancer
SH4YL59_Cell1


title: Breast Cancer BC1365

description:
Breast Cancer
SH4YL60_Cell1


title: Breast Cancer BC1357

description:
Breast Cancer
SH4YL59_Cell4


title: Breast Cancer BC1437

description:
Breast Cancer
SH4YL64_Cell4


title: Breast Cancer BC1436

description:
Breast Cancer
SH4YL64_Cell3


title: Breast Cancer BC1352

description:
Breast Cancer
SH4YL59_Cell2


title: Breast Cancer BC1345

description:
Breast Cancer
SH4YL58_Cell1


title: Breast Cancer BC1341

description:
Breast Cancer
SH4YL57_Cell4


title: Breast Cancer BC1334

description:
Breast Cancer
SH4YL57_Cell2


title: Kidney_fresh_tissue_donor_85

source_name: fresh kidney tissue endothelial cells donor 85 (M, 122 d)


title: Kidney_fresh_tissue_donor_80

source_name: fresh kidney tissue endothelial cells donor 80 (M, 135 d)


title: Breast Cancer BC1331

description:
Breast Cancer
SH4YL57_Cell1


title: Heart_cultured_donor_51

source_name: cultured heart endothelial cells

value: Cultured


title: Breast Cancer BC1330

description:
Breast Cancer
SH4YL55_Cell4


title: RB668 organoids_P1

city: Bangkok

first: Rossukon

last: Kaewkhaw

address: 270 Rama VI Road Ratchathewi

country: Thailand

institute: Mahidol University

data_processing:
[Read Filtering]  High-quality RNA-seq reads were selected by using Trimmomatic (v0.36) using default parameters.
[Gene Expression Computation]  Kallisto (v0.43) was used to compute transcript-level counts on the Ensembl V84 transcriptome (coding and non-coding sequences were included to compute index with Kallisto). To compute gene level expression, the “tximport” R package was used. Initially, gene level count data was TMM (trimmed mean of M-values); it was normalized and then underwent CPM (counts per million) computation.
[Differential Expression]  To account for differences in sequencing, we modeled the data with two batches representing poly-A-tail-pulldown vs. total RNA sequencing protocols. We incorporated these batches in our design matrix and implemented a generalized linear modeling approach for differential expression (“estimateDisp,” followed by “glmFit” functions in the “edgeR” package). Genes with log2 fold-change of 2 and Benjamini-Hochberg-adjusted p-values ≤ 0.01 were selected as differentially expressed genes.
Genome_build: GRCh38.p3 (Ensembl release 82)
Supplementary_files_format_and_content: Tab delimited text file containing annotation and raw gene counts of samples

source_name: Culture of retinal tumor

growth_protocol: Tissue was mechanically and enzymatically dissociated; dissociated cells were mixed in Matrigel® solution and plated as adherent Matrigel® drops which were overlaid with culture medium

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq stranded mRNA 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: tumor

value: RB organoid cells

tag: passage

tag: genotype


title: RB668 Tumor tissue

source_name: Retinal tumor

value: RB tissue


title: RB668 organoids_P3


title: Breast Cancer BC1313

description:
Breast Cancer
SH4YL55_Cell3


title: Liver_cultured_donor_51

source_name: cultured liver endothelial cells


title: Heart_fresh_tissue_donor_80

source_name: fresh heart tissue endothelial cells donor 80 (M, 135 d)


title: Liver_fresh_tissue_donor_80

source_name: fresh liver tissue endothelial cells donor 80 (M, 135 d)


title: Lung_fresh_tissue_donor_80

source_name: fresh lung tissue endothelial cells donor 80 (M, 135 d)


title: Breast Cancer BC1304

description:
Breast Cancer
SH4YL55_Cell2


title: Lung_cultured_donor_51

source_name: cultured lung endothelial cells


title: Kidney_cultured_donor_51

source_name: cultured kidney endothelial cells


title: Heart_cultured_donor_48


title: OX_rep3

city: Beijing

first: Bin

last: Yin

address: Tsinghua East Road

country: China

institute: Beijing Forestry University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based onthe clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Genome_build: Poptr2_0 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000002775.3)
Supplementary_files_format_and_content: FPKMs and DEGs

organism: Populus tomentosa

source_name: untreated overexpression cells

growth_protocol: All cell lines grew in bed temperature incubator at 25 ℃ (140 rpm, 24 h dark).

extract_protocol:
Total RNA was isolated from suspension cells of populus tomentosa, using EASYspin Plant RNA kit RN09 (Aidlab, China) according to the manufacturer's instructions.
In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: H2O2 treatment (10 mM, 3 h dark, 25 ℃， 140 rpm); AsA treatment (1 mM, 3 h dark, 25℃, 140 rpm)

value: PtomitAPX-overexpression transgenic

tag: treatment

value: untreated

tag: Stage

value: 5 days after subculturing

value: suspension cells


title: anti_A_rep2

source_name: antisense cells treated with AsA (1mM, 3h)

value: PtomitAPX-antisense

value: AsA


title: OX_H_rep2

source_name: overexpression cells treated with H2O2 (10mM, 3h)


title: anti_A_rep3


title: OX_H_rep3


title: OX_H_rep1


title: anti_A_rep1


title: Breast Cancer BC1298

description:
Breast Cancer
SH4YL54_Cell3

source_name: Serum


title: VRE treated [18]

city: St. Lucia

first: Lisa

last: Bohlmann

address: University of Queensland

country: Australia

institute: University of Queensland

data_processing:
An average of 45 million reads per sample were generated and mapped to the reference genome using the 2-passmethod of the STAR aligner with default parameters.
Duplicate reads were denoted with the MarkDuplicates tool of Picard (http://broadinstitute.github.io/picard)
Differential gene expression was analysed using Degust (http://victorian-bioinformatics-438 consortium.github.io/degust/)
genome build: Streptococcus pyogenes: NZ_AFRY01000001.1, Staphylococcus aureus: NC_007793.1, Enterococcus faecium: Bioproject PRJNA497960
Supplementary_files_format_and_content: xlsx files for each bacterial strain, CPM

organism: Enterococcus faecium

source_name: Bacteria

growth_protocol: Bacteria were grown in cation-adjusted Mueller-Hinton broth

extract_protocol:
RNA was isolated using the FastRNA® Pro Blue Kit (MP Biomedicals) and the SV Total RNA Isolation System (Promega)
RNASeq analysis was performed at the Australian Genome Research Facility. The library was prepared using a Ribo-zero stranded protocol. Libraries were sequenced with a HiSeq 2500 ultra-high-throughput sequencing system (Illumina) to produce 100-base-paired end reads.

treatment_protocol: Bacteria were grown in the presence or absense of PBT2 and zinc

tag: strain

tag: agent

value: PBT2 and zinc


title: OX_rep1


title: OX_rep2


title: Breast Cancer BC1293

description:
Breast Cancer
SH4YL54_Cell1


title: Breast Cancer BC1292

description:
Breast Cancer
SH4YL53_Cell4


title: Breast Cancer BC1288

description:
Breast Cancer
SH4YL53_Cell2


title: VRE treated [17]


title: Breast Cancer BC1286

description:
Breast Cancer
SH4YL53_Cell1


title: Breast Cancer BC1301

description:
Breast Cancer
SH4YL55_Cell1


title: Breast Cancer BC1281

description:
Breast Cancer
SH4YL52_Cell3


title: Lung_cultured_donor_37


title: Liver_cultured_donor_37


title: Lung_cultured_donor_48


title: Liver_cultured_donor_48


title: Kidney_cultured_donor_48


title: anti_rep2

source_name: untreated antisense cells


title: Heart_cultured_donor_37


title: Kidney_cultured_donor_37


title: VRE treated [16]


title: anti_rep1


title: VRE untreated [14]


title: VRE untreated [13]


title: VRE untreated [15]


title: WT_rep3

description: anti_3vsWT_anti_1p5_001.DEG; anti_3_AvsWT_antiA_1p5_001.DEG; OXvsWT_ox_1p5_001.DEG; OX_HvsWT_oxH_1p5_001.DEG

source_name: untreated wild type cells

value: WT


title: WT_rep1


title: anti_rep3


title: mms21-S2

city: London

first: Vanessa

last: Dumeaux

state: Ontario

address: Elgin Dr

department: Anatomy and Cell Biology

country: Canada

institute: Western University

data_processing:
Raw reads were pre-processed with the sequence-grooming tool cutadapt version 0.4.1{Martin, 2011 #723} with the following quality trimming and filtering parameters (`--phred33 --length 36 -q 5 --stringency 1 -e 0.1`. Each set of paired-end reads was mapped against the C. albicans SC5314 haplotype A, version A22 downloaded from the Candida Genome Database (CGD) (www.candidagenome.org) using HISAT2 version 2.0.4. SAMtools was then used to sort and convert SAM files. The read alignments and C. albicans SC5314 genome annotation were provided as input into StringTie v1.3.3 (Pertea et al., 2015) which returns gene abundances for each sample.
Genome_build: C. albicans SC5314 haplotype A, version A22
Supplementary_files_format_and_content: Tab-delimited gene abundances files

organism: Candida albicans

source_name: yeast cells

growth_protocol: YPD medium at 30°C

extract_protocol:
Total RNA isolation was performed as previously described (Tebbji et al, PloSGenetics 2014)
Libraries were prepared according to Illumina's mRNASeq stranded library preparation kit

treatment_protocol: YPD medium at 30°C

value: mms21 deletion


title: mms21-S1


title: SN148-S1

value: wild type SN148


title: SN148-S2


title: SMAD4KO_WT_01

status: Public on Oct 22 2018

city: Hangzhou

first: Mu

last: Xiao

state: Zhejiang

address: 866 Yuhangtang Road

department: Life Sciences Institute

institute: Zhejiang University

data_processing:
Sequenced reads were trimmed to 50bp and mapped to the human genome (hg19) using Tophat v2.1.1.
Mapped reads (~95% of total reads) were subsequently assembled into transcripts guided by the reference annotation (UCSC gene models) with Cufflinks v2.2.1.
Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments)
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Bedgraph

source_name: Human immortalized keratinocytes

growth_protocol: HaCaT cells were cultured in MEM-EBSS medium with 10% FBS.

extract_protocol:
RNA was harvested using Trizol reagent.  VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (NR601-01) 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: Cells were treated with TGF-b (2 ng/ml) for 24 hours

tag: cell line

value: HaCaT cell

value: without TGF-beta treatment

value: SMAD4 KO cells stably expressing SMAD4


title: SMAD4KO_Y95F_T_01

value: with TGF-beta treatment

value: SMAD4 KO cells stably expressing SMAD4 Y95F


title: SMAD4KO_Y95E_01

value: SMAD4 KO cells stably expressing SMAD4 Y95E


title: SMAD4KO_Y95F_01


title: Parental_T_01

value: Parental


title: SMAD4KO_T_01

value: SMAD4 KO cells stably expressing GFP


title: SMAD4KO_01


title: SMAD4KO_WT_T_01


title: SMAD4KO_Y95E_T_01


title: Parental_01


title: WT_rep2

value: untreated


title: 17_APseq_6Gy_30min_rep2_enrichment

first: Anna

middle: R

last: Poetsch

address: 1 Midland Rd

country: United Kingdom

institute: The Francis Crick Instutute

library_source: genomic

data_processing:
Basecalls performed using CASAVA
AP-seq reads were aligned to the hg19 genome assembly using Bowtie2 with standard settings, allowing for 2 mismatches and random assignment of non-uniquely mapping reads.
Paired reads were imported into R using the “GenomicAlignments” and “rtracklayer” packages. Paired reads mapping more than 1kb apart were discarded.
Inter-library normalization was performed using only genomic areas of low damage. It was necessary to consider that increased exposure to DNA damage leads to increased library sizes. A global scaling factor was calculated as the mean read coverage in a low-damage subset (10%) of 100kb bins, which were identified by their read coverage as the lowest decile of 100kb bins over the mean of all samples.
Relative Enrichment of DNA damage was assessed through the normalised log2 fold change of the enriched sample over input (termed Relative Enrichment). This should account for biases derived from DNA amounts after genomic DNA extraction, as well as GC content biases from sequencing, which would affect the pull-down samples and inputs alike.
Genome_build: hg19
Supplementary_files_format_and_content: bam files were generated, aligning the reads to the hg19 genome built using Bowtie2. From these, bigwig files were generated using the "GenomicRanges" and "rtracklayer" packages in R. Scores represent the unsmoothed  and non-normalised counts of read coverage.

molecule: genomic DNA

growth_protocol: HepG2 cells were cultivated at 37°C and 5% CO2 in Dulbecco’s Modified Eagle Medium (DMEM; Invitrogen) supplemented with 1% essential amino acids, 1% pyruvate, 2% penicillin/streptavidin and 10% heat-inactivated fetal bovine serum (FBS).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Total genomic DNA was extracted using a Blood and Tissue Kit (Qiagen, catalogue number 69506) and genomic DNA was kept on ice during the process. Antioxidants were not applied in this experiment to avoid artefacts through sequence specific effects. Since treated samples and the untreated control are exposed to the same technical artefacts from sample processing, these should be accounted for in the data analysis. 5.7mg of genomic DNA was tagged with biotin using 5mM Aldehyde Reactive Probe (ARP; Life Technologies, catalogue number A10550) in phosphate buffered saline (PBS) for 2h at 37°C. Genomic DNA was then purified using AMPure beads (Agencourt, catalogue number A63882) with 1.8x bead solution, 2x 70% ethanol washing; beads were not allowed to dry to prevent DNA from sticking. Both the damage-enriched and input DNA were in vitro repaired using PreCR (NEB catalogue number M0309L). The input DNA and supernatant of the pull-down were purified using AMPure beads. The purified pull-down was recombined with the beads and library preparation was performed on the re-pooled sample containing the supernatant and the beads. A 125bp paired-end ChIP-Seq library preparation kit (KAPA Biosystems catalogue number KK8504) was used and sequencing performed using an Illumina HiSeq 2000 on first a rapid and then a high-output run (catalogue number FC-401-4002). The resulting data were subsequently combined.

treatment_protocol: ~1x106 cells were exposed to 6Gy X-ray using a SOFTEX M-150WE in triplicates. Triplicate samples of untreated control cells were processed in parallel, excluding irradiation. Cells were harvested 30 minutes post-treatment.

value: hepatocellular carcinoma cell line

value: X-rays, 6Gy, 30min

tag: processing

value: aldehyde reactive probe

tag: enrichment

value: biotin-streptavidin-ARP-enrichement


title: 18_APseq_6Gy_30min_rep3_enrichment


title: 19_OGG1-APseq_control_rep1_enrichment

value: control

value: OGG1 digest/ aldehyde reactive probe


title: 20_OGG1-APseq_control_rep2_enrichment


title: 23_OGG1-APseq_6Gy_30min_rep2_enrichment


title: 22_OGG1-APseq_6Gy_30min_rep1_enrichment


title: 24_OGG1-APseq_6Gy_30min_rep3_enrichment


title: 16_APseq_6Gy_30min_rep1_enrichment


title: 21_OGG1-APseq_control_rep3_enrichment


title: 14_APseq_control_rep2_enrichment


title: 13_APseq_control_rep1_enrichment


title: 11_OGG1-APseq_6Gy_30min_rep2_input

value: input


title: 12_OGG1-APseq_6Gy_30min_rep3_input


title: 09_OGG1-APseq_control_rep3_input


title: 10_OGG1-APseq_6Gy_30min_rep1_input


title: 08_OGG1-APseq_control_rep2_input


title: 06_APseq_6Gy_30min_rep3_input


title: 07_OGG1-APseq_control_rep1_input


title: Secondary gliomas derived from transplantation in NOD/SCID of early onset glioma; biological rep 3

city: Genoa

first: Paolo

last: Malatesta

address: Largo Rosanna Benzi 10

country: Italy

institute: IRCCS Ospedale Policlinico San Martino

description: Tumor generated from transplantation of early-onset primary glioma induced by PDGF-B overexpression

hyb_protocol: cDNA was hybridized at 45°C for 16 hours by using the affymetrix hybridization, wash and stain kit.

scan_protocol: Scanned using an Affymetrix GeneChip scanner following manufacturer's instructions on Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed with the R3.4.0 software and BioConductor version 3.5. Expression values were extracted from raw data files using the RMA method built in the affy 1.54.0 library package. Differentially expressed genes were ranked by using RankProd 3.2.0 library

label: biotin

organism: Mus musculus

source_name: Secondary glioma

label_protocol: 5ug of cDNA was fragmented and botin labelled by using the Encore® Biotin Module (NuGEN)

growth_protocol: NOD/SCID mice were transplanted with early onset/ low-grade glioma cells and their brains were dissected at the onset of glioma symptoms

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. cDNA was obtained from 30 ng of RNA by using the Ovation® Pico WTA System V2 kit (NuGEN).

treatment_protocol: Gliomas were visualized under a fluorescence microscope thanks to the EGFP expression and dissected in HBSS medium. Tumor cells were dissociated with enzymatic digestion in Trypsin/EDTA and mechanical dissociation with a Pasteur pipette in 10% FBS and after centrifugation at 500xg for 5 minutes, the pellet was suspended in PBS supplemented with 1% FBS and 1.5mM EDTA and EGFP expressing cells were sorted with a FACSAria II cell sorter.

tag: glioma cell background strain

tag: glioma cell genotype/variation

value: PDGF-B/EGFP overexpression

value: EGFP-positive glioma cells

tag: host mouse strain

value: NOD/SCID


title: Secondary gliomas derived from transplantation in NOD/SCID of early onset glioma; biological rep 2

tag: tissue


title: 15_APseq_control_rep3_enrichment

tag: cell type


title: eSAS

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: five repetitive selections of parental human tongue squamous-cell carcinoma cells

hyb_protocol: Before hybridization, 1650 ng labeled cRNA was fragmented and mixed with hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65˚C. The slides were washed according to the manufacturer's manual.

scan_protocol: The array was scanned using Agilent G2505C DNA microarray scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (v 10.7.3.1).

label_protocol: 200 ng of total RNAs were independently reverse-transcribed using oligo-dT primers containing the T7 RNA polymerase promoter sequence to generate cDNAs and AffinityScript, RTase, which were then subjected to in vitro transcription using T7 RNA polymerase to label the cRNAs with Cy3-CTP (Amersham Pharmacia Biotech, Piscataway, NJ) using a Low input Quick-Amp Labeling Kit (Agilent Technologies).

growth_protocol: A human oral squamous cell carcinoma cell line derived from a tongue tumor, SAS cells, were obtained from the Human Science Resource Cell Bank (Osaka, Japan). SAS cells were cultured with Dulbecco’s modified Eagle’s medium (DMEM, Sigma, St. Louis, MO) supplemented with 10% fetal bovine serum (FBS, Hyclone, Logan, UT), 100 U/mL penicillin, and 100 μg/mL streptomycin, and incubated at 37 °C and 5% CO2.

extract_protocol: Total RNA was extracted using mIRNeasy kit (Qiagen). The quality of the RNAs was estimated by using the RNA 6000 Nano LabChip Kit (p/n 5065-4476) on the Agilent 2100 Bioanalyzer (G2940BA; Agilent Technologies, Santa Clara, CA).

treatment_protocol: Three-dimensional (3D) cell culture system have been used to obtain multicellular spheroidal cell aggregates, or spheroids. We manufactured a tool, named Spheroid-catch, for selection of large-sized and/or size-matched spheroids. After five-round selection process, we obtained five kinds of SAS cell populations.

value: eSAS


title: Tertiary gliomas derived from transplantation of secondary glioma in NOD/SCID; biological rep 2

description: Tumor generated from transplantation of a secondary glioma generated in NOD/SCID from transplantation of primary glioma

source_name: Tertiary glioma


title: Secondary gliomas derived from transplantation in NOD/SCID of early onset glioma; biological rep 1


title: Secondary gliomas derived from transplantation in NOD/SCID of early onset glioma; biological rep 4


title: Late onset glioma; biological rep 2

description: Gene expression data from high-grade murine glioma cells

hyb_protocol: Fragmented cRNA from two samples was hybridized to the mouse MoGene-1_0-st-v1 array for 16 hours at 45 Celsius.The array was then washed and stained with streptavidin-phycoerythrin (SAPE) using the fluidics station

scan_protocol: Scanned with GeneChip Scanner 3000

data_processing: Expression values were extracted by using the RMA function from the Bioconductor package affy 3.4.2 (Gautier et al. 2004) in R (R Core Team 2017; https://www.R-project.org/).

source_name: Cells explanted from one late onset PDGF-induced murine glioma

label_protocol: One-Cycle Target Labelling Assay: Biotinylated cRNA was prepared and fragmented according to the Affymetrix protocol.

growth_protocol: Embryos injected at embryonic day 14 with PDGF/EGFP expressing retrovirus were let to develop until delivery and then pups were let to grow until the onset of glioma symptoms

extract_protocol: Total RNA was extracted following the double extraction protocol: RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction (Trizol Invitrogen) followed by a Qiagen RNeasy clean-up procedure.

tag: background strain

tag: genotype/variation

tag: tumor stage

value: high-grade


title: Late onset glioma; biological rep 1


title: Tertiary gliomas derived from transplantation of secondary glioma in NOD/SCID; biological rep 3


title: SAS

description: a human tongue squamous-cell carcinoma cells

value: SAS


title: Tertiary gliomas derived from transplantation of secondary glioma in NOD/SCID; biological rep 1


title: 05_APseq_6Gy_30min_rep2_input


title: 03_APseq_control_rep3_input


title: 02_APseq_control_rep2_input


title: 04_APseq_6Gy_30min_rep1_input


title: SW 2 7 D1

city: Rochester

first: YS

last: Prakash

state: MN

address: 200 1st St

institute: Mayo Clinic

description: Control

data_processing:
The Illumina’s RTA version 1.17.21.3 was used for base calling.
Libraries were sequenced at 8 samples per lane to generate ~30-45 million reads per sample following Illumina’s standard protocol using the Illumina cBot and cBot Paired end cluster kit version 3.
The flow cells were sequenced as 51 X 2 paired end reads on an Illumina HiSeq 2000 using TruSeq SBS sequencing kit version 3 and HCS v2.0.12data collection software.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited files includes RKPM values for each sample.

source_name: Lung

growth_protocol: Cells were grown on 6 well plates in DMEM/F12 media supplemented with 10% fetal bovine serum and 1% antibotic/antimyotic. Once cells reached 80% confluency, they were serum starved with DMEM/F12 media supplemented with 0% fetal bovine serum and 1% antibotic/antimyotic for 48 h.

extract_protocol:
RNA from cell lysates was isolated using the Qiagen RNeasy Mini kit. 200 ng RNA from each sample were used to prepare RNA libraries.
RNA libraries were perpared using the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA) following manufacturer instructions. The concentration and size distribution of completed libraries was determined using an Agilent Bioanalyzer DNA 1000 chip (Santa Clara, CA) and Qubit fluorometry (Invitrogen, Carlsbad, CA).

value: Lung

value: Airway Smooth Muscle

tag: disease

value: Asthmatic

tag: age

tag: Sex

value: M


title: SW 2 7 J1

description: Control

value: F


title: SW 2 7 E1

description: Control

value: Nonasthmatic


title: 01_APseq_control_rep1_input

value: hepatocellular carcinoma cell line

tag: treatment

value: aldehyde reactive probe


title: SW 2 7 H1

description: Control


title: SW 2 7 G1

description: Control


title: SW 2 7 M1

description: Control


title: SW 2 7 K1

description: Control


title: SW 2 7 F1

description: Control


title: SW 2 7 C1

description: Control


title: Early onset glioma pool; biological rep 1

description: Gene expression data from low-grade murine glioma cells

source_name: Pool of cells explanted from two early onset PDGF-induced murine gliomas

value: low-grade


title: RDB 2-103-61

description: Control


title: SW 2 7 A1

description: Control


title: RDB 2-103-45

description: Control


title: Early onset glioma pool; biological rep 2


title: RDB 2-103-49

description: Control


title: SW 2 7 L1

description: Control

value: Unknown


title: SW 2 7 I1

description: Control


title: RDB 2-103-37

description: Control


title: RDB 2-103-33

description: Control


title: RDB 2-103-29

description: Control


title: RDB 2-103-41

description: Control


title: RDB 2-103-21

description: Control


title: RDB 2-103-25

description: Control


title: RDB 2-103-1

description: Control


title: 13D [reanalysis]

first: Alice

last: Gao

state: London

address: 237 Fulham Road

department: Breast Cancer Now

institute: The Institute of Cancer Research

hyb_protocol: Hybridized to the Illumina HumanHT-12 V4.0 expression BeadChip or Illumina HumanWG-6 v3.0 expression BeadChip using the standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol of iScan.

data_processing: The data was filtered to remove any non-expressed probes using the detection p-value from Illumina. Across all samples probes for which the intensity values were not significantly different (p>0.01) from the negative controls were removed from the analysis. Following filtering the data was transformed and normalized using variance-stabilizing transformation and robust spline normalization (RSN) method in the lumi package in R. The RSN combines the features of quantile and loess normalization

source_name: breast tumour, LumA, diagnostic

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

extract_protocol: mRNA from untreated paired biopsies were extracted with RNeasy Mini Kit (Qiagen), as per the manufacturer's instructions, and quantification performed using the Agilent 2100 Bioanalyzer (Santa Clara, CA, USA).

value: female

value: primary ER+ breast carcinoma

tag: group

value: untreated

tag: sampling time

value: diagnosis

tag: subtype

value: LumA

value: breast tumour


title: 50D [reanalysis]


title: 6D [reanalysis]

source_name: breast tumour, LumB, diagnostic

value: LumB


title: 10D [reanalysis]


title: H324CB

city: Vancouver

first: Davide

last: Pellacani

state: British Columbia

address: Terry Fox Laboratory BC Cancer research centre

department: Terry Fox Laboratory

institute: BC Cancer Agency

description: Bisulphite converted genomic DNA

data_processing:
Fastq files were trimmed using Trim Galore! v0.4.1 with the following parameters: --fastqc --illumina --paired --rrbs --non_directional.
Trimmed sequences were aligned to the human genome (hg19) using bsmap v2.90 and the following parameters: -m 0 -x 1000 -n 1 -p 8 -S 1.
bam files were sorted and indexed using samtools v0.1.19
methylation and coverage calls for each CpG site were calculated using the methratio.py script in the bsmap software
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited txt file with the following columns: chromorome; coordinate (1-based); strand; sequence context (CG|CHG|CHH); methylation ratio, calculated as #C_counts / #eff_CT_counts; number of effective total C+T counts on this locus (#eff_CT_counts = #CT_counts * (#rev_G_counts / #rev_GA_counts)); number of total C counts on this locus (#C_counts); number of total C+T counts on this locuso (#CT_counts); number of total G counts on this locus of reverse strand (#rev_G_counts); number of total G+A counts on this locus of reverse strand (#rev_GA_counts); lower bound of 95% confidence interval of methylation ratio, calculated by Wilson score interval for binomial proportion; upper bound of 95% confidence interval of methylation ratio, calculated by Wilson score interval for binomial proportion.

source_name: FACS purified EpCAM+CD49f+CD24- cells from prostate cancer tissue

extract_protocol:
DNA was extracted from FACS sorted populations using phenol/chloroform extraction and ethanol precipitation.
Bisulphite conversion, library preparation, sequencing, and initial bioinformatics analyses were performed by Zymo Research following the Methyl-MiniSeq pipeline.

tag: donor

tag: sample type

value: prostate cancer tissue

tag: cell population


title: H324NL

description: Bisulphite converted genomic DNA

source_name: FACS purified EpCAM+CD49f-CD24+ cells from normal prostate tissue

value: normal prostate tissue


title: H324CL

description: Bisulphite converted genomic DNA

source_name: FACS purified EpCAM+CD49f-CD24+ cells from prostate cancer tissue


title: H329CL

description: Bisulphite converted genomic DNA


title: H324NB

description: Bisulphite converted genomic DNA

source_name: FACS purified EpCAM+CD49f+CD24- cells from normal prostate tissue


title: H329CB

description: Bisulphite converted genomic DNA


title: SW 2 7 B1

description: Control

value: Lung

value: Airway Smooth Muscle


title: 54D [reanalysis]


title: 52D [reanalysis]

source_name: breast tumour, normal, diagnostic

value: Normal


title: 56S [reanalysis]

source_name: breast tumour, LumB, surgical

value: surgery


title: H329NL

description: Bisulphite converted genomic DNA


title: H309CL

description: Bisulphite converted genomic DNA


title: H323CL

description: Bisulphite converted genomic DNA


title: H323CB

description: Bisulphite converted genomic DNA


title: 47D [reanalysis]


title: 52S [reanalysis]

source_name: breast tumour, LumA, surgical


title: 54S [reanalysis]


title: 55S [reanalysis]


title: 55D [reanalysis]


title: 51D [reanalysis]


title: H309NB

description: Bisulphite converted genomic DNA


title: H309CB

description: Bisulphite converted genomic DNA


title: 53D [reanalysis]


title: H309NL

description: Bisulphite converted genomic DNA


title: H329NB

description: Bisulphite converted genomic DNA


title: 51S [reanalysis]


title: 56D [reanalysis]


title: 53S [reanalysis]


title: 49S [reanalysis]


title: 46S [reanalysis]


title: 48D [reanalysis]


title: 45D [reanalysis]


title: 50S [reanalysis]


title: 47S [reanalysis]


title: 49D [reanalysis]


title: 48S [reanalysis]


title: 3887-1

city: Halifax

first: Paola

last: Marcato

state: Nova Scotia

address: PO Box 15000

department: Pathology

institute: Dalhousie University

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: CHP files generated by Transcriptome Analysis Console

label_protocol: standard Affymetrix protocol

extract_protocol: Trizol and PureLink RNA kit

tag: replicate

value: PDX


title: 4D [reanalysis]


title: 45S [reanalysis]


title: 3887-3


title: 1D [reanalysis]


title: P5 NT 3

data_processing:
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HuGene-2_0-st
program-name = Expression Console
program-version = 1.4.1.46

source_name: P5_no treatment

extract_protocol: standard Affymetrix protocol

tag: tissue/cell type

value: patient-derived xenograft

value: no treatment


title: 2665-3


title: 2665-1


title: P49 NT 1

source_name: P49_no treatment


title: 42D [reanalysis]

tag: tissue


title: 43D [reanalysis]


title: 44D [reanalysis]


title: 3887-2


title: 46D [reanalysis]


title: 41S [reanalysis]


title: HCC1937 RA 3

source_name: HCC1937_100 nM all-trans retinoic acid

tag: cell line

value: triple-negative breast cancer cell line

value: 100 nM all-trans retinoic acid


title: 38S [reanalysis]

value: female

value: primary ER+ breast carcinoma


title: P49 NT 3


title: P5 NT 1


title: P49 NT 2


title: 43S [reanalysis]

value: untreated


title: 42S [reanalysis]


title: 40S [reanalysis]

value: LumA


title: 39S [reanalysis]

value: breast tumour


title: 44S [reanalysis]

value: LumB


title: P5 NT 2


title: 37S [reanalysis]


title: 2665-2


title: MDA-MB-436 RA 3

source_name: MDA-MB-436_100 nM all-trans retinoic acid


title: HCC1937 NT 2

source_name: HCC1937_no treatment


title: 37D [reanalysis]

value: diagnosis


title: 41D [reanalysis]


title: 40D [reanalysis]


title: 39D [reanalysis]


title: HCC1937 RA 2


title: HCC1937 NT 3


title: 33S [reanalysis]


title: 38D [reanalysis]


title: MDA-MB-453 NT 3

source_name: MDA-MB-453_no treatment


title: HCC1937 NT 1


title: MDA-MB-436 RA 2


title: MDA-MB-436 NT 3

source_name: MDA-MB-436_no treatment


title: MDA-MB-453 RA 3

source_name: MDA-MB-453_100 nM all-trans retinoic acid


title: MDA-MB-436 RA 1


title: 36S [reanalysis]


title: 36D [reanalysis]


title: 31S [reanalysis]


title: MDA-MB-436 NT 1


title: MDA-MB-453 RA 2


title: 34D [reanalysis]

source_name: breast tumour, LumA, diagnostic


title: HCC1937 RA 1


title: MDA-MB-453 NT 2


title: MDA-MB-436 NT 2


title: 35S [reanalysis]


title: MDA-MB-453 NT 1


title: 35D [reanalysis]

source_name: breast tumour, LumB, diagnostic


title: SUM159 RA 2

source_name: SUM159_100 nM all-trans retinoic acid


title: HCC38 NT 1

source_name: HCC38_no treatment


title: 32S [reanalysis]


title: 34S [reanalysis]


title: 30S [reanalysis]


title: 29D [reanalysis]


title: 30D [reanalysis]


title: 33D [reanalysis]


title: SUM159 RA 1


title: 32D [reanalysis]


title: SUM159 RA 3


title: 29S [reanalysis]


title: SUM159 NT 1

source_name: SUM159_no treatment


title: 27S [reanalysis]


title: SUM159 NT 2


title: 28S [reanalysis]


title: 28D [reanalysis]


title: SUM149 RA 3

source_name: SUM149_100 nM all-trans retinoic acid


title: MDA-MB-453 RA 1


title: SUM159 NT 3


title: 31D [reanalysis]


title: SUM149 NT 3

source_name: SUM149_no treatment


title: SUM149 NT 2


title: SUM149 RA 2


title: 27D [reanalysis]


title: 26S [reanalysis]


title: 25S [reanalysis]


title: HCC38 NT 3


title: HCC38 NT 2


title: 22S [reanalysis]


title: 24S [reanalysis]

source_name: breast tumour, LumB, surgical


title: SUM149 RA 1


title: HCC70 RA 3

source_name: HCC70_100 nM all-trans retinoic acid


title: HCC70 NT 3

source_name: HCC70_no treatment


title: 25D [reanalysis]


title: 24D [reanalysis]


title: 20D [reanalysis]


title: 23S [reanalysis]


title: HCC38 RA 2

source_name: HCC38_100 nM all-trans retinoic acid


title: HCC70 NT 2


title: HCC70 RA 1


title: 22D [reanalysis]


title: HCC38 RA 1


title: 20S [reanalysis]

source_name: breast tumour, LumA, surgical


title: HCC70 RA 2


title: BT20 RA 1

source_name: BT20_100 nM all-trans retinoic acid


title: BT20 NT 2

source_name: BT20_no treatment


title: HCC70 NT 1


title: 23D [reanalysis]

source_name: breast tumour, Her2, diagnostic


title: SUM149 NT 1


title: 21S [reanalysis]


title: 26D [reanalysis]


title: 21D [reanalysis]


title: HCC38 RA 3


title: BT20 NT 1


title: 19D [reanalysis]


title: HCC1187 RA 4

source_name: HCC1187_100 nM all-trans retinoic acid


title: 16D [reanalysis]


title: HCC1187 RA 3


title: 18S [reanalysis]


title: 17S [reanalysis]


title: Du4475 RA 2

source_name: Du4475_100 nM all-trans retinoic acid


title: 19S [reanalysis]


title: Du4475 NT 3

source_name: Du4475_no treatment


title: HCC1806 RA 3

source_name: HCC1806_100 nM all-trans retinoic acid


title: Du4475 RA 3


title: HCC1187 RA 1


title: 12S [reanalysis]


title: 15D [reanalysis]

source_name: breast tumour, LumA, diagnostic


title: 14S [reanalysis]


title: HCC1187 NT 4

source_name: HCC1187_no treatment


title: Du4475 NT 2


title: 15S [reanalysis]


title: HCC1806 NT 3

source_name: HCC1806_no treatment


title: Du4475 NT 1


title: Du4475 RA 1


title: 18D [reanalysis]

source_name: breast tumour, LumB, diagnostic


title: 13S [reanalysis]


title: 14D [reanalysis]


title: 17D [reanalysis]


title: 16S [reanalysis]


title: HCC1187 NT 3


title: HCC1806 NT 1


title: 11D [reanalysis]


title: HCC1806 RA 2


title: 10S [reanalysis]


title: BT20 NT 3


title: 8S [reanalysis]


title: POS aTreg 2

city: New York

first: Alexander

middle: Y

last: Rudensky

state: New York (NY)

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
UMI-based grouping of sequencing reads covering the same starting cDNA molecules was performed using MIGEC software (Shugay et al., Nat. Methods 2014).
TCRα repertoire extraction was performed using MiXCR software (Bolotin et al., Nat. Methods 2015).
Dendrogram clustering using the F2 overlap metric was performed using VDJtools (Shugay et al., PLoS Comput. Biol. 2015).

source_name: Spleen

extract_protocol:
Singlet Vβ8+ NK-1.1− CD1d Tetramer− CD4+ CD8α− Foxp3+ Treg or Foxp3− Tconv of 3 different activation states (naive/resting, CD49b-NEGative activated, or CD49b-POSitive activated) were FACS-purified from CD4-enriched mouse splenocytes and resuspended in Buffer RLT Plus. RNA was purified using the RNeasy Micro Kit.
Purified RNA was reverse transcribed and tagged with barcodes to generate Tcra cDNA libraries, using a previously published method (Feng et al., Nature 2015).

tag: genetic background

tag: genotype

value: Foxp3GFP Tcra+/- DO11.10tg

value: Male

value: 3 months old

value: Spleen

tag: cell type

value: Treg

tag: subset activation markers

value: CD4+ Foxp3+ CD44hi CD49b+

tag: purification

value: CD4 pos selection + FACS


title: POS aTreg 4

tag: Sex

tag: age


title: 8D [reanalysis]

tag: disease

tag: group


title: BT20 RA 3

tag: treatment


title: 12D [reanalysis]

tag: sampling time

tag: subtype


title: POS aTreg 3


title: HCC1806 NT 2

value: no treatment


title: HCC1806 RA 1

value: triple-negative breast cancer cell line


title: BT20 RA 2

value: 100 nM all-trans retinoic acid


title: 5D [reanalysis]

value: female


title: 7D [reanalysis]

value: primary ER+ breast carcinoma


title: 7S [reanalysis]

source_name: breast tumour, LumB, surgical

value: untreated

value: surgery


title: 9S [reanalysis]

source_name: breast tumour, normal, surgical

value: Normal

value: breast tumour


title: 5S [reanalysis]

value: LumA


title: HCC1187 NT 1


title: NEG aTreg 3

value: Foxp3GFP Tcra+/- DO11.10tg

value: CD4+ Foxp3+ CD44hi CD49b-


title: POS aTreg 1

value: Male

value: 3 months old


title: NEG aTreg 2

value: Spleen

value: Treg


title: NEG aTreg 1

value: CD4 pos selection + FACS


title: Resting Treg 4

value: CD4+ Foxp3+ CD62Lhi CD44lo CD49b-


title: 9D [reanalysis]

value: diagnosis


title: Resting Treg 3


title: Resting Treg 2


title: POS Teff 4

value: Tconv

value: CD4+ Foxp3- CD44hi CD49b+


title: Resting Treg 1


title: 11S [reanalysis]

value: female

value: primary ER+ breast carcinoma


title: 4S [reanalysis]

value: untreated

value: surgery


title: 3D [reanalysis]

value: breast tumour


title: POS Teff 3


title: POS Teff 2


title: 2S [reanalysis]

value: LumA


title: 3S [reanalysis]

value: LumB


title: 1S [reanalysis]


title: 2D [reanalysis]


title: 6S [reanalysis]


title: POS Teff 1

value: Foxp3GFP Tcra+/- DO11.10tg


title: NEG Teff 4

value: Male

value: CD4+ Foxp3- CD44hi CD49b-


title: NEG Teff 3

value: 3 months old

value: Spleen


title: NEG Teff 1

value: CD4 pos selection + FACS


title: Tnaive 4

value: CD4+ Foxp3- CD62Lhi CD44lo CD49b-


title: NEG Teff 2


title: Tnaive 3


title: Tnaive 2


title: Tnaive 1


title: AI.Treated.193S

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol of iScan

source_name: breast tumour

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

extract_protocol: mRNA from baseline (B) and surgery (S) tumour biopsies were extracted with RNeasy Mini Kit (Qiagen), as per the manufacturer's instructions, and quantification performed using the Agilent 2100 Bioanalyzer (Santa Clara, CA, USA).

value: treated

tag: timepoint

value: surgery (S)

value: Negative


title: AI.Treated.191S

value: female


title: AI.Treated.192S


title: AI.Treated.188S


title: AI.Treated.194S


title: AI.Treated.196S


title: parental line of Drosha KO mESC, I-PpoI [16_DroKO_cut.rrna]

city: Solna

first: Franziska

last: Bonath

state: Stockholm

address: Tomtebodavägen 23A

department: Department for Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratories

country: Sweden

institute: Stockholm University

data_processing:
removing adatper, pre-mapping to a hand-curated list of ribosomal cDNA and miRNA libraries and collapsing reads with identical sequence using an in-house pipeline allowing one mismatch and discarding reads below 18nt
remapping to ribosomal RNA (custom cDNA library) using bowtie (version 1.12) with the options “-v 0 –q –k 1 –best”
Genome_build: The reference we used to map was not from a genome build but from a curated ribosomal RNA library:We curated a ribosomal RNA library based on RNA sequences retrieved from NCBI (www.ncbi.nlm.nih.gov, accessed: 2015-02-17), Silva (https://www.arb-silva.de, 23193283) and the Ensembl database (www.ensembl.org, accessed: 2015-02-17).
Supplementary_files_format_and_content: standard bowtie output format, reads mapped to ribosomal cDNA library

source_name: mouse embryonic stem cells

extract_protocol:
TRIZOL
TruSeq small RNA library preparation, Illumina, using 1ug of total RNA as input, addition of Exiqon small RNA spike-ins

tag: growth protocol

value: LIF+Serum, gelatin coated wells

tag: incubation after plasmid or mock transfection

tag: sirna

tag: i-ppoi transfection

value: 2.5 μg pOPRSVI-IPpoI (Lipofectamin)

tag: miRNA spike-ins (exiqon)

value: 1/3 of recommended amount


title: parental line of Drosha KO mESC, I-PpoI [18_DroKO_cut.rrna]


title: parental line of Drosha KO mESC, I-PpoI [17_DroKO_cut.rrna]


title: parental line of Drosha KO mESC, no I-PpoI [15_DroKO_unc.rrna]

value: Mock


title: AI.Treated.189S


title: AI.Treated.197S


title: AI.Treated.198S


title: AI.Treated.190S


title: AI.Treated.195S


title: AI.Treated.185S


title: AI.Treated.183S


title: AI.Treated.181S


title: parental line of Drosha KO mESC, no I-PpoI [14_DroKO_unc.rrna]


title: parental line of Drosha KO mESC, no I-PpoI [13_DroKO_unc.rrna]


title: Drosha KO mESC, I-PpoI [11_cont_cut.rrna]


title: NEG aTreg 4

tag: genetic background

tag: genotype

tag: tissue

value: Treg

value: CD4+ Foxp3+ CD44hi CD49b-


title: Drosha KO mESC,I-PpoI [10_cont_cut.rrna]


title: Drosha KO mESC, no I-PpoI [7_cont_unc.rrna]


title: Drosha KO mESC, no I-PpoI [8_cont_unc.rrna]


title: parental line of Drosha KO mESC, I-PpoI, Cordycepin treated [35-mESCd-cut-Cord.fastq]

value: recommended amount


title: AI.Treated.186S


title: AI.Treated.180S


title: AI.Treated.179S


title: Drosha KO mESC, I-PpoI [12_cont_cut.rrna]


title: AI.Treated.175S


title: parental line of Drosha KO mESC, no I-PpoI, Cordycepin treated [31-mESCd-unc-Cord.fastq]


title: parental line of Drosha KO mESC, no I-PpoI, Cordycepin treated [32-mESCd-unc-Cord.fastq]


title: parental line of Drosha KO mESC, I-PpoI, Cordycepin treated [34-mESCd-cut-Cord.fastq]


title: AI.Treated.178S


title: AI.Treated.187S


title: AI.Treated.176S


title: AI.Treated.173S


title: DGCR8 KO mESC, I-PpoI [18_DGCR8KO_cut]


title: Drosha KO mESC, no I-PpoI [9_cont_unc.rrna]


title: DGCR8 KO mESC, I-PpoI [16_DGCR8KO_cut]


title: DGCR8 KO mESC, no I-PpoI [14_DGCR8KO_unc]


title: AI.Treated.177S


title: AI.Treated.170S


title: AI.Treated.174S


title: AI.Treated.167S


title: AI.Treated.165S


title: DGCR8 KO mESC, no I-PpoI [13_DGCR8KO_unc]


title: AI.Treated.166S


title: AI.Treated.168S


title: parental line of Drosha KO mESC, I-PpoI [5_mESC_cut]


title: AI.Treated.172S


title: parental line of Drosha KO mESC, no I-PpoI [2_mESC_unc]


title: parental line of Drosha KO mESC, no I-PpoI [1_mESC_unc]


title: parental of Dicer KO mESC, I-PpoI [C_DcrPar_cut]


title: parental of Dicer KO mESC, I-PpoI [D_DcrPar_cut]


title: AI.Treated.161S


title: parental of Dicer KO mESC, no I-PpoI [B_DcrPar_unc]


title: parental line of Drosha KO mESC, I-PpoI [4_mESC_cut]


title: Dicer KO mESC, I-PpoI [23_DcrKO_cut]


title: AI.Treated.160S


title: AI.Treated.155S


title: AI.Treated.147S


title: Dicer KO mESC, no I-PpoI [19_DcrKO_unc]


title: AI.Treated.153S


title: AI.Treated.151S


title: Dicer KO mESC, I-PpoI [22_DcrKO_cut]


title: Dicer KO mESC, no I-PpoI [20_DcrKO_unc]


title: AI.Treated.163S


title: AI.Treated.159S


title: AI.Treated.149S


title: AI.Treated.154S


title: AI.Treated.146S


title: parental of Dicer KO mESC, no I-PpoI [A_DcrPar_unc]


title: AI.Treated.143S


title: AI.Treated.142S


title: AI.Treated.140S


title: Biotin

city: xianyang

first: Fayang

last: Liu

state: shannxi

address: taicheng street

institute: Northwest A&F University

data_processing:
Basecalls performed using R package developed by shanghai biotechnology corporation.
Fastx(version:0.0.13) was used to clean reads, including: 1. Remove reads with lower overall quality and remove reads with a mass greater than 20 bases less than 50%. 2. The base having a mass Q of less than 20 at the 3' end is removed, that is, the base error rate is less than 0.01, wherein Q=‐10 logerror_ratio. 3.Remove the linker sequence contained in reads. 4. Remove sequencing fragments whose lengths less than 20. Remove N-base-containing reads.
Bowtie (version: 0.12.8) was used for genome mapping (Genome version mm10, modified parameters number-m=1).
MACS (version: 1.4.2) was used to perform peak enrichment on the bam file obtained from mapping.diffScore>=30 ie pvalue<=1e‐3(diffScore= ‐10*LOG10(pvalue)
MEME-ChIP online pattern annotation tool was used to performs motif of the peaks.
Genome_build: mm10

growth_protocol: The RAW264.7 mouse macrophage cell line purchased from ATCC (Manassas, VA, USA) was cultured in Dulbecco's Modified Eagle's Medium containing 10% fetal bovine Serum Replacement.And maintained at 37︒C and 5% CO2 in a humidified incubator.

extract_protocol:
ChIP assays were performed with an Enzymatic Chromatin IP Kit (pierce) according to the manufacturer’s instructions.Anti-Flag and Streptavidin were used for protein-DNA complex isolation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RAW264.7 cells were transfected with the lentiviral pCDH-Puro constructs BAP-Sp110-P2A-BirA-T2A-PuroR and BAP-P2A-BirA-T2A-PuroR, containing a Flag tag (MDYKDDDDK) BAP (MAGLNDIFEAQKIEWHE), and P2A (GSGATNFSLLKQAGDVEENPGP).Cells were screened with 5 μg/mL puromycin (Amresco, USA).

tag: cell types

tag: chip antibody

value: Streptavidin

tag: strain

value: Balb/c


title: Flag-Ipr1

value: anti-Flag


title: IgG


title: AI.Treated.139S

tag: Sex


title: Patient 5 Total Liver Homogenate

city: Toronto

first: Jeff

address: 101 College Street, RM 4-601

department: Princess Margaret Cancer Center

institute: University Health Network

data_processing:
Raw sequencing data (bcl files) were converted to fastq files with Illumina bcl2fastq, version 2.19.1
The CellRanger (10X Genomics) secondary analysis pipeline was used to generate a digital gene expression matrix
Cells with a very small library size (< 1500) and a very high (> 0.5) mitochondrial genome transcript ratio were removed.  Genes detected (UMI count > 0) in less than three cells were removed.
Normalization by scran R package
Clustering and Gene Expression Analysis by Seurat package
Genome_build: GRCh38
Supplementary_files_format_and_content: log2CPM gene expression values for filtered cells in CSV text format

source_name: Liver

extract_protocol:
The caudate lobe was cannulated with two or three 1.2-2mm diameter irrigation cannulae with olive tips, which were inserted into exposed vessels in the cut surface if the liver lobe (cannulae manufacturer: Ernst Kratz GmbH cat no: 1464LL, 1465LL). The lobe was flushed with HBS+EGTA at 4°C (perfusion rate of 10mL/min/cannulae), which removed any residual non-liver resident cells. Single cell isolation from the resected caudate liver lobe was performed with a modified  “two-step” collagenase procedure6,97 as described in Fig. 1b. Eight to 12 million viable cells were recovered per gram of tissue as determined by Beckman Vi-Cell trypan blue exclusion. Viability for TLHs by trypan blue exclusion varied between 50-90% viable for the five livers profiled. Caudate lobes weighed on average 30.2 g +/-SD of 8.367g. TLHs were taken directly after dissociation for scRNA Seq.
10X Genomics Single Cell 3' v2 Reagent Kit

value: Total Liver Homogenate


title: Patient 4 Total Liver Homogenate


title: AI.Treated.138S

tag: group


title: NEG aTreg 4

data_processing:
Trimmomatic v0.32 was run with standard settings to remove low-quality reads and adaptor contamination.
Trimmed reads were aligned to Ensembl assembly GRCm38 using TopHat2 v2.0.11 implementing Bowtie2 v2.2.2 with default settings.
Read alignments were sorted with SAMtools v0.1.19.
Raw read counts were generated using HTSeq v0.6.1p1.
Read counts were normalized by library size.
Genome_build: GRCm38

molecule: polyA RNA

extract_protocol:
TCRβ+ NK-1.1− CD1d Tetramer− CD4+ CD8α− Foxp3+ Treg or Foxp3− Tconv of different activation states were doubly FACS-purified from mouse spleens and resuspended in TRIzol.
Total RNA was extracted and underwent SMARTer amplification, poly(A) selection, and Illumina TruSeq paired-end library preparation following manufacturer’s protocols.

value: Male

tag: age

value: 8 weeks old

value: Spleen

tag: cell type

tag: subset activation markers

value: CD4+ Foxp3+ CD44hi CD49b−

tag: purification

value: CD4 pos selection + FACS


title: Patient 2 Total Liver Homogenate


title: POS aTreg 4

value: CD4+ Foxp3+ CD44hi CD49b+


title: NEG aTreg 3


title: POS aTreg 2


title: POS aTreg 3


title: POS aTreg 1


title: NEG aTreg 2


title: AI.Treated.144S

value: treated

value: female

tag: timepoint

value: surgery (S)

value: Negative


title: Patient 1 Total Liver Homogenate


title: AI.Treated.137S


title: AI.Treated.133S


title: AI.Treated.134S


title: AI.Treated.127S


title: AI.Treated.132S


title: AI.Treated.130S


title: AI.Treated.125S


title: AI.Treated.124S


title: AI.Treated.128S


title: AI.Treated.126S


title: AI.Treated.122S


title: AI.Treated.121S


title: Activin 12h

first: Albert

last: Ruzo

state: NY

address: 1230 York Avenue

department: Laboratory of Stem Cell Biology and Molecular Embryology

institute: The Rockefeller University

data_processing:
Reads were aligned using the STAR aligner
featureCounts was used to assign reads to Gencode v18 gene annotations.
DESeq2 was used to normalize the count matrix.
Genome_build: NCBI genome build 37
Supplementary_files_format_and_content: raw counts file and normalized gene count matrix

source_name: Embryonic stem cells

growth_protocol: hESCs were cultured as single cells in E7 medium.

extract_protocol:
Trizol and Rneasy mini kit (QIAGEN)
Illumina TruSeq RNA Sample Prep Kit v2

treatment_protocol: A group of 3 samples were kept in E7 medium (controls) and 5 other samples were switched to E7 medium + 10 ng/ml Activin A. Samples were collected at the specified times.

value: Embryonic stem cells

tag: treatment

value: Activin

tag: time of collection


title: AI.Treated.120S


title: Activin 8h


title: AI.Treated.123S


title: Activin 4h


title: Resting Treg 4

value: Treg

value: CD4+ Foxp3+ CD62Lhi CD44lo CD49b−


title: NEG aTreg 1


title: Resting Treg 3


title: Activin 2.5h


title: Resting Treg 2


title: Resting Treg 1


title: Control 12h

value: Control


title: POS Teff 4

value: Tconv

value: CD4+ Foxp3− CD44hi CD49b+


title: Control 6h


title: POS Teff 3

value: Male


title: AI.Treated.112S


title: AI.Treated.118S


title: AI.Treated.111S


title: AI.Treated.115S


title: AI.Treated.119S


title: Control 0h


title: AI.Treated.116S


title: AI.Treated.109S


title: AI.Treated.108S


title: AI.Treated.105S


title: AI.Treated.107S


title: NEG Teff 4

value: 8 weeks old

value: CD4+ Foxp3− CD44hi CD49b−


title: POS Teff 2

value: Spleen


title: POS Teff 1

value: CD4 pos selection + FACS


title: Activin 1h


title: AI.Treated.94S


title: AI.Treated.96S


title: AI.Treated.97S


title: AI.Treated.95S


title: NEG Teff 3


title: AI.Treated.92S


title: NEG Teff 2


title: AI.Treated.169S


title: Tnaive 4

value: CD4+ Foxp3− CD62Lhi CD44lo CD49b−


title: AI.Treated.93S

value: treated


title: NEG Teff 1


title: AI.Treated.90S

value: female


title: AI.Treated.84S

value: surgery (S)


title: AI.Treated.91S

value: Negative


title: AI.Treated.104S


title: AI.Treated.87S


title: AI.Treated.88S


title: AI.Treated.85S


title: AI.Treated.81S


title: AI.Treated.78S


title: AI.Treated.82S


title: Tnaive 2


title: Tnaive 1


title: AI.Treated.80S


title: Spleen Foxp3minus 3

description: Spleen Tconv 3

data_processing:
Trimmomatic v0.32 was run with standard settings to remove low-quality reads and adaptor contamination.
Trimmed reads were aligned to Ensembl assembly GRCm38 using TopHat2 v2.0.11 implementing Bowtie2 v2.2.2 with default settings.
Read alignments were sorted with SAMtools v0.1.19.
Raw read counts were generated using HTSeq v0.6.1p1.
Genome_build: GRCm38

source_name: Spleen (pool of 3)

extract_protocol:
Live CD45+ TCRβ+ NK-1.1− CD1d Tetramer− CD4+ CD8α− Foxp3+ Treg or Foxp3− Tconv were FACS-purified from the indicated tissues and resuspended in TRIzol.
Total RNA was extracted and underwent SMARTer amplification, poly(A) selection, and Illumina TruSeq paired-end library preparation following manufacturer’s protocols.

value: 5 months old

value: CD4+ Foxp3Thy1.1−


title: Spleen Foxp3plus 3

description: Spleen Treg 3

value: Treg

value: CD4+ Foxp3Thy1.1+


title: AI.Treated.79S


title: Biotin-Ipr1

value: Streptavidin

value: Balb/c


title: Spleen Foxp3plus 2

description: Spleen Treg 2


title: Spleen Foxp3minus 2

description: Spleen Tconv 2

value: Tconv


title: AI.Treated.76S


title: AI.Treated.77S


title: Spleen Foxp3minus 1

description: Spleen Tconv 1

value: Male


title: AI.Treated.75S


title: 956Tumor

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: Gene expression data from microdissected ovarian tumor epthelial component

hyb_protocol: For each sample, 15 microgram of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array

scan_protocol: GeneChip Scanner 3000 (Affymetrix) was used for array scanning and data collection

data_processing: Microarray data analysis software, GeneSpring V.14.9 (Agilent Technologies Inc.) was used to perform the primary data analysis. RMA summerization algorithm was used and baseline transformation to median of all samples were performed.

label: Biotin

source_name: Microdissected ovarian tumor epthelial component

label_protocol: RNA samples were amplified and labeled using the two-cycle amplification protocol (Affymetrix).

extract_protocol: Frozen sections were affixed onto FRAME slides (Leica, Wetzlar, Germany), fixed in 70% alcohol and stained by 1% methyl green. Air-dried tissue sections were then taken for microdissection using a MD LMD laser microdissecting microscope (Leica). Different types of tissues were dissected and harvested. Total RNA was isolated using the RNeasy Micro kit (Qiagen).

treatment_protocol: Cancer specimens were obtained from the primary tumors of previously untreated ovarian cancer patients. All specimens were collected under protocols approved by the institutional review boards.

value: Human ovarian tissue


title: 799Tumor


title: AI.Treated.135S


title: AI.Treated.71S


title: AI.Treated.74S


title: 794Tumor


title: 780Tumor


title: AI.Treated.69S


title: AI.Treated.70S


title: AI.Treated.136S


title: PBMC Foxp3minus 3

description: PBMC Tconv 3

source_name: PBMC (pool of 3)

value: PBMC


title: AI.Treated.64S


title: 691Tumor


title: AI.Treated.66S


title: AI.Treated.67S


title: AI.Treated.59S


title: AI.Treated.73S


title: Spleen Foxp3plus 1

description: Spleen Treg 1

value: Spleen


title: 645Tumor


title: PBMC Foxp3plus 3

description: PBMC Treg 3

value: CD4 pos selection + FACS


title: PBMC Foxp3minus 2

description: PBMC Tconv 2


title: PBMC Foxp3plus 2

description: PBMC Treg 2


title: AI.Treated.63S


title: 412Tumor


title: 778Tumor


title: AI.Treated.62S


title: AI.Treated.57S


title: 402Tumor


title: AI.Treated.68S


title: 396Tumor


title: 388Tumor


title: PBMC Foxp3minus 1

description: PBMC Tconv 1


title: AI.Treated.56S


title: PBMC Foxp3plus 1

description: PBMC Treg 1


title: AI.Treated.53S


title: AI.Treated.55S


title: AI.Treated.54S


title: AI.Treated.58S


title: AI.Treated.50S


title: AI.Treated.49S


title: Liver Foxp3minus 3

description: Liver Tconv 3

source_name: Liver (pool of 3)

value: Liver


title: Liver Foxp3plus 3

description: Liver Treg 3


title: AI.Treated.48S

value: treated


title: Liver Foxp3minus 2

description: Liver Tconv 2


title: 386Tumor


title: AI.Treated.45S

value: female


title: AI.Treated.47S

value: surgery (S)


title: Liver Foxp3plus 2

description: Liver Treg 2


title: Liver Foxp3minus 1

description: Liver Tconv 1


title: 389Tumor


title: Liver Foxp3plus 1

description: Liver Treg 1


title: AI.Treated.40S

value: Negative


title: AI.Treated.42S


title: AI.Treated.43S


title: AI.Treated.44S


title: 380Tumor


title: 377Tumor


title: AI.Treated.52S


title: AI.Treated.39S


title: LDLN Foxp3minus 3

description: LDLN Tconv 3

source_name: Liver-draining lymph node (pool of 3)

value: 5 months old

value: Liver-draining lymph node


title: AI.Treated.38S


title: 358Tumor


title: LDLN Foxp3plus 3

description: LDLN Treg 3

value: Treg


title: 349Tumor


title: LDLN Foxp3minus 2

description: LDLN Tconv 2

value: CD4+ Foxp3Thy1.1−


title: AI.Treated.37S


title: AI.Treated.35S


title: 1064Tumor


title: 1312Tumor


title: AI.Treated.34S


title: AI.Treated.33S


title: AI.Treated.32S


title: 324Tumor


title: LDLN Foxp3plus 2

description: LDLN Treg 2

value: CD4+ Foxp3Thy1.1+


title: LDLN Foxp3minus 1

description: LDLN Tconv 1


title: AI.Treated.31S


title: AI.Treated.30S


title: AI.Treated.36S


title: 934Tumor


title: LDLN Foxp3plus 1

description: LDLN Treg 1


title: AI.Treated.27S


title: 786Tumor


title: AI.Treated.25S

value: Positive


title: AI.Treated.26S


title: AI.Treated.24S


title: AI.Treated.22S


title: AI.Treated.21S


title: AI.Treated.28S


title: AI.Treated.23S


title: VL3-3M2 WT DamID

city: Durham

first: Michael

middle: S

last: Krangel

state: NC

address: 207 Research Drive, Jones Building, Room 316

institute: Duke University

description: DamID against Lamin B1

data_processing:
library strategy; DNA adenine methyltransferase identification (DamID)-seq
DamID-seq reads were processed using LADetector (available at https://github.com/thereddylab/pyLAD), an updated Python implementation of LADetector described in (Harr et al., 2015) with incorporated sequence mapping. pyLAD was run with the parameters “--multimapping --quality-trim –unalignable --count-overlaps –seed 5”.
Reads were quality trimmed using a sliding window quality score average over 3 bases and a minimum score cutoff of 30. This was followed by trimming any matching overlap between read-ends and sequencing or DamID adapter-primer sequence. Reads containing a DamID adapter-primer sequence were split and adapter-primer sequence removed. All resulting reads greater than 20 bp were aligned to mm9 using Bowtie (Langmead et al., 2009) with parameters “—tryhard –best --m 1”. Unaligned reads had 10 bases trimmed from the 5' end and remapped, and the resultant unmapped reads were trimmed 10 bases from the 3’ end and remapped.
Total aligned reads were assigned to DpnI bins, with reads straddling bin boundaries counting towards both. Prior to scoring, a value of 0.5 was added to bins with no reads. Bins falling in unaligned regions were removed prior to analysis. DamID scores were calculated for all non-zero bins as the log2 ratio of Dam-Lamin B1 over unfused Dam.
Scores were partitioned using circular binary segmentation using the DNAcopy package in R (Seshan and Olshen, 2018).
LADs were classified as regions >100 kb in size of positive signal, allowing for smaller regions of negative signal <10 kb in size.
Genome_build: mm9
Supplementary_files_format_and_content: DamID files in .bedgraph, binned on DpnI cut sites. LAD calls based on DamID tracks in .bed.

source_name: VL3-3M2 cell line (wild-type)

growth_protocol: VL3-3M2 cells were maintained in RPMI 1640 with L-glutamine supplemented with 10% fetal bovine serum, 50 U/mL penicillin-streptomycin and 55 uM 2-mercaptoethanol.

extract_protocol:
Genomic DNA was harvested from VL3-3M2 cells transduced with either unfused Dam or Dam-Lamin B1 retroviruses. DamID enrichment was performed as described in Vogel et al., 2007.
1-2 μg DamID material was subjected to end repair using the NEBNext End Repair Module (New England Biolabs) and cleaned up using DNA Clean and Concentrator -5 (Zymo Research). Cleaned up DNA was ligated with 5U T4 DNA ligase (Roche) per 1 μg material in 20 μL to generate a library of large DNA fragments. This DNA library was diluted to 200 μL in H2O, sonicated for one hour in 1.5 mL in DNA LoBind tubes (Eppendorf) using a Bioruptor (Diagenode), then transferred to 1.5 mL TPX tubes (Diagenode) for four rounds of 10 min sonication to yield fragments of 150-300 bp in size. Samples were transferred to new TPX tubes between each round of sonication to minimize loss of DNA fragments. The sonicated DNA was transferred to 1.5mL DNA LoBind tubes, ethanol precipitated and resuspended in 10 μL of 10 mM Tris-HCl pH 8.0. Samples were quantified using Qubit and sequencing libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: dusRC VL3-3M2 line was obtained by CRISPR/Cas9-mediated deletion of regulatory elements

tag: cell line

tag: genotype/variation

value: wild type


title: 656Tumor


title: AI.Treated.19S


title: 477Tumor


title: 660Tumor


title: AI.Treated.14S


title: 692Tumor


title: AI.Treated.18S


title: 715Tumor


title: AI.Treated.17S


title: AI.Treated.20S


title: 486Tumor


title: AI.Treated.16S


title: 4C_MEF2C_recVP7_SHSY5Y_rep2

city: Gent

first: Sarah

last: Vergult

address: Corneel Heymanslaan 10

department: Department of Biomolecular Medicine

country: Belgium

institute: Ghent University

data_processing:
Base-calling was performed on the NextSeq 500 system by RTA v2.
Sequencing libraries were demultiplexed based on the presence of the viewpoint-specific reading primer sequence, which precedes the captured DNA sequence.
Captured sequences were mapped to the hg19 reference genome using Bowtie2.
For the cis chromosome, mapped read counts were summarized per DpnII restriction fragment.
4C coverage profiles were obtained by normalizing the per fragment coverage to reads per million (RPM) on the cis chromosome and smoothing the normalized coverage using the rollmean function from the R ‘zoo’ package with a window size of 21 fragments.
Genome_build: hg19
Supplementary_files_format_and_content: 4C-seq interaction profiles in bedgraph format. The file contains the normalized counts per restriction fragment after rolling-mean smoothing.

source_name: SH-SY5Y cell line

growth_protocol: Cell lines were cultured in complete RPMI 1640 medium (10%FBS, 1%P/S, 1% glutamine, 1% kanamycine). Cells were passaged every 3-4 days. We allowed at least two passages before using cells in experiments.

extract_protocol:
4C templates were prepared according to the protocol by Van de Werken et al. (Methods Enzymol., 2012). In brief, for each template 1x10^7 cells were detached, counted, resuspended and crosslinked by incubating them with 2% formaldehyde for 10 min at room temperature. Following cell lysis, crosslinked DNA was digested with 400U of DpnII restriction enzyme (NEB #R0543L) and nearby DNA fragments were ligated using 50U of T4 DNA ligase (Roche #10799009001). Ligated DNA circles were de-crosslinked overnight using proteinase K and purified with NucleoMag P-Beads (Macherey-Nagel) to obtain an intermediate 3C template. A second round of digestion and ligation, using 50U of Csp6I restriction enzyme (Thermo Scientific #ER0211), resulted in 4C templates.
Adaptor-containing reading and non-reading primers, specific to the viewpoints of interest, were designed to amplify all captured, interacting DNA fragments. For each viewpoint, 16 PCR reactions, each using 200 ng of input 4C template, were pooled. Resulting 4C sequencing libraries were purified using High Pure PCR Product Purification kit (Roche #11732676001) and QIAquick PCR Purification kit (Qiagen #28106). Approximately 15-20 different 4C sequencing libraries were pooled and sequenced simultaneously on an Illumina NextSeq 500 (single-end, 75 nt, loading concentration 1.6 pM).

tag: 4c viewpoint (vp)

value: MEF2C reciprocal VP 7

tag: assay


title: 4C_MEF2C_recVP7_SHSY5Y_rep1


title: 4C_MEF2C_recVP6_SHSY5Y_rep2

value: MEF2C reciprocal VP 6


title: AI.Treated.15S


title: 4C_MEF2C_recVP6_SHSY5Y_rep1


title: 4C_MEF2C_recVP5_SHSY5Y_rep2

value: MEF2C reciprocal VP 5


title: Treg

data_processing:
FASTQ files were demultiplexed using the SEQC pipeline (https://github.com/ambrosejcarr/seqc.git).
Cell filtering was performed using the following QC metrics: # of UMIs, # of genes, and % mitochondrial content per cell.
R1 files contain the barcode and the R2 files are the read sequences.
Genome_build: GRCm38
Supplementary_files_format_and_content: Cell x gene unnormalized count matrices

extract_protocol:
Singlet CD4+ Foxp3+ (Treg) or CD4+ Foxp3− (Tconv) cells were FACS-purified from CD4-enriched Foxp3GFP splenocytes from 3 pooled mice and resuspended in TRIzol.
scRNA-seq libraries were prepared using the 10x Genomics Chromium instrument and Chromium Single Cell 3' Reagent Kit v2 following manufacturer's protocols. Paired-end sequencing was performed on the Illumina HiSeq 2500.

tag: genetic background

value: Male

value: 8 weeks old

tag: tissue

value: Spleen x 3 (pooled)


title: 4C_MEF2C_recVP5_SHSY5Y_rep1


title: Tconv

value: Tconv

value: CD4 pos selection + FACS


title: AI.Treated.13S

value: treated

value: female

value: surgery (S)


title: AI.Treated.12S


title: 4C_MEF2C_recVP4_SHSY5Y_rep1

value: MEF2C reciprocal VP 4


title: 410Tumor

value: Human ovarian tissue


title: 393Tumor


title: AI.Treated.9S


title: AI.Treated.3S


title: 367Tumor


title: 351Tumor


title: 431Tumor


title: AI.Treated.5S


title: AI.Treated.7S


title: AI.Treated.10S


title: AI.Treated.197B

value: baseline (B)

value: Negative


title: 332Tumor


title: AI.Treated.198B


title: AI.Treated.8S

value: Positive


title: AI.Treated.1S


title: AI.Treated.196B


title: AI.Treated.195B


title: AI.Treated.194B


title: 2199Stroma

description: Gene expression data from microdissected ovarian cancer stroma

source_name: Microdissected ovarian cancer stroma


title: 326Tumor


title: AI.Treated.192B


title: 4C_MEF2C_recVP3_HEK_rep1

source_name: HEK cell line

value: HEK

value: MEF2C reciprocal VP 3


title: 4C_MEF2C_recVP3_SHSY5Y_rep1


title: 4C_MEF2C_recVP2_HEK_rep1

value: MEF2C reciprocal VP 2


title: 4C_MEF2C_recVP3_HEK_rep2


title: 4C_MEF2C_recVP2_HEK_rep2


title: 4C_MEF2C_recVP2_SHSY5Y_rep1


title: 4C_MEF2C_recVP1_HEK_rep2

value: MEF2C reciprocal VP 1


title: 4C_MEF2C_recVP3_SHSY5Y_rep2


title: 1933Stroma


title: 1660Stroma


title: AI.Treated.191B


title: AI.Treated.193B


title: AI.Treated.187B


title: AI.Treated.189B


title: 4C_MEF2C_recVP1_SHSY5Y_rep2


title: 4C_MEF2C_recVP1_HEK_rep1


title: AI.Treated.188B


title: 4C_MEF2C_recVP1_SHSY5Y_rep1


title: 1557Stroma


title: 4C_MEF2C_HEK_rep2

value: MEF2C promoter


title: AI.Treated.190B


title: AI.Treated.186B


title: 1223Stroma


title: AI.Treated.185B


title: 1231Stroma


title: 1653Stroma


title: 1109Stroma


title: 4C_MEF2C_HEK_rep1


title: 1686Stroma


title: 4C_MEF2C_SHSY5Y_rep2


title: 4C_MEF2C_SHSY5Y_rep1


title: LL-6: CBR-470-1 rep 3

city: La Jolla

first: Padma

last: Natarajan

state: CA

address: 10550 N.Torrey Pines Road

department: CCBB

institute: The Scripps Research Institute

data_processing:
Illumina bcl2fastq software used for basecalling.
Quantification of transcript abundance was obtained from sequenced reads using Salmon v.0.7.2
Abundance measurements in transcripts per million (TPM) units were calculated at the gene-level.
Genome_build: GRCh38 release 25 (GENCODE)
Supplementary_files_format_and_content: exel file includes measure of abundance in TPM (transcripts per million) units

source_name: IMR32 cell line

growth_protocol: IMR32 human neuroblastoma cells were originally obtained from ATCC and maintained in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted using an RNeasy kit (Qiagen).
RNAseq libraries were prepared from polyA selected RNA using the NEBNext Ultra RNA Library Prep Kit for Illumina.

treatment_protocol: IMR32 cells, plated at 10^6 cells per well in 6-well plates, were treated for 24 hours with 5 µM CBR-470-1 or an equivalent volume of DMSO vehicle control.


title: LL-5: CBR-470-1 rep 2


title: LL-4: CBR-470-1 rep 1


title: LL-3: DMSO rep 3


title: LL-1: DMSO rep 1


title: 799Stroma


title: HeLa cells, control siRNA, I-PpoI, Cordycepin treated [29_siCont_cut_Cord]

data_processing:
removing adatper, pre-mapping to a hand-curated list of ribosomal cDNA and miRNA libraries and collapsing reads with identical sequence using an in-house pipeline allowing one mismatch and discarding reads below 18nt
remapping to ribosomal RNA (custom cDNA library) using bowtie (version 1.12) with the options “-v 0 –q –k 1 –best”
Genome_build: custom
Supplementary_files_format_and_content: standard bowtie output format, reads mapped to ribosomal cDNA library

source_name: HeLa

value: HeLa

tag: growth protocol

value: DMEM + FBS + Pen/Strep

tag: incubation after plasmid or mock transfection

tag: sirna

value: 25nM of control siRNA (Thermo Fisher, CatNo:4390844) was transfected with Lipofectamine RNAiMAX 12 hrs prior to I-PpoI transfection

tag: ip, antibody

tag: i-ppoi transfection

value: 2.5 μg pOPRSVI-IPpoI (Lipofectamin)

tag: miRNA spike-ins (exiqon)

value: recommended amount


title: HeLa cells, control siRNA, I-PpoI, Cordycepin treated [28_siCont_cut_Cord]


title: 794Stroma


title: 956Stroma


title: HeLa cells, control siRNA, I-PpoI, Cordycepin treated [30_siCont_cut_Cord]


title: 1064Stroma


title: 744Stroma


title: 778Stroma


title: 780Stroma


title: 402Stroma


title: 412Stroma


title: 645Stroma


title: HeLa cells, control siRNA, no I-PpoI, Cordycepin treated [27_siCont_unc_Cord]

value: Mock


title: AI.Treated.163B

data_processing: The data was filtered to remove any non-expressed probes using the detection p-value from Illumina. Across all samples probes for which the intensity values were not significantly different (p>0.01) from the negative controls were removed from the analysis. Following filtering the data was transformed and normalized using variance-stabilizing transformation and robust spline normalization (RSN) method in the lumi package in R. The RSN combines the features of quantile and loess normalization

tag: group

value: treated

tag: Sex

value: female


title: 388Stroma

value: Human ovarian tissue


title: LL-2: DMSO rep 2


title: 389Stroma


title: 386Stroma


title: 691Stroma


title: 396Stroma


title: 380Stroma


title: HeLa cells, control siRNA, no I-PpoI, Cordycepin treated [26_siCont_unc_Cord]


title: IGG control 3, no I-PpoI [unc-IGG-16]

extract_protocol:
Magna RIP RNA-Binding Protein Immunoprecipitation Kit
TruSeq small RNA library preparation, Illumina, using RNA returned from RIP as input

value: Igg (control, Magna RIP™ kit)


title: 377Stroma


title: 349Stroma


title: 358Stroma


title: AgoRIP 3, antibody A, no I-PpoI [unc-AgoIP-abc-5]

value: abcam (ab57113)


title: AgoRIP 3, antibody B, no I-PpoI [unc-AgoIP-dia-10]

value: diagenode (Cat. No. C15200167)


title: AgoRIP 2, antibody B, no I-PpoI [unc-AgoIP-dia-8]


title: AgoRIP 1, antibody A, no I-PpoI [unc-AgoIP-abc-2]


title: IGG control 1, no I-PpoI [unc-IGG-12]


title: HeLa cells, control siRNA, no I-PpoI, Cordycepin treated [25_siCont_unc_Cord]


title: AgoRIP 2, antibody A, no I-PpoI [unc-AgoIP-abc-4]


title: Input 3, no I-PpoI [Input-III-unc-22]

extract_protocol:
Magna RIP RNA-Binding Protein Immunoprecipitation Kit
TruSeq small RNA library preparation, Illumina, using RNA returned from RIP as input, addition of Exiqon small RNA spike-ins

value: 1/3 of recommended amount


title: Input 2, no I-PpoI [Input-II-unc-20]


title: IGG control 2, no I-PpoI [unc-IGG-14]


title: Input 1, no I-PpoI [Input-I-unc-18]


title: IGG control 3, I-PpoI [cut-IGG-15]

value: 2.5 μg pOPRSVI-IPpoI (Lipofectamin)/well (6-well plate)


title: IGG control 2, I-PpoI [cut-IGG-13]


title: AgoRIP 3, antibody B, I-PpoI [cut-AgoIP-dia-9]


title: AgoRIP 2, antibody B, I-PpoI [cut-AgoIP-dia-7]


title: AgoRIP 3, antibody A, I-PpoI [cut-AgoIP-abc-6]


title: AgoRIP 2, antibody A, I-PpoI [cut-AgoIP-abc-3]


title: 1217Stroma


title: 317Stroma


title: 324Stroma


title: AgoRIP 1, antibody A, I-PpoI [cut-AgoIP-abc-1]


title: 2389Stroma


title: 1890Stroma


title: 1916Stroma


title: 786Stroma


title: 2068Stroma


title: 1214Stroma


title: IGG control 1, I-PpoI [cut-IGG-11]


title: 692Stroma


title: 694Stroma


title: 1923Stroma


title: 934Stroma


title: 970Stroma


title: 718Stroma


title: Input 3, I-PpoI [Input-III-cut-21]


title: Input 2, I-PpoI [Input-II-cut-19]


title: Input 1, I-PpoI [Input-I-cut-17]


title: 715Stroma


title: HeLa cells, control siRNA, I-PpoI [17_siCont_cut_rrna]


title: 660Stroma


title: HeLa cells, control siRNA, no I-PpoI [15_siCont_unc_rrna]


title: HeLa cells, control siRNA, no I-PpoI [14_siCont_unc_rrna]


title: HeLa cells, control siRNA, no I-PpoI [13_siCont_unc_rrna]


title: 656Stroma


title: 486Stroma


title: 477Stroma


title: HeLa cells, Drosha KD, I-PpoI [6_siDro_cut_rrna]

value: 25nM of siDro (Silencer siRNA, ID:126719) was transfected with Lipofectamine RNAiMAX 12 hrs prior to I-PpoI transfection


title: HeLa cells, control siRNA, I-PpoI [18_siCont_cut_rrna]


title: HeLa cells, Drosha KD, I-PpoI [5_siDro_cut_rrna]


title: HeLa cells, Drosha KD, I-PpoI [4_siDro_cut_rrna]


title: HeLa cells, Drosha KD, no I-PpoI [2_siDro_unc_rrna]


title: HeLa cells, Drosha KD, no I-PpoI [3_siDro_unc_rrna]


title: HeLa cells, control siRNA, I-PpoI [16_siCont_cut_rrna]


title: 478Stroma


title: 431Stroma


title: 393Stroma


title: HeLa cells, Drosha KD, no I-PpoI [1_siDro_unc_rrna]


title: 384Stroma


title: 367Stroma


title: 423Stroma


title: 410Stroma


title: HeLa cells, I-PpoI, 120 hrs after transfection [JP12_5d_BC20_GTGGCC_rrna]


title: 351Stroma


title: AI.Treated.57B

tag: timepoint

value: baseline (B)

value: Negative


title: 344Stroma


title: HeLa cells, I-PpoI, 48 hrs after transfection [JP9_48h_BC17_GTAGAG_rrna]

value: HeLa


title: 326Stroma


title: 332Stroma


title: 312Stroma


title: ChIP_H3K4me1_CPP_2

city: Cincinnati

first: Jeffrey

middle: D

last: Steimle

email: jeffrey.steimle@cchmc.org, jeffrey.steimle@bcm.edu, jsteimle@uchicago.edu, jsteimle@alumni.nd.edu

state: OH

address: 240 Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Medical Hospital Center

data_processing:
Raw sequencing reads were aligned to the mm10 genome using Bowtie2 (Langmead and Salzberg 2012, Nat Methods) and SAMtools (Li et al 2009 Bioinformatics, Li 2011 Bioinformatics) requiring a minimum mapping quality of 10 (-q 10).
For ChIP-seq, pooled peak calling was performed using default settings of MACS2 callpeak (Zhang et al 2008 Genome Biol, Feng et al 2012 Nat Protoc) with a q-value set to 0.05 and tag size set to 6 (-q 0.05 -s 6). For ATAC-seq, peak calling was performed using MACS2 callpeak (Zhang et al 2008 Genome Biol, Feng et al 2012 Nat Protoc) using the settings --nomodel --shift -100 --extsize 200 -q 0.05.
A fold-enrichment track was generated using MACS2 using the bdgcmp function (-m FE) for visualization on the genome browser (Zhang et al 2008 Genome Biol, Feng et al 2012 Nat Protoc).
Genome_build: mm10
Supplementary_files_format_and_content: .bw files are bigWig files generated by MACS2 of the fold enrichment

source_name: embryonic CPP

extract_protocol:
To prepare chromatin extract, micro-dissected tissue from E9.5 CD-1 mouse embryos (2x from 50 embryo pools each) obtained from Charles River were cross-linked in PBS containing 1% formaldehyde at 25°C for 10 minutes. The reaction was quenched by 125 mM glycine. The cross-linked tissues were incubated in LB1 (50 mM HEPES-KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA; 10% Glycerol; 0.5% NP-40; 0.25% Triton X-100) with protease and phosphatase inhibitors on ice for 10 minutes. The tissues were then sonicated in LB3 (10 mM Tris-HCl, pH 8.0; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% sodium deoxycholate; 0.5% N-lauroyl sarcosine; 1% Triton X-100) with protease and phosphatase inhibitors. Chromatin extract was then cleared by centrifugation at 14,000g, 4°C for 10 minutes. For immunoprecipitation, the chromatin extract was incubated with 5ug of the anti-TBX5 antibody (Santa Cruz Biotechnology sc-17866; Lot #G1516), 1μg of anti-H3K4me3 (Wako Chemicals #305-34819; Lot #14004), or 1μg of anti-H3K4me1 (Abcam ab8895; Lot #GR257926-1) at 4°C for >12 hours in a total volume of 200 μL. The immune-complexes were captured by Protein G-conjugated magnetic beads (Life Technologies, 1003D), washed in sequence by LB3, LB3 with 1 M NaCl, LB3 with 0.5 M NaCl, LB3, and TE (10 mM Tris-HCl, pH 8.0; 1 mM EDTA). The captured chromatin was eluted in ChIP Elution Buffer (10 mM Tris-HCl, pH 8.0; 1 mM EDTA; 1% SDS; 250 mM NaCl) at 65°C. After RNase and proteinase K treatment and reverse cross-linking, DNA were purified.
High-throughput sequencing libraries from ChIP and input DNA were prepared using NEBNext Ultra DNA Library Prep Kit (New England Biolabs, E7370S). During library preparation, adaptor-ligated DNA fragments of 200-650 bp in size were selected before PCR amplification using Sera-Mag magnetic beads (GE, 6515-2105-050-250). DNA libraries were sequenced using Illumina Hi-seq instruments (single-end 50 base) by the Genomics Core Facility at the University of Chicago.

tag: strain

tag: embryonic day

tag: micro-dissected tissue

value: CPP


title: ChIP_H3K4me3_CPP_2


title: ChIP_Input_CPP_1


title: ChIP_Input_Heart_1

source_name: embryonic heart

value: Heart


title: AI.Treated.42B

source_name: breast tumour


title: HeLa cells, I-PpoI, 96 hrs after transfection [JP11_4d_BC19_GTGAAA_rrna]

value: DMEM + FBS + Pen/Strep

tag: cell line

value: 2.5 μg pOPRSVI-IPpoI (Lipofectamin)


title: HeLa cells, I-PpoI, 72 hrs after transfection [JP10_3d_BC18_GTCCGC_rrna]


title: ChIP_H3K4me3_HT_1


title: HeLa cells, I-PpoI, 24 hrs after transfection [JP7_24h_BC16_CCGTCC_rrna]


title: ChIP_H3K4me3_CPP_1


title: HeLa cells, I-PpoI, 16 hrs after transfection [JP6_16h_BC15_ATGTCA_rrna]


title: ChIP_H3K4me3_HT_2


title: ChIP_H3K4me1_HT_2


title: ChIP_H3K4me1_HT_1


title: ChIP_TBX5_HT_2


title: HeLa cells, I-PpoI, 8 hrs after transfection [JP5_8h_BC14_AGTTCC_rrna]


title: ATAC_CPP_4

extract_protocol:
ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) was performed as previously described (Buenrostro et al 2015, Curr Protoc Mol Bio). Nuclei were isolated from micro-dissected tissue from E9.5 CD-1 mouse embryos (2x from 5 embryo pools each) from Charles River according to published protocols and transposition reaction performed by published methods (Buenrostro et al 2015, Curr Protoc Mol Bio).
Libraries were amplified and normalized with the Illumina Nextera DNA Library prep kit (FC-121–1031) according to the manufacturer's protocols. Libraries were quantitated using the Agilent Bio-analyzer, pooled in equimolar amounts, and sequenced with 50-bp single-end reads on the Illumina HiSeq following the manufacturer's protocols through the Genomics Core Facility at the University of Chicago.


title: ATAC_CPP_3


title: ChIP_H3K4me1_CPP_1


title: ChIP_TBX5_HT_1


title: HeLa cells, Mock transfected [JP2_M0h_BC11_GGCTAC_rrna]

value: Mock


title: ATAC_HT_3


title: ATAC_CPP_2


title: ATAC_HT_1


title: ATAC_HT_2


title: ATAC_CPP_1


title: VL3-3M2 dusRC DamID

description: DamID against Lamin B1

source_name: VL3-3M2 cell line (dusRC)

tag: genotype/variation

value: dusRC


title: AI.Treated.26B

value: treated

value: female

value: Positive


title: AI.Treated.25B


title: AI.Treated.21B


title: ATAC_HT_4


title: VL3-3M2 dusRC input

description: Used to normalize H3K9me2

data_processing:
Demultiplexed .fastq files were trimmed using the fastqFilter command in the R dada2 (1.8.0) package with the parameters “truncLen = 0, trimLeft = 0, maxN = 0, minQ = 0, rm.phix = TRUE”
The trimmed files were aligned to the mm9 genome using the qAlign command in the R QuasR (1.20.0) package with the parameters “aligner = “Rbowtie”, maxHits = 1, paired = NULL”.
Duplicate and replicate .bam files were merged using the mergeBam command in the R Rsamtools (1.32.0) package.
Reads were placed into 200 bp bins using the constructBins command in the R mosaics (2.18.0) package with the parameters “fragLen = 150, binSize = 200, capping = 50, PET = FALSE”. Reads that corresponded to chromosome Y, chromosome M or unmapped parts of the chromosome were excluded.
Bins were assembled into tracks in the .bedgraph format.
H3K27ac tracks were normalized to reads per million.
H3K9me2 tracks were normalized for read count relative to the input sample and a value of 1 was added to bins with no reads. Log2 ratios of the H3K9me2 sample over input were then plotted.
Genome_build: mm9
Supplementary_files_format_and_content: .bedgraph in 200bp bins. Bins with a value of 0 were deleted to reduce file size.

extract_protocol:
Nucleosomes were obtained by micrococcal nuclease digestion and antibody added. Pulldown was performed using protein A-agarose and bound DNA was purified by phenol-chloroform extraction
Library preparation and high-throughput sequencing were performed by the Duke Center for Genomic and Computational Biology Core Facility

treatment_protocol: Derivative VL3-3M2 cell lines were obtained by CRISPR/Cas9-mediated deletion of regulatory elements (usRC or Eb)

tag: sample type

value: Cell line

tag: cell type/line

tag: age

tag: antibody


title: VL3-3M2 dEb input

description: Used to normalize H3K9me2

source_name: VL3-3M2 cell line (dEb)

value: dEb


title: VL3-3M2 WT input

description: Used to normalize H3K9me2

value: wild-type


title: VL3-3M2 dEb H3K9me2

value: H3K9me2 (abcam ab1220)


title: VL3-3M2 dEb H3K27ac

value: H3K27ac (abcam ab4729)


title: VL3-3M2 dusRC H3K27ac


title: VL3-3M2 dusRC H3K9me2


title: VL3-3M2 WT H3K27ac


title: DP H3K27ac

description: DP thymocytes obtained by anti-CD3e injection

source_name: Rag2-/- thymocyte, anti-CD3e-injected

value: Primary cell

value: thymocyte

value: 4 weeks

value: Rag2-/- thymocyte, anti-CD3e-injected


title: DP input

description: DP thymocytes obtained by anti-CD3e injection, used to normalize H3K9me2


title: DP H3K9me2


title: 5637C1

city: Madrid

first: Monica

last: Martinez-Fernandez

address: Avda Complutense 40

country: Spain

institute: CIEMAT

description: 5637 cell line control 1

hyb_protocol: Following fragmentation, 5,5 ug of fragmented and labeled ss-DNA were hybridized for 16 hr at 45ºC at 60 rpm on Hybridization Oven 640 de Affymetrix. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 7G de Affymetrix

data_processing: Expression data were normalized, background-and batch corrected using the Guanine Cytosine Count Normalization (GCCN) and Signal Space Transformation (SST), and prior to summarizing using the Robust Multi-Array Average (RMA) algorithm implemented in the Affymetrix Expression Console software. In order to combine the different microarray data sets, possible batch effects were corrected by using the Bioconductor Combat package in R environment (Johnson et al., 2007)

source_name: 5637 cell line control

label_protocol: cRNA is converted to biotinylated sense-strand DNA prepared according to the standard Affymetrix protocol from 12 ngs total RNA (GeneChip Whole Trasncript WT Expression Arrays, Affymetrix).

growth_protocol: The bladder cancer cell lines were maintained in Dulbecco's Modified Eagle Medium GlutaMAX™ (Gibco-BRL Life Technologies) with 10% fetal bovine serum (Hyclone) and 1% antibiotic-antimycotic (Gibco-BRL Life Technologies) at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol: Extraction of total RNA was performed using miRNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Control (PBS-treated) and palbociclib-treated (IC50) RT112, J82 and 5637 cells, were analyzed. Cell pool transcriptomes were obtained from 3 different p100 dishes grown to 70-80% confluence.

tag: cell type

value: Bladder cell line

tag: treated with

value: PBS (control)


title: 5637C3

description: 5637 cell line control 3


title: 5637PB1

description: 5637 cell line treated with palbociclib (IC50) replicate 1

value: palbociclib (IC50)


title: RT112C3

description: RT112 cell line control 3

source_name: RT112 cell line control


title: VL3-3M2 WT H3K9me2


title: 5637PB2

description: 5637 cell line treated with palbociclib (IC50) replicate 2


title: RT112C1

description: RT112 cell line control 1


title: RT112PB3

description: RT112 cell line treated with palbociclib (IC50) replicate 3


title: RT112PB2

description: RT112 cell line treated with palbociclib (IC50) replicate 2


title: 5637PB3

description: 5637 cell line treated with palbociclib (IC50) replicate 3


title: RT112PB1

description: RT112 cell line treated with palbociclib (IC50) replicate 1


title: 5637C2

description: 5637 cell line control 2


title: DN input

description: Used to normalize H3K9me2

source_name: Rag2-/- thymocyte

value: Rag2-/- thymocyte


title: DN H3K27ac


title: J82PB2

description: J82 cell line treated with palbociclib (IC50) replicate 2


title: RT112C2

description: RT112 cell line control 2


title: DN H3K9me2


title: J82PB3

description: J82 cell line treated with palbociclib (IC50) replicate 3


title: J82PB1

description: J82 cell line treated with palbociclib (IC50) replicate 1


title: J82C2

description: J82 cell line control 2

source_name: J82 cell line control