title: NRF1_3H3

description: ChIP-seq


title: liver_12mo_wt_NJ_1

status: Public on Sep 01 2020

type: SRA

city: Iowa City

first: Jesse

last: Riordan

state: IA

address: 375 Newton Road

country: USA

institute: University of Iowa

library_source: transcriptomic

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts derived with Subread:featureCount 1.45.  RPKM and CPM calculated from gene counts with custom R scripting.
Genome_build: Ensembl Release 76 GRCm38.76
Supplementary_files_format_and_content: Gene counts in tab-delimitted text format

molecule: polyA RNA

organism: Mus musculus

source_name: Liver

growth_protocol: Studies in primary hepatocytes: Livers were perfused and digested with 0.05% collagenase (Type IV, C5138, Sigma) and hepatocytes plated on collagen-coated dishes overnight.

extract_protocol:
Total RNA was extracted using TRIzol and treated with DNAse. For each genotype and condition, 3 pools were prepared, each containing RNAs from 3-4 separate mice, for a total of 10 mg RNA per final pool.
RNA pools were subjected to oligo(dT) selection and cDNA library preparation and whole transcriptome sequencing on an Illumina HiSeq2000.

tag: strain

tag: age

value: 12 months

tag: tissue

value: Liver


title: NRF1_3H1_sh2

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: ChIP-seq

library_source: genomic

data_processing:
Basecalls were performed using  bcl2fastq v2.17 for NextSeq output.
ChIP-seq reads were trimmed from the 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: HCT116 cells (ATCC CCL-247) were grown at 37 °C in DMEM supplemented with 10% FBS (Fisher Scientific, 35-015-CV).

extract_protocol:
1x10^8 cells were fixed in 1% formaldehyde (Sigma, 252549) in PBS for 15- 20 min at room temperature and quenched with 1/10th volume of 1.25 M glycine for 5 minutes at room temperature. Cells were collected at 1,000xg for 5 minutes, washed in PBS, pelleted at 1,000xg for 5 min and pellets were flash frozen in liquid nitrogen and stored at -80°C until use. Pellets were thawed on ice and resuspended in 10 ml lysis buffer 1 (50 mM HEPES, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% IGEPAL CA-630, 0.25% Triton X-100 with 5μl/ml Sigma 8340 protease inhibitor cocktail incubated on ice 10 minutes, pelleted 1,500xg and subsequently washed in lysis buffer 2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and 5ul/ml protease inhibitor) as with lysis buffer 1 before resuspending in 1 ml lysis buffer 3 (10 mM tris-HCl pH 8.0, 1 mM EDTA, 0.1% SDS and 5 ul/ml protease inhibitors) for sonication. Chromatin was sheared in a 1 ml milliTUBE with AFA fiber on a Covaris E220 using 10% duty factor for 2 min. The sheared chromatin concentration was estimated with Nanodrop at OD 260 and diluted to 1 mg/ml in ChIP Dilution Buffer (10% Triton X-100, 1M NaCl and 1% Sodium deoxycholate). 1 mg chromatin was combined with 4 μg hybridoma tissue culture supernatant and rotated overnight at 4°C. 40 μl protein A/G Dynabeads was added and incubated for 2-4 hr rotating at 4°C. Samples were washed 5 times with 1 ml RIPA buffer, 2 times with TE with 50 mM NaCl. Chromatin was eluted with 800 μl elution buffer (50 mM Tris pH 8.0, 1 mM EDTA, 0.1% SDS) for 30 min at 65°C shaking at 1,500 rpm in a ThermoMixer (Eppendorf). Supernatants were collected, digested with 20 μl of 20 mg/ml Proteinase K and incubated overnight at 65°C. DNA was purified with phenol chloroform extraction. 500 μl of the aqueous phase was precipitated with 20 μl 5M NaCl, 1.5 μg glycogen and 1 ml EtOH on ice for 1 hr or at -20°C overnight.
Sequencing libraries were prepared with the KAPA HTP library prep kit (Roche) using 1-10 ng DNA and libraries were size selected with AMPure XP beads (Beckman Coulter).

treatment_protocol:
Heat shock and non-heat shock HCT116 cells were washed with PBS before fixing with 1% formaldehyde (Sigma, 252549) in PBS for 15 minutes and processing for ChIP-seq.
For RNAi, Lentiviruses were mixed with an equal volume of fresh media supplemented with 10% FBS and polybrene was added at a final concentration of 5 µg/mL to increase infection efficiency. The medium was changed 6 hours after infection. Cells were selected with 2 µg/ml puromycin for three days before processing for ChIP-seq.

tag: cell line

tag: cell type

value: colorectal carcinoma

tag: treatment

value: NRF1targeting shRNA #2

tag: antibody


title: liver_12mo_wt_NJ_2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A8_AD010_indexed

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: MOp

tag: Sex

value: male


title: 134_S9_L002_R1_001_W4_LS

city: New York

first: Ana

last: Pavel

state: NY

address: One Gustave L. Levy Place

department: Dermatology

institute: Icahn School of Medicine at Mount Sinai

description: exp.csv

data_processing:
RNA-seq sample quality was assessed using FastQC and MultiQC.
Samples were aligned to human reference genome based on STAR RNA-sequencing aligner and sequencing reads were assigned to genomic features by featureCounts.
Genomic features with 0 counts in more than 20% of the samples were filtered out.
Data was then transfromed to log2-counts per million by voom-transform.
Fold changes (FCHs) vs. baseline were estimated and hypothesis testing was conducted with contrasts under the general framework for linear models in limma package. P-values were adjusted using the Benjamini-Hochberg procedure, which controls False Discovery Rate (FDR).
Genome_build: GRCh38

molecule: total RNA

source_name: Skin biopsy

extract_protocol:
Total RNA was extracted from skin biopsy samples using Qiagen miRNeasy Mini kit.
The libraries were generated using TruSeq Stranded mRNA Library Prep kit following manufactory protocol. Briefly, mRNA was first extracted from 240ng of total RNA using oligo-dT magnetic beads and fragmented at high temperature. A cDNA library was then prepared from the fragemented mRNA by revervse transcription, second strand synthesis and ligation of specific adapters.
Next generation sequencing was performed on Illumina Hiseq 4000 with single-ended 100 red cycles. Image analysis and bases calling was conducted in real-time by the Illumina analysis pipeline.

tag: ptid

tag: timepoint

value: Placebo

tag: tissuetype

value: LS


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B10_AD004_indexed


title: liver_12mo_acf_ko_3


title: NRF1_3H1_sh1

description: ChIP-seq

value: NRF1targeting shRNA #1


title: 133_S8_L001_R1_001_BL_LS

description: exp.csv

value: BL


title: liver_12mo_acf_ko_2


title: hepatocyte_CLIP-seq_acf_tg_3

description: Primary hepatocytes isolated from 12 week-old A1cf +/Tg mice were seeded on 10 mm collagen-coated plates, washed and exposed to 400mJ/cm2 of 254 nm UV light in a Stratalinker 2400 (Stratagene). Hepatocytes were scraped in 1ml Lysis buffer containing 50 mM HEPES pH 7.5, 150 mM KCL, 2 mM EDTA, 1 mM NaF, 0.5% (v/v) NP40, 1 mM DTT, 1x protease inhibitors, 2 mM Na3VO4, 5 mM Sodium Pyrophosphate and RNAsin (Promega), incubated 5 min on ice and frozen at -80 °C. Cell lysis was completed by homogenization and the lysate cleared by centrifugation at 13,000g 15 min at 4 °C. RNAsin-treated lysates were treated with RQ1 DNAse (Promega) 5 min at 37 °C followed by 15 min incubation at room temperature with RNAse T1 (Fermentas). A1CF-RNA complexes were immunoprecipitated, washed and treated on-beads with RNAse-T1, ligated with RNA adapters (RL5a-TYE705 and RL3-biotin), resolved on SDS-PAGE and transferred to nitrocellulose. The RNP complexes were excised and treated with Proteinase K (Thermo Scientific). Phenol/chloroform-purified RNA was subjected to cDNA synthesis using DP3 primer, followed by PCR amplification using DP5a and DP3 primers and Platinum Pfx DNA polymerase (Invitrogen). PCR conditions were as followed: 94 °C 2 min, 40 cycles at 94 °C 30 sec, 58 °C 30 sec, 68 °C 30 sec, 68 °C 10 min. PCR products were gel-purified and subjected to a second round of amplification using DSFP5a and indexed DSFP3 primer (RPIX-D3) (one per template) with the following conditions: 94 °C 2 min, 35 cycles at 94 °C 30 sec, 62 °C 45 sec, 68 °C 45 sec, 68 °C 10 min.  Final PCR products were gel purified and submit for High throughput sequencing using sequencing primer SSP1. Primer sequences are as follows: RL5a-TYE705: 5’-AGGGAGGACGAUGCGG-3’; RL3-biotin: 5’-GGCGACCUUCACUGACUGUG-3’; DP5a: 5’-AGGGAGGACGATGCGG-3’; DP3: 5’-CCGCTGGAAGTGACTGACAC-3’; DSFP5a: 5’-AATGATACGGCGACCACCGACTATGGATACTTAGTCAGGGAGGACGATGCGG-3’; RPIX1-DP3: 5’-CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCACCGCTGGAAGTGACTGACAC-3’.

source_name: Isolated hepatocytes

value: 12 weeks

value: Isolated hepatocytes


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A9_AD007_indexed


title: 132_S7_L001_R1_001_BL_NL

description: exp.csv

value: NL


title: 136_S11_L002_R1_001_BL_LS

description: exp.csv

value: Secukinumab


title: liver_12mo_acf_ko_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A8_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B10_AD008_indexed


title: liver_12mo_wt_4


title: 131_S6_L001_R1_001_W16_LS

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A9_AD008_indexed


title: NRF1_3D4_sh1

description: ChIP-seq


title: 13_S13_L003_R1_001_W4_LS

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A9_AD004_indexed


title: liver_12mo_wt_2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A8_AD008_indexed


title: NFE2L2_3D2

description: ChIP-seq

tag: associated input


title: NRF1_3D4_sh2

description: ChIP-seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A6_AD010_indexed


title: NFE2L2_1D12

description: ChIP-seq


title: liver_12mo_wt_3


title: 128_S3_L001_R1_001_BL_LS

description: exp.csv


title: NRF1_3H1_NonT

description: ChIP-seq

value: Non-targeting shRNA


title: MLLT3_2B6

description: ChIP-seq


title: 129_S4_L001_R1_001_W4_LS

description: exp.csv


title: 127_S7_L001_R1_001_BL_NL

description: exp.csv


title: liver_12mo_acf_tg_4


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A6_AD012_indexed


title: MLLT10_1D4

description: ChIP-seq


title: 126_S2_L001_R1_001_W16_LS

description: exp.csv


title: 130_S5_L001_R1_001_W16_NL

description: exp.csv


title: liver_12mo_acf_tg_3


title: liver_12mo_acf_tg_2


title: NRF1_3D4_NonT

description: ChIP-seq


title: 125_S1_L001_R1_001_W16_NL

description: exp.csv


title: MEN1_2B1

description: ChIP-seq


title: MLLT10_1C10

description: ChIP-seq


title: liver_12mo_wt_1


title: liver_12mo_acf_tg_1


title: 124_S58_L007_R1_001_W4_LS

description: exp.csv


title: 123_S57_L007_R1_001_BL_LS

description: exp.csv


title: hepatocytes_wt_3


title: 122_S10_L002_R1_001_BL_NL

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A8_AD004_indexed


title: hepatocytes_wt_2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A7_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A7_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A7_AD002_indexed


title: hepatocytes_wt_1


title: MED8_1B4

description: ChIP-seq


title: MED8_1A4

description: ChIP-seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A6_AD006_indexed


title: hepatocytes_acf_tg_3


title: 120_S55_L007_R1_001_W16_NL

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A8_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A7_AD012_indexed


title: MED7_1C4

description: ChIP-seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A8_AD007_indexed


title: 12_S12_L003_R1_001_BL_LS

description: exp.csv


title: MED7_1B8

description: ChIP-seq


title: 119_S54_L007_R1_001_W4_LS

description: exp.csv


title: hepatocytes_acf_tg_1


title: MEN1_1H6

description: ChIP-seq


title: MED9_1D6

description: ChIP-seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A7_AD006_indexed


title: MED6_3D10

description: ChIP-seq


title: 118_S53_L007_R1_001_BL_LS

description: exp.csv


title: 121_S56_L007_R1_001_W16_LS

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A5_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A6_AD004_indexed


title: Brg1 KO rep2

city: Boston

first: Manav

last: Gupta

state: MASSACHUSETTS

address: 1 Blackfan Circle

department: Genetics

institute: Harvard University

description:
KO_Ctr_vs_WT_Ctr_DE
KO_Ctr_vs_WT_Ctr_DE_mm_HUGO for GSEA

data_processing:
Illumina HiSeq 2000 40-nt single-ended reads were mapped to the UCSC mm9 mouse genome build (http://genome.ucsc.edu/) using RSEM (v1.2.12) (deweylab.github.io/RSEM) using RSEM’s default Bowtie (v1.0.1) alignment program
RSEM estimated read counts were used to perform pairwise differential gene expression analysis between experimental conditions using EBSeq with median-by-ratio normalization.
Mouse gene symbols were updated to their most-recent nomenclature using data from the Mouse Genome Informatics (MGI) batch query utility (www.informatics.jax.org/batch) and subsequently mapped to orthologous human gene symbols using mouse-human ortholog assignments (www.informatics.jax.org/downloads/reports/index.html) from MGI
The RNA-seq pairwise analysis differential expression signature consisting of genes up-regulated and down-regulated in KO-control versus WT-control conditions was used to score expression profiles.
Ranked gene lists by fold change were analyzed through a pre-ranked gene set enrichment analysis (GSEA) algorithm against Gene Ontology (GO) and Reactome databases using MsigDB (36, 37), using default conditions.
Genome_build: mm9
Supplementary_files_format_and_content: KO_Ctr_vs_WT_Ctr_DE.xlsx:  Strict Open XML Spreadsheet for raw and normalized counts for each sample and each gene (all genes)
Supplementary_files_format_and_content: KO_Ctr_vs_WT_Ctr_DE_FC_1.5_sig.xlsx:  Strict Open XML Spreadsheet for raw and normalized counts for each sample and each gene (FDR < 0.05, FC > 1.5)
Supplementary_files_format_and_content: KO_Ctr_vs_WT_Ctr_DE_mm_HUGO for GSEA.xlsx:  Strict Open XML Spreadsheet for raw and normalized counts for each sample and each gene (pre-ranked gene list for Gene Set Enrichment analysis)
Supplementary_files_format_and_content: Analysis_guide.txt:  Tab-delimited text file showing guide for processed files

source_name: Lung cancer cells

growth_protocol: Lung cancer cell lines grown in adherent plastic dishes in Advanced DMEM medium with 10% FBS, 1% L-Glutamine, and 0.5% Pencillin/Streptomycin

extract_protocol:
Standard RNA extraction protocols
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment. Samples are either Brg1 wildtype or Brg1 knockout.

value: lung adenocarcinoma cells

value: CRISPR/Cas9 - sgBrg1

tag: genotype

value: Brg1 KO


title: Brg1 KO rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A5_AD006_indexed


title: 117_S52_L007_R1_001_BL_NL

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A7_AD008_indexed


title: MED30_1B12

description: ChIP-seq


title: Brg1 KO rep3


title: 116_S51_L007_R1_001_W4_LS

description: exp.csv


title: MED30_1C3

description: ChIP-seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A5_AD012_indexed


title: Brg1 WT rep3

value: CRISPR/Cas9 - sgTomato

value: Brg1 WT


title: hepatocytes_acf_tg_2


title: 115_S50_L006_R1_001_BL_LS

description: exp.csv


title: MED22_2A7

description: ChIP-seq

value: colorectal carcinoma


title: Brg1 WT rep2


title: 114_S49_L006_R1_001_W4_LS

description: exp.csv


title: MED22_1E4

description: ChIP-seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A6_AD002_indexed

value: MOp


title: Brg1 WT rep1


title: 113_S48_L006_R1_001_BL_LS

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A6_AD007_indexed

value: male


title: MED4_1A6

description: ChIP-seq


title: MED21_4F3

description: ChIP-seq


title: 112_S47_L006_R1_001_BL_NL

description: exp.csv


title: MED21_4B5

description: ChIP-seq


title: D18-6298-5-3240A

city: Cambridge

first: Forest

last: White

state: Massachusetts

address: 500 Main Street, MIT Room 76-353

department: Biological Engineering

institute: MIT

data_processing:
Illumina Pipeline version RTA / OLB / CASAVA (v2.8.0 / v1.8.0 / v1.7.0) was used for base calling and trimming adaptor sequences.
Sequenced were mapped to mm10 transcriptome using RSEM (v1.3.0) and STAR (v2.5.3a) with command: rsem-calculate-expression --star -p 16 --output-genome-bam --forward-prob 0
log2 transcripts per million (l2tpm) and comparisons between groups were calculated using DESeq2.
Gene set enrichment and pathway analysis were performed using ssGSEAProjection (v4) and PROGENy web server (v1.0).
Genome_build: mm10
Supplementary_files_format_and_content: Excel table contains read counts and differential expression calculations, ssGSEA, and PROGENy gene pathway analyses.

source_name: hSiglec-5 2xY->F

growth_protocol: BV-2 cells were cultured in a 6-well plate with 5 mL RPMI media (10% FBS + P/S).

extract_protocol:
Cells were lysed after 48 hours in 500 μL TRIzol and pipetted repeated through a P1000 to sheer DNA. RNA was extracted by adding 180 μL chloroform, vortexing for 15 seconds, and then centrifuging at 12,000 g for 15 minutes at 4°C. The top, clear, RNA-containing phase was then transferred to a new tube, mixed 1:1 with 100% Ethanol and purified using a Direct-zol RNA MicroPrep kit.
RNA-seq libraries were prepared from 50 ng of RNA using Kapa mRNA Hyperprep Kits.
RNA-Seq analyses were performed by The MIT BioMicro Center. Library sequencing was multiplexed on two lanes of a HiSeq 2000 (Illumina) using paired-end sequencing for 40 bp.

treatment_protocol: BV-2 cells were transduced with retrovirus to generate stable Siglec expression lines. Cells were split once

tag: passage

value: P10, 1 passage post transduction

value: Human Siglec-5 2xY->F


title: D18-6299-5-3240A

value: Human Siglec-8


title: 111_S46_L006_R1_001_W4_LS

description: exp.csv

value: Placebo

value: LS


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A5_AD010_indexed


title: 110_S45_L006_R1_001_BL_LS

description: exp.csv

value: BL


title: 11_S11_L003_R1_001_BL_NL

description: exp.csv

value: NL


title: D18-6297-5-3240A

source_name: Empty

value: Empty Vector


title: D18-6296-5-3240A

value: Human CD33


title: MED1_1A11

description: ChIP-seq


title: D18-6295-5-3240A


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A5_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A4_AD006_indexed


title: MED1_1A9

description: ChIP-seq


title: LDB1_1C5

description: ChIP-seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A4_AD002_indexed


title: KDM1A_1B2

description: ChIP-seq


title: D18-6294-5-3240A

source_name: mSiglec-F 2xY->F

value: Mouse Siglec-F 2xY->F


title: 108_S43_L006_R1_001_W16_LS

description: exp.csv

value: Secukinumab


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A4_AD001_indexed


title: KDM1A_1A4

description: ChIP-seq


title: D18-6293-5-3240A


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A4_AD010_indexed


title: 107_S42_L005_R1_001_W16_NL

description: exp.csv


title: D18-6292-5-3240A

source_name: hCD33 2xY->F

value: Human CD33 2xY->F


title: KDM1A_1A10

description: ChIP-seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A3_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A4_AD004_indexed


title: 106_S41_L005_R1_001_W4_LS

description: exp.csv


title: 105_S40_L005_R1_001_BL_LS

description: exp.csv


title: JAZF1_1C1

description: ChIP-seq


title: JAZF1_1C2

description: ChIP-seq


title: 109_S44_L006_R1_001_BL_NL

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A3_AD008_indexed


title: D18-1730097-5-3240A

source_name: mSiglec-F

value: Mouse Siglec-F


title: D18-1730098-5-3240A


title: 104_S39_L005_R1_001_BL_NL

description: exp.csv


title: 103_S38_L005_R1_001_W4_LS

description: exp.csv


title: JAZF1_1A5

description: ChIP-seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A3_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A3_AD006_indexed


title: D18-1730093-5-3240A


title: HSF2_2C1_43

description: ChIP-seq

value: One hour heat shock


title: D18-1730094-5-3240A


title: 101_S33_L004_R1_001_BL_NL

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A3_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A3_AD002_indexed


title: HSF2_2C1_37

description: ChIP-seq

value: colorectal carcinoma


title: D18-1730092-5-3240A

value: Human Siglec-5


title: 100_S32_L004_R1_001_W16_LS

description: exp.csv


title: HSF1_1D11_43

description: ChIP-seq


title: D18-1730091-5-3240A


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A3_AD001_indexed

value: MOp

value: male


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A2_AD012_indexed


title: HSF1_1D11_37

description: ChIP-seq


title: D18-1730090-5-3240A

value: P10, 1 passage post transduction


title: 1_S1_L002_R1_001_BL_NL

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A2_AD010_indexed


title: JAZF1_1B8

description: ChIP-seq


title: D18-1730089-5-3240A


title: 102_S37_L005_R1_001_BL_LS

description: exp.csv


title: D18-1730088-5-3240A


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A2_AD007_indexed


title: HSF1_1C1_37

description: ChIP-seq


title: HSF1_1C1_43

description: ChIP-seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A2_AD006_indexed


title: HSF1_1A9_43

description: ChIP-seq


title: HSF1_1A9_37

description: ChIP-seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A2_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A2_AD002_indexed


title: HSF1_1A8_43

description: ChIP-seq


title: 10_S10_L003_R1_001_W16_LS

description: exp.csv


title: HSF1_1A8_37

description: ChIP-seq


title: D18-1730083-5-3240A


title: D18-1730087-5-3240A


title: D18-1730086-5-3240A

source_name: hSiglec-8 2xY->F

value: Human Siglec-8 2xY->F


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A1_AD012_indexed


title: D18-1730082-5-3240A


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A2_AD001_indexed


title: HSF1_1A6_43

description: ChIP-seq


title: HSF1_1A6_37

description: ChIP-seq


title: D18-1730080-5-3240A


title: D18-1730079-5-3240A


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A1_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A11_AD006_indexed


title: D18-1730078-5-3240A


title: D18-1730084-5-3240A

value: Human Siglec-5 2xY->F


title: HSF1_1A10_43

description: ChIP-seq


title: HSF1_1A10_37

description: ChIP-seq


title: Gonadal white adipose tissue, fed, replicate 7

type: RNA

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 2.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

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

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.52.0).

label: biotin

source_name: Gonadal white adipose tissue, fed condition

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

growth_protocol: Animal studies were performed using 3 to 4-month-old pure-bred male mice on a C57Bl/6 background. The study was approved by the Local Animal Ethics Committee of Wageningen University.

extract_protocol: RNA was isolated using Qiagen RNeasy Mini Kit (Qiagen), quantified using NanoDrop, and quality was checked with the Agilent 2100 bioanalyzer (Agilent Technologies). Samples were only included for further analyses in case of intact bands corresponding to 18S and 28S ribosomal subunits and absence of chromosomal peaks or RNA degradation products.

treatment_protocol: Mice were fed, or fasted for 16 hours, prior to sacrifice. Gonadal white adipose tissue was collected for microarray analysis.

tag: sex (female=1, male=0)

value: 3-4 months

tag: nutritional status

value: Fed

tag: moment of sampling

value: morning

value: Gonadal white adipose tissue


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A11_AD004_indexed

tag: age

tag: strain


title: HMG20B_1B5

description: ChIP-seq

tag: cell line


title: Gonadal white adipose tissue, fast, replicate 6

source_name: Gonadal white adipose tissue, after 16hrs of fasting

value: Fast

tag: tissue


title: D18-1730076-5-3240A

tag: treatment

value: Human Siglec-8


title: GTF2H2C_2C9

description: ChIP-seq

tag: cell type

tag: antibody


title: D18-1730077-5-3240A


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A1_AD007_indexed

tag: brain region

tag: Sex


title: Gonadal white adipose tissue, fast, replicate 5


title: Gonadal white adipose tissue, fast, replicate 4


title: Gonadal white adipose tissue, fed, replicate 5


title: D18-1730095-5-3240A


title: Gonadal white adipose tissue, fed, replicate 6


title: Gonadal white adipose tissue, fast, replicate 7


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A1_AD010_indexed


title: Gonadal white adipose tissue, fast, replicate 3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A1_AD006_indexed


title: Gonadal white adipose tissue, fed, replicate 4


title: GTF2F2_1B4

description: ChIP-seq


title: GTF2H2_1B9

description: ChIP-seq


title: D18-1730074-5-3240A


title: D18-1730073-5-3240A


title: D18-1730072-5-3240A

value: Human CD33


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A11_AD010_indexed


title: FOS_1A7

description: ChIP-seq


title: D18-1730071-5-3240A

value: Mouse Siglec-F 2xY->F


title: Gonadal white adipose tissue, fed, replicate 3


title: Gonadal white adipose tissue, fast, replicate 2


title: EZH2_1B3

description: ChIP-seq


title: Gonadal white adipose tissue, fed, replicate 2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A10_AD012_indexed


title: D18-1730070-5-3240A

value: Mouse Siglec-F


title: GTF2F2_1B3

description: ChIP-seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A1_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A10_AD004_indexed


title: D18-1730069-5-3240A

value: Empty Vector


title: 4228_sIRI-sNx

city: Budapest

first: Pál

last: Tod

state: Budapest

address: Szigony utca 43

country: Hungary

institute: Institute of Experimental Medicine

description: Biological replicate 3 of 4 from the sham IRI-sham Nx group, 8 days after the first intervention

hyb_protocol: Hybridization wascarried out according to the miRCURY LNA™ microRNA Array Instruction manual utilizing a Tecan HS4800™ hybridization station (Tecan, Austria)

scan_protocol: Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA)

data_processing:
Image analysis: ImaGene® 9 (miRCURY LNA™ microRNA Array Analysis Software, Exiqon, Denmark)
Quantified signals were background corrected with Normexp method (offset value 10), for normalization the global Lowess (Locally Weighted Scatterplot Smoothing) regression algorithm was used
normalized data matrix contains the log2 normalized Hy3/Hy5 ratio

source_name: sIRI-sNx

label_protocol: Total RNA (750 ng) from both the test and pooled reference samples were labelled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark)

growth_protocol: animal housing: Mice were kept under standard animal-house conditions with free access to standard rodent chow and tap water ad libitum

extract_protocol: Mice were anticoagulated with 10 ml/kg (550 IU/mL) heparin intraperitoneally 2 min prior to cervical dislocation. The post-ischemic or sham operated left kidney was removed, snap frozen in liquid nitrogen and stored at -80°C

treatment_protocol: On day 0 mice were anasthesised with 4 mg/kg ketamine-xylazin. Unilateral IRI was performed using atraumatic vascular clip or sham operation was performed.  7 days later mice were again anasthetised and the contralateral kidney was removed or sham operation was performed. On day 8 all mice were sacrificed.

value: kidney

value: NMRI

tag: gender

value: Male

source_name: kidney pooled reference


title: DPF1_1B6

description: ChIP-seq

value: colorectal carcinoma


title: Gonadal white adipose tissue, fed, replicate 1


title: DPF1_1B3

description: ChIP-seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A11_AD001_indexed

value: MOp

value: male


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A4_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A1_AD001_indexed


title: D18-1730068-5-3240A

value: P10, 1 passage post transduction

value: Human Siglec-8 2xY->F


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A10_AD007_indexed


title: DPF1_1A9

description: ChIP-seq


title: 4227_IRI-Nx

description: Biological replicate 6 of 6 from the IRI-Nx group, 8 days after the first intervention

source_name: IRI-Nx


title: D18-1730067-5-3240A


title: D18-1730066-5-3240A

value: Human Siglec-5 2xY->F


title: D18-1730065-5-3240A

value: Human Siglec-5


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A1_AD002_indexed


title: 4225_IRI-sNx

description: Biological replicate 6 of 6 from the IRI-sham Nx group, 8 days after the first intervention

source_name: IRI-sNx


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A11_AD002_indexed


title: 4226_sIRI-Nx

description: Biological replicate 4 of 4 from the sham IRI-Nx group, 8 days after the first intervention

source_name: sIRI-Nx


title: DNMT3L_1E3

description: ChIP-seq


title: DNMT3A_1E2

description: ChIP-seq


title: DPF1_1A4

description: ChIP-seq


title: 4223_IRI-sNx

description: Biological replicate 4 of 6 from the IRI-sham Nx group, 8 days after the first intervention


title: 4231_sIRI-sNx

description: Biological replicate 4 of 4 from the sham IRI-sham Nx group, 8 days after the first intervention


title: Gonadal white adipose tissue, fast, replicate 1

value: 3-4 months

value: morning

value: Gonadal white adipose tissue


title: 4224_IRI-sNx

description: Biological replicate 5 of 6 from the IRI-sham Nx group, 8 days after the first intervention


title: 4222_IRI-Nx

description: Biological replicate 5 of 6 from the IRI-Nx group, 8 days after the first intervention


title: DCP2_1D6

description: ChIP-seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A10_AD006_indexed

source_name: C57BL/6J Male P56 Mouse Brain


title: D18-1730064-5-3240A

value: Human CD33 2xY->F


title: CXXC1_2D3

description: ChIP-seq


title: D18-1730061-5-3240A


title: 4221_IRI-sNx

description: Biological replicate 3 of 6 from the IRI-sham Nx group, 8 days after the first intervention


title: tet2 -/-_meDIP_rep3

city: North York

first: Vinothkumar

last: Rajan

state: ON

address: 2075 Bayview Ave, Room # M7-413

department: Biological Sciences

country: Canada

institute: Sunnybrook Research Institute

description: methylation

data_processing:
Sequencing reads were aligned to danRer10 zebrafish reference genome using BWA mem v0.7.6 with option -M. Sambamba v0.5.5 was used for bam sorting and duplicates marking.
Bed files were generated using MACS v2.1.2 (https://github.com/taoliu/MACS) with the following parameters: -f BAMPE -q 0.01 -g 1369631918 . Tet2-/- libraries were used as 'treatment' and 'casper control' as control.
Genome_build: danio rerio GRCz10
Supplementary_files_format_and_content: bigwig

organism: Danio rerio

source_name: Kidney Marrow

extract_protocol:
Kidney marrow extracted from adult zebrafish, followed by single-cell suspension generation by vigrous pipetting and passing through 70 micron filter.
Genomic DNA was sonicated to 200bp with a Covaris E220 Focused-ultrasonicator followed by end repair for 30 minutes at room temperature.  A-tailing was performed for 30 minutes at 37°C and adapters were ligated overnight at room temperature.  SPRI bead clean-ups were performed after end repair, a-tailing, and adapter ligation.  Three spike-in DNA controls were used to assess immunoprecipitation (IP) specificity: unmethylated ƛ, fully methylated T7, and fully hydroxymethylated M13.  Spike-in controls were sheared into libraries and adapter ligated as previously described. Spike-in controls were added in a 1:1000 ratio to the sample libraries prior to template denaturation.  100ng (meDIP) and 150ng (hmeDIP) adapter ligated libraries were denatured at 95°C for 10 minutes and snap-cooled on ice for two minutes to allow antigen accessibility.  5ng of each sample library (with spike-in added) was removed and reserved as input (no-IP) control DNA.  Primary IP reactions were performed overnight at 4°C with overhead rotation using anti-5-methylcytosine antibody (Eurogentec BI-MECY-0100) or anti-5-hydroxymethylcytosine antibody (Eurogentec BI-HMCY-0100).  Secondary IP reactions were performed for 2 hours at 4°C with overhead rotation with M-280 sheep anti-mouse Dynabeads (ThermoFisher 11201D).  The library-bound magnetic beads were washed on a magnet six times with IP buffer (10mM Sodium Phosphate buffer, 140mM NaCl, 0.05% Triton X-100) to remove non-specific fragments.  Proteinase K digestion in TE buffer with 0.25% SDS was performed at 55°C for 2 hours with gentle rotation on a Thermomixer (1250 rpm).  Samples were purified with a SPRI bead clean-up and the reserved input (no-IP) control DNA wells were added back to the sample plate before PCR.  To complete library generation, a 7-cycle PCR reaction with Phusion HotStart II DNA Polymerase (ThermoFisher) was performed to add i7 indices and Illumina flow cell adapter sequences.  Qubit High Sensitivity DNA quants, Agilent Bioanalyzer High Sensitivity DNA traces, and qPCR against spike-in controls (unmethylated ƛ, fully methylated T7, and fully hydroxymethylated M13) were used as quality control (QC) metrics to assess the quality of the final libraries.  Libraries that passed QC were pooled and sequenced as paired-end 125nt reads on the Illumina HiSeq 2500 platform.

tag: Stage

value: 3-5 months


title: tet2 -/-_meDIP_rep2

description: methylation


title: D18-1730063-5-3240A

value: Human CD33


title: 4220_sIRI-sNx

description: Biological replicate 2 of 4 from the sham IRI-sham Nx group, 8 days after the first intervention


title: D18-1730059-5-3240A


title: tet2 -/-_meDIP_rep1

description: methylation


title: CXXC1_2C3

description: ChIP-seq

tag: associated input


title: CXXC1_2A7

description: ChIP-seq


title: D18-1730058-5-3240A

value: Human Siglec-8


title: 4117_IRI-sNx

description: Biological replicate 2 of 6 from the IRI-sham Nx group, 8 days after the first intervention

value: kidney


title: CXXC1_2A1

description: ChIP-seq


title: tet2 wt/wt_meDIP_rep3

description: methylation

tag: genotype

value: tet2 wt/wt


title: 4116_IRI-Nx

description: Biological replicate 4 of 6 from the IRI-Nx group, 8 days after the first intervention

value: NMRI

value: Male


title: 4114_sIRI-Nx

description: Biological replicate 3 of 4 from the sham IRI-Nx group, 8 days after the first intervention


title: CXXC1_1E5

description: ChIP-seq

value: colorectal carcinoma


title: tet2 wt/wt_meDIP_rep1

description: methylation


title: tet2 wt/wt_meDIP_rep2

description: methylation


title: CXXC1_1C7

description: ChIP-seq


title: D18-1730053-5-3240A

tag: passage

value: Mouse Siglec-F 2xY->F


title: D18-1730054-5-3240A

value: P10, 1 passage post transduction


title: 4113_IRI-sNx

description: Biological replicate 1 of 6 from the IRI-sham Nx group, 8 days after the first intervention


title: D18-1730052-5-3240A

value: Mouse Siglec-F


title: tet2-/-_hmeDIP_rep3

description: hydroxy methylation


title: CXXC1_1B6

description: ChIP-seq


title: CIZ1_1A2

description: ChIP-seq


title: tet2-/-_hmeDIP_rep2

description: hydroxy methylation


title: D18-1730051-5-3240A

value: Empty Vector


title: 4110_IRI-Nx

description: Biological replicate 3 of 6 from the IRI-Nx group, 8 days after the first intervention


title: 4105_sIRI-Nx

description: Biological replicate 2 of 4 from the sham IRI-Nx group, 8 days after the first intervention


title: tet2 wt/wt_hmeDIP_rep3

description: hydroxy methylation


title: Dicer1-AS

city: Los Angeles

first: Vassilios

last: Papadopoulos

address: 1985 Zonal Avenue

department: Department of Pharmacology and Pharmaceutical Sciences, School of

institute: University of Southern California

data_processing:
A Roche 454 sequencer at the McGill University and Genome Quebec Innovation Centre for B2-AS spesific RNAs or Illumina Casava1.7 software used for basecalling of total RNA samples.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
For the RNA-seq data, the *.BAM files were used as input for further quantification analysis using SeqMonk software packages (http://www.bioinformatics.bbsrc.ac.uk/projects/seqmonk/; Babraham Bioinformatics, Cambridge, UK). The number of reads falling in the exons were counted and normalized by the size of database.
The Base Pair quantitation was used to count the actual number of bases. This gives a more fine grained view of the data.
The Mapping of B2-AS from 454 sequencer was crossinlgy compared with the featured genetic elements of SINE B2.
Genome_build: mm9
Supplementary_files_format_and_content: base pair quantitation counts in text format

source_name: testes

growth_protocol: MA-10 mouse Leydig tumor cells, a gift from Dr. M. Ascoli (University of Iowa), were maintained in Dulbecco modified Eagle medium/Ham F-12 medium supplemented with 5% heat-inactivated fetal bovine serum and 2.5%  horse serum at 37°C and 5% CO2.

extract_protocol:
MA-10 cell lysates were collected and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard 454 sequencer or Illumina protocols

value: MA-10 cells

value: testes

value: Leydig cell tumor

value: WT-with Dicer1 knockdown


title: tet2-/-_hmeDIP_rep1

description: hydroxy methylation


title: CBX5_2A7

description: ChIP-seq


title: 4103_IRI-Nx

description: Biological replicate 1 of 6 from the IRI-Nx group, 8 days after the first intervention


title: WT-MA-10

value: WT


title: 4104_IRI-Nx

description: Biological replicate 2 of 6 from the IRI-Nx group, 8 days after the first intervention


title: tet2 wt/wt_hmeDIP_rep2

description: hydroxy methylation

value: 3-5 months


title: CBX3_2E1

description: ChIP-seq


title: D18-1730056-5-3240A

value: Human Siglec-5


title: CBX5_2D8

description: ChIP-seq


title: 4102_sIRI-sNx

description: Biological replicate 1 of 4 from the sham IRI-sham Nx group, 8 days after the first intervention


title: S34_tumor_3207_wt_2

first: Dylan

middle: Derik

last: Skola

address: 9500 Gilman Dr.

department: Cellular and Molecular Medicine

institute: UCSD

data_processing:
FASTQ files from sequencing experiments were mapped to mouse genome build mm10 using STAR with default parameters.
HOMER was used to convert aligned reads into tag directories for further analysis.
The analyzeRepeats function of HOMER was used to generate a table of read counts for each experiment using the parameters “-raw -count exons -strand both -pc 3  condenseGenes”.
All gene transcripts with length < 250 nt were excluded from further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-separated values (tsv) format containing number of exonic reads in most abundant transcript for each gene in each sample.

source_name: Tumor cells, SRX3207 treated, Syk WT

growth_protocol: LLC cells were obtained from the American Type Culture Collection (ATCC). All cell lines were tested for mycoplasma and mouse pathogens and checked for authenticity against the International Cell Line Authentication Committee (ICLAC; http://iclac.org/databases/cross-contaminations/) list. LLC cells (1 x 105) were injected subcutaneously into syngeneic 4-6 week old mice. Tumors were isolated, minced and then enzymatically dissociated in Hanks Balanced Salt Solution containing 0.5 mg/ml Collagenase IV (Sigma), 0.1 mg/ml Hyaluronidase V (Sigma), 0.6 U/ml Dispase II (Roche) and 0.005 MU/ml DNAse I (Sigma) at 37°C for 30-45 min as described before (12). Cell suspensions were filtered through a 70μm cell strainer and red blood cells were lysed with red cell lysis buffer (Pharm Lyse, BD Biosciences, San Jose, CA). Cells were then washed with PBS and were used for flow cytometry analysis or magnetic bead purification of CD11b, Gr1 or CD90.2 cells (Miltenyi Biotech MACS Microbeads) according to manufacturer’s protocol. Arginase and iNOS activity on sorted macrophages were done as described before (12). For flow cytometry staining, single cells isolated from tumors were incubated with Aqua Live Dead fixable stain (Life Technologies, Carlsbad, CA) followed by FcR-blocking (BD Biosciences, San Jose, CA) and incubation with fluorescently labeled antibodies directed against CD45 (30-F11), CD11b (M1/70), Gr1 (RB6-8C5), F4/80 (BM8), MHC-II (AF6-120.1) from BD Pharmingen.

extract_protocol:
Total RNA was isolated from BMDMs and sorted tumor macrophages using the Qiagen RNAeasy kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions. cDNA was prepared from 1 ug RNA sample using iscript cDNA synthesis kit (Bio-Rad, Hercules, CA). cDNA (2 µL) was amplified by RT-PCR reactions with 1× SYBR green supermix (Bio-Rad, Hercules, CA) in 96-well plates on an CFX96 Real time system (Bio-Rad, Hercules, CA), using the program: 5 min at 95°C, and then 40 cycles of 20 s at 95°C, 1 min at 58°C and 30 sec at 72°C.
For RNA sequencing, RNA libraries were prepared and sequenced using standard Illumina protocols. RNA sequencing was performed by the University of California, San Diego Institute for Genomic Medicine. mRNA profiles were generated by single read deep sequencing, in triplicate, using Illumina HiSeq2000.

treatment_protocol: Mice were treated daily with vehicle or by oral gavage with 10mg/kg SRX3207 (in DMSO, administered intraperitoneally), until tumors were harvested.

value: Tumor cells

tag: stimulation


title: Supt16h Mutant

first: David

last: Traver

state: California

address: 9500 Gilman Drive, MC 0380

department: Division of Biological Sciences

data_processing:
Basecalls were performed using Illumina's CASAVA (v1.8)
Reads were then aligned, assembled, and analyzed for differential expression using the Tuxedo Suite (TopHat [v2.1.1], Cufflinks [v2.2.1], and CummeRbund [v2.7.2])
Assembled transcripts were inputted into the RNAmapper pipeline to map the mutants through linkage analysis of SNP haplotype blocks and identify candidate mutations using the Variant Effect Predictor tool from Ensembl.
A list of candidate SNPs causal for the mutation was then generated using the RNAidentifie.R custom R script.
Genome_build: Zv9
Supplementary_files_format_and_content: Excel file for "Cuffdiff_gene differential expression testing" lists all genes mapped along with their FPKM value, log2(fold_change), and p-value/significance. Excel file for "SnpEff" provides the chromosome, position, and gene for all identified SNPs as well as their variant effect. HTML file provides a complied report of the RNAmapper pipeline identifying the linkage region as well as high impact SNPs and most affected transcripts.

source_name: Whole embryo

growth_protocol: Zebrafish were grown at 28°C and collected at 32hpf

extract_protocol:
Whole embryo was collected and RNA was extracted using TriZol reagent. llumina TruSeq Stranded mRNA Library Prep Kit (Cat# RS-122-2101) was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries were prepared according to Illumina's instructions accompanying the mRNA Sample Kit (Part# 15031047). Briefly, mRNA was purified using poly-T oligo magnetic beads and fragmented. Samples were subjected to first strand cDNA synthesis using SuperScript II, which was then followed by a second strand cDNA synthesis using DNA Pol I and Rnase H. The 3’ ends were then adenylated and adapters are attached. The products were finally purified and PCR amplified to create the final cDNA library. Paired end 50 libraries were sequenced on the Illumina HiSeq2500.

tag: developmental stage

value: whole embryo

value: MUT


title: Wildtype Sibling


title: S33_tumor_3207_wt_1


title: BRWD1_2C12

description: ChIP-seq


title: S32_tumor_vehicle_wt_2

source_name: Tumor cells, vehicle treated, Syk WT

value: SRX3207 Vehicle only


title: mvp-7dpa_rep3

city: Nanjing

first: Yuxi

last: Yang

state: Jiangsu

address: Room 402, 12 Xuefu Road, Nanjing University

department: Medical School

country: China

institute: Nanjing University

data_processing:
Illumina bcl2fastq2-v 2.20.0.422 software was used for base calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Read quality was checked for each sample by using FastQC v 0.11.8.
High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10.
Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0.
Genome_build: GRCz11
Supplementary_files_format_and_content: Tab-delimited text files include raw counts for each sample

source_name: adult heart

extract_protocol:
Sham surgeried and resected zebrafish ventricles were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
NEBNext Single Cell_Low Input RNA Library Prep Kit for Illumina was used with 200 ng of total RNA for the construction of sequencing libraries.

treatment_protocol: Ventricle resection or sham surgeries to wild type and mvp mutant adult zebrafish hearts were perfomed. At 7 days post amputation, ventricle samples below the surgery plane were collected in triplicate.

value: mvp mutant

value: adult heart

value: 7 days post amputation


title: S31_tumor_vehicle_wt_1


title: BRWD1_1E12

description: ChIP-seq

value: colorectal carcinoma


title: mvp-7dpa_rep2


title: S30_TAM_notx_cre_3

source_name: Tumor-associated macrophages, not stimulated, Syk cre

value: Tumor-associated macrophages

value: cre


title: BRD9_1H8

description: ChIP-seq


title: S29_TAM_notx_cre_2


title: mvp-sham_rep2

value: sham


title: S28_TAM_notx_cre_1


title: tet2 wt/wt_hmeDIP_rep1

description: hydroxy methylation

value: tet2 wt/wt


title: mvp-7dpa_rep1


title: BRD3_1D12

description: ChIP-seq


title: BRD1_2B7

description: ChIP-seq


title: mvp-sham_rep3


title: 4101_sIRI-Nx

description: Biological replicate 1 of 4 from the sham IRI-Nx group, 8 days after the first intervention

value: kidney

value: NMRI

value: Male


title: BRD3_1C12

description: ChIP-seq


title: CBX1_1A4

description: ChIP-seq


title: WT-7dpa_rep3

value: wild type


title: S27_TAM_notx_flox_3

source_name: Tumor-associated macrophages, not stimulated, Syk flox

value: flox-flox


title: mvp-sham_rep1


title: BACH1_2G3

description: ChIP-seq


title: WT-7dpa_rep1


title: H9 ESC

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

country: Germany

institute: Universitätsklinikum Düsseldorf

description: Replicate 2

hyb_protocol: Standard Affymetrix hybridization protocol.

scan_protocol: Standard Affymetrix scanning protocol for PrimeView Human Gene Expression Array.

data_processing: The data were normalised using RMA normalisation from R/Bioconductor.

source_name: embryonic stem cells H9

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

growth_protocol: Primary patient-derived cells were cultured as organoids in growth-factor-reduced Matrigel (Corning, phenol red-free) droplets (5,000 cells per 50 µl Matrigel droplet). Matrigel droplets were covered with 500 µl Cancer Stem Cell Medium (CSCM) consisting of Advanced DMEM/F12, 10 mM Hepes, 1% GlutaMAX, B-27 media supplement without retinoic acid, N-2 media supplement, 2 µg/ml Heparin, 1 mM N-Acetylcystein, 50 ng/ml human EGF, 50 ng/ml human FGF2, 10 µM Y-27632 and antibiotics/antimycotics. Medium was changed every other day. After 48 h of culturing, Y-27632 was omitted from the media and antibiotics/ antimycotics treatment was reduced to 100 U/ml Penicillin and 100 µg/ml Streptomycin.

extract_protocol: The RNA was extracted using TRIzol reagent (Thermo Fisher Scientific) and the manufacturer's protocol. The quality of the RNA was checked with a NanodropTM spectrophotometer (Thermo Scientific).

treatment_protocol: For FGFR-inhibition experiments, FGF2 and EGF were omitted from the medium and 10 µM SU-5402 (Sigma) was added. SU-5402 powder was solved in DMSO (30 mM) according to the manufacturer’s protocol and was diluted 1:3,000 for a working concentration. The same DMSO dilution was equally added to control experiments.

value: embryonic stem cells


title: H1 ESC

description: Replicate 1

source_name: embryonic stem cells H1


title: S25_TAM_notx_flox_1


title: BMI1_1H1

description: ChIP-seq


title: BACH1_1A2


title: S26_TAM_notx_flox_2


title: S22_tumor_notx_cre_1

source_name: Tumor cells, not stimulated, Syk cre

value: LLC tumor cells


title: BMI1_1G9

description: ChIP-seq


title: S23_tumor_notx_cre_2


title: S20_tumor_notx_flox_2

source_name: Tumor cells, not stimulated, Syk flox


title: Patient 2 CSC-Media

description: Replicate 4

source_name: colon cancer organoids patient 2

value: colon cancer organoids

tag: patient


title: c-Jun ippt

city: Edmonton

first: Robert

middle: J

last: Ingham

state: Alberta

address: Katz Building

department: Medical Microbiology and Immunology

institute: University of Alberta

description: Karpas 299 is an ALK+ ALCL cell line.

data_processing:
Peak calling was done with MACS 2.1.0. MACS default cutoff is pvalue 1e-7 for narrow peaks and 1e-1 for broad.
Peak filtering was performed by removing false ChIP-Seq peaks as defined within the ENCODE blacklist.
Standard normalization is achieved by down-sampling the usable number of tags for each sample in a group to the level of the sample in the group with the fewest usable number of tags.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig

source_name: ALK+ ALCL tumour

growth_protocol: Karpas 299 cells were grown to exponential phase in RPMI 1640 media supplemented with 10% FBS, 1mM sodium pyruvate, 2mM L-glutamine, and 50uM 2-ME.

extract_protocol:
Lysates were clarified from sonicated nuclei and c-Jun/JunB-DNA complexes were isolated with antibodies.
Libraries were constructed by Active Motif using Illumina sequencing.

value: Karpas 299

tag: chip antibody

value: H-79; Santa Cruz Biotechnology


title: WT-sham_rep3

value: adult heart


title: WT-sham_rep2


title: Patient 4 SU-5402 treated

description: Replicate 2

source_name: colon cancer organoids patient 4

value: colon cancer organoids with FGFR inhibition


title: Patient 3 SU-5402 treated

description: Replicate 1

source_name: colon cancer organoids patient 3


title: Patient 4 CSC-Media

description: Replicate 2


title: Patient 1 SU-5402 treated

description: Replicate 3

source_name: colon cancer organoids patient 1


title: JunB ippt

description: Karpas 299 is an ALK+ ALCL cell line.

value: C37F9 mAb; Cell Signalling Technology


title: WT-sham_rep1


title: S19_tumor_notx_flox_1

tag: strain


title: S18_BMDM_IL4_cre_2

source_name: BMDMs, IL4-stimulated, Syk cre

growth_protocol: Bone marrow-derived macrophages (BMDMs) were generated by flushing the bone marrow cavity with culture media (IMDM, Invitrogen, Rockville, MD). Following centrifugation at 1500 rpm, resuspended cells were lysed in red blood cell lysis buffer (0.155 M ammonium chloride, 0.01 M potassium bicarbonate, and 0.1 M EDTA) and kept at room temperature for 5 min. Following centrifugation, cells were resuspended in macrophage medium (IMDM) supplemented with 20% fetal bovine serum, 1% penicillin/streptomycin, and 50 ng/ml M-CSF. Fibroblasts were allowed to adhere for 4 h at 37 °C, and the nonadherent cells were transferred to another flask. This step was repeated after overnight incubation at 37 °C. On day 8, most of the adhering cells are macrophages (>80% MAC1-positive cells and 100% phagocytic activity via FcγRII/III). All cells were cultured in DMEM media containing 10% FBS.

treatment_protocol: For LPS or IL4 stimulations, on day 7, BMDMs were treated with 100ng/ml of LPS or 20ng/ml IL4 respectively for 10 hrs.

value: Bone-marrow-derived macrophages


title: SUPT16H_3

data_processing:
Illumina Casava1.8 software used for basecalling.
RSeQC and FastQC was used to determine quality control of sequencing data
Reads were aligned using Burrows-Wheeler transformation and mapped using TopHat
Differential expression was calculated using Cufflinks and assessed by DEGseq
Genome_build: GRCz11
Supplementary_files_format_and_content: file containing differential expression data that includes p-value, q-value, and log2FoldChange

source_name: whole embryo

growth_protocol: Embryos grown at 28 degrees celsius and collected at 32 hpf

extract_protocol:
Whole embryos were collected and RNA was harvested using Trizol RNA-extraction
RNA libraries were prepared for sequencing using standard Illumina protocols for the TruSeq Stranded mRNA kit

treatment_protocol: WT vs MUT

tag: age

value: supt16h mutant

value: whole embryo


title: WT-7dpa_rep2

tag: tissue

value: 7 days post amputation


title: S15_BMDM_IL4_flox_2

source_name: BMDMs, IL4-stimulated, Syk flox


title: SUPT16H_1


title: UCH1_K27me3_DMSO_2

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

description: H3K27me3 IP

data_processing:
The ChIP-Rx data was aligned to a concatenated genome sequence of human (GRCh37-hg19) and spike-in of drosophila (BDGP5.25) using bowtie2 with --very-sensitive option. Only uniquely mapped reads and properly-paired reads (for paired-end data) were used for the downstream analysis. PCR duplicates were removed using samtools. Spike-in calibration was performed according to the methodology suggested by (https://doi.org/10.1016/j.molcel.2019.03.024). The replicates were merged using samtools. Genome coverage tracks were obtained for the merged samples using MACS2 pileup function.
Genome_build: human GRCh37-hg19, drosophila (BDGP5.25)
Supplementary_files_format_and_content: Bigwig

source_name: UCH1 chordoma cells

growth_protocol: UCH1 cells were cultured as described previously (doi: 10.1002/path.4729).

extract_protocol:
Cells were fixed in 1% formaldehyde for 10 minutes prior to quenching with excess glycine. Cells were resuspended on ice in a cell lysis buffer (10 mM Tris-HCL, 10 mM Nacl, 0.5 % NP-40, all reagents were from Sigma-Aldrich) for 15 minutes, centrifuged, and resuspended in nuclear lysis buffer (50 mM Tris-HCl, 10 mM EDTA, 1 % SDS, all from Sigma-Aldrich) for 10 minutes.  Samples were diluted with 2 volumes of dilution buffer (16.7 mM Tris-HCL, 167 mM NaCl, 1.2 mM EDTA, 0.01 % SDS, all from Sigma-Aldrich) and sonicated on a Bioruptor Pico (Diagenode, Belgium) for 10 cycles of 30 seconds on/30 seconds off. Sonication efficiency was checked by running a sample of de-crosslinked material on a 2 % agarose gel.
Libraries were prepared using the NEBNext Ultra 2 DNA Library Preparation Kit (New England Biolabs, MA, USA)

treatment_protocol: Cells were treated with KDOBA67 (5 uM) or DMSO (0.1 %, as control) for 48hours.

tag: cell line

value: chordoma

tag: treatment

value: DMSO


title: input control

description: Karpas 299 is an ALK+ ALCL cell line.


title: UCH1_K27me3_KDOBA67_2

description: H3K27me3 IP

tag: cell type


title: SUPT16H_2


title: S16_BMDM_IL4_cre_1

value: cre


title: UCH1_K27me3_KDOBA67_1

description: H3K27me3 IP


title: TCP-replicate3

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C to PrimeView Affymetrix Human Gene Expression Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Data was summarized and normalized with the bioconductor package affy version 1.34.0 running under R version 2.15.0

source_name: Mesenchymal Stem Cells (hMSC)

label_protocol: Biotinylated cDNA were prepared with Nugen Applause kits according to manufacturer's protocols.

growth_protocol: hMSCs were obtained from the Center for the Preparation and Distribution of Adult Stem Cells (medicine.tamhsc.edu/irm/msc-distribution.html) and cultured in complete culture medium (CCM) containing alpha modified Eagle’s medium (αMEM) (Invitrogen, Carlsbad, CA) with 20% lot-selected fetal bovine serum (FBS; Atlanta Biologicals, Lawrenceville, GA), and 1% penicillin-streptomycin (P/S) (Invitrogen) at 37°C in a humidified atmosphere of 5% CO2 at a density of 3,500 cells per cm2.

extract_protocol: RNA was isolated with Qiagen RNAeasy kits.

treatment_protocol: hMSCs were seeded at 3,500 cells per cm2 and cultured for 7 days.  After 7 days medium was switched to CCM with ascorbic acid (50 μM) (Sigma, St. Louis, MO) to enhance matrix production.  After an additional 8 days, plates were washed with PBS and decellularized with 1ml/cm2 of PBS with 0.5 % Triton X- 100 (Sigma) containing 11 mM ammonium hydroxide for 7 minutes at 37 °C.  After repeated washes with PBS plates were dried and then stored at 4 °C until use.  For cross-linker conditions, Sulfo-SANPAH (N-Sulfosuccinimidyl-6-(4’-azido-2’-nitrophenylamino) hexanoate (Thermo Fisher Scientific, Waltham, MA) was diluted in water to 10mM.  Twelve mL was added to each TCP T75 plate and UV incubation was performed for 5 min followed by rinsing with copious amounts of water.  Plates were stored in a humidified environment until addition of hMSCs.

tag: substrate

value: Tissue Culture Plastic


title: S11_BMDM_LPS_cre_2

source_name: BMDMs, LPS-stimulated, Syk cre

value: Lipopolysaccharide


title: Patient 1 CSC-Media

description: Replicate 3


title: TCP-replicate2


title: Patient 3 CSC-Media

description: Replicate 1


title: WT_3

value: WT


title: S10_BMDM_LPS_cre_1


title: WT_2


title: TCP-replicate1


title: hMCS-ECM-replicate1

value: hMSC Depositied ECM


title: UCH1_input_K27me3_KDOBA67_2

description: Input for H3K27me3


title: S12_BMDM_LPS_cre_3


title: UCH1_K27me3_DMSO_1

description: H3K27me3 IP


title: WT_1


title: hMCS-ECM-replicate2


title: S9_BMDM_LPS_flox_3

source_name: BMDMs, LPS-stimulated, Syk flox

value: flox-flox


title: scRNA seq of mus musculus, 10w female bone marrow, vehicle, sorted CD3neg CD19neg [CT26_marrow_veh]

city: Farmington

first: Marmar

last: Moussa

state: CT

address: Farmington

department: School of Medicine

institute: University of Connecticut

data_processing:
10x Genomics pipeline
Genome_build: mm10
Supplementary_files_format_and_content: h5 containing 10x output filtered count matrix

source_name: marrow

extract_protocol:
Single cell suspensions from each sample were prepared from spleen or bone marrow of SNS-ablated or control CT26-bearing wild-type BALB/c mice eighteen days after tumor challenge. Viable, CD3−CD19− cells were sorted on a BD FACSAria II Cell Sorter (BD Biosciences) into RPMI media containing 10% FBS. The cells were washed and resuspended in PBS containing 0.04% BSA, and immediately processed as follows. Cells were counted on a Countess II automated cell counter (ThermoFisher), and 12,000 cells were loaded into one lane of a 10X Chromium microfluidic chip.
Single cell capture, barcoding and library preparation were performed using the 10X Chromium version 3 chemistry, according to the manufacturer’s protocol (#CG000183). cDNA and libraries were checked for quality on an Agilent 4200 TapeStation, quantified by KAPA qPCR, and sequenced on a single lane of a HiSeq4000 (Illumina) to an average depth of 50,000 reads per cell.

treatment_protocol: Wild-type BALB/c mice were injected i.p. with 100 mg/kg 6-hydroxydopamine hydrochloride (Sigma-Aldrich) on Day -4, and 200 mg/kg 6-OHDA on Day -2 and Day 0 to ablate sympathetic nerves. CT26 (5x10^5) cells were implanted intradermally into the right flank four hours after Day 0 6-OHDA injection. Subsequent of injections of 200 mg/kg 6-OHDA or vehicle control were administered every 6 days for the duration of the experiment to maintain sympathetic denervation. Mice were euthanized eighteen days after tumor challenge and spleen and bone marrow were harvested.

value: CT26 tumor-bearing BALB/c

value: 10 weeks

tag: Sex

value: female

value: Bone Marrow

value: Treated with vehicle control

value: FACS-sorted CD3neg CD19neg single cells


title: UCH1_input_K27me3_KDOBA67_1

description: Input for H3K27me3


title: S13_BMDM_IL4_flox_1

value: Bone-marrow-derived macrophages


title: hMCS-ECM-replicate3


title: S8_BMDM_LPS_flox_2


title: UCH1_input_K27me3_DMSO_1

description: Input for H3K27me3


title: hMSC-ECM-Xlink-FN-replicate3

value: hMSC Depositied ECM Plus Crosslinker and Fibronectin


title: hMCS-ECM-FN-replicate2

value: hMSC Depositied ECM Plus Fibronectin


title: hMCS-ECM-FN-replicate1


title: hMCS-ECM-FN-replicate3


title: S7_BMDM_LPS_flox_1


title: UCH1_input_K27me3_DMSO_2

description: Input for H3K27me3

value: chordoma


title: S4_BMDM_NS_cre_1

source_name: BMDMs, not stimulated, Syk cre


title: P0_Chromium_v1_WT_scRNA-Seq

city: Irvine

first: Bogi

last: Andersen

address: 205 Sprague Hall

institute: University of California, Irvine

data_processing:
Alignment of 3’ end counting libraries from droplet-enabled scRNAseq analyses was completed utilizing 10x Genomics Cell Ranger 1.3.1
Each library was aligned to an indexed mm10 genome using Cell Ranger Count. “Cell Ranger Aggr” function was used to normalize the number of confidently mapped reads per cells across the libraries from different samples.
Genome_build: mm10
Supplementary_files_format_and_content: Processed files include the standard 'filtered gene bc matrices' found in the outs folder, which can be easily read into Seurat for analysis.

source_name: Skin

growth_protocol: Mice were housed in animal facility.

extract_protocol:
Normal or Grhl3 -/-  mouse skin were isolated, made into a single cell suspension, and then processed as per 10X Genomics 3' scRNA-Seq v2 protocol.
Cells were washed in PBS with 0.04% BSA and resuspended at a concentration of approximately 1000 cells/µl. Library generation for 10x Genomics v2 chemistry was performed following the Chromium Single Cell Kits User Guide
Quantification of cDNA libraries was performed using Qubit dsDNA HS Assay Kit (Life Technologies Q32851) and high-sensitivity DNA chips (Agilent. 5067-4626). Quantification of library construction was performed using KAPA qPCR (Kapa Biosystems KK4824)

value: Skin

value: All cells from epidermis of skin


title: scRNA seq of mus musculus, 10w female spleen, 6-OHDA, sorted CD3neg CD19neg [CT26_spleen_OHDA]

source_name: spleen

value: Spleen

value: Treated with 6-OHDA


title: P0_KO1_scRNA-Seq

value: KO


title: scRNA seq of mus musculus, 10w female bone marrow, 6-OHDA, sorted CD3neg CD19neg [CT26_marrow_OHDA]


title: scRNA seq of mus musculus, 10w female spleen, vehicle, sorted CD3neg CD19neg [CT26_spleen_veh]


title: UCH1_K4me3_KDOBA67_2

description: H3K4me3 IP


title: S5_BMDM_NS_cre_2

value: cre


title: P0_KO2_scRNA-Seq


title: S6_BMDM_NS_cre_3


title: UCH1_K4me3_KDOBA67_1

description: H3K4me3 IP


title: UCH1_K4me3_DMSO_1

description: H3K4me3 IP

value: DMSO


title: UCH1_input_K4_KDOBA67_1

description: Input for H3K4me3


title: hMSC-ECM-Xlink-FN-replicate2


title: UCH1_input_K4_KDOBA67_2

description: Input for H3K4me3


title: hMSC-ECM-Xlink-replicate3

value: hMSC Depositied ECM plus Crosslinker


title: hMSC-ECM-Xlink-FN-replicate1


title: hMSC-ECM-Xlink-replicate2


title: S1_BMDM_NS_flox_1

source_name: BMDMs, not stimulated, Syk flox

value: flox-flox


title: hMSC-ECM-Xlink-replicate1


title: S2_BMDM_NS_flox_2


title: E16.5_KO2_scRNA-Seq

value: All cells from skin


title: P0_WT2_scRNA-Seq

value: WT


title: E16.5_KO1_scRNA-Seq


title: Total_RNA_LSD1_WT_mES_rep1

city: Ann Arbor

first: Shigeki

last: Iwase

address: 1241 E. Catherine St.

institute: University of Michigan

description: Total RNA

data_processing:
Reads were mapped to mm9 using Tophat 2 (v2.1.0) and Bowtie 2 (v2.2.6) allowing upto two mismatches. Only uniquely mapping reads were analyzed further.
BAM Files were converted to Bigwig files in a strand specific manner using Bedtools v2.25.0. Bigwigs were normalized to 10 million non-rRNA and non-mitochondrial reads.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files represent genome coverage by the reads in a strand specific manner after normalizing to 10 million non-rRNA non-mtRNA reads.

source_name: mouse embryonic stem cells

growth_protocol: mES were cultured on gelatin-coated dishes in high-glucose DMEM containing 15% ES-qualified FBS (Chemicon), 2 mM glutamine, 1 × penicillin-streptomycin, 1 × NEAA, 10 mM HEPES, 143 μM β-mercaptoethanol (Sigma) and 1,000 U ml−1 of LIF (Chemicon) in a humidified incubator at 37°C with 5% CO2. Medium was replaced every day and Trypsin-EDTA was used for dissociation during passaging.

extract_protocol:
Cells or nuclei were dissolved in Trizol and homogenized with a qiashredder.
Direct Ligation of Adaptors to First Strand cDNA (DLAF,PMID: 25607527)
Ribosomal RNA was depleted using Eukaryote Ribominus kit. RNA was reverse-transcribed, treated with RNases, ligated to splinted adaptors, treated with USER and PCR amplified. Libraries were pooled and 280-500 bp fragments were gel purified for sequencing.

treatment_protocol: Nuclei were isolated as described in PMID:21572438 with minor modifications.

tag: strain of origin


title: TCP-Xlink-replicate3

value: Tissue Culture Plastic plus Crosslinker


title: TCP-Xlink-replicate2


title: S3_BMDM_NS_flox_3


title: P0_WT1_scRNA-Seq


title: UCH1_input_K4_DMSO_2

description: Input for H3K4me3


title: UCH1_input_K4_DMSO_1

description: Input for H3K4me3


title: Total_RNA_LSD1_GT_mES_rep2

description: Total RNA


title: E16.5_WT1_scRNA-Seq


title: UCH1_K4me3_DMSO_2

description: H3K4me3 IP


title: Total_RNA_LSD1_WT_mES_rep2

description: Total RNA


title: UCH1_H3K27ac_KDOBA67_3

description: H3K27ac IP


title: UCH1_H3K27ac_KDOBA67_1

description: H3K27ac IP


title: TCP-Xlink-replicate1


title: Total_RNA_LSD1_GT_mES_rep1

description: Total RNA


title: UCH1_H3K27ac_KDOBA67_2

description: H3K27ac IP


title: E14.5_KO2_scRNA-Seq


title: E16.5_WT2_scRNA-Seq


title: UCH1_H3K27ac_DMSO_3

description: H3K27ac IP


title: wdr-23 mutant control RNAi, biological rep2

city: Gainesville

first: Keith

last: Choe

state: Florida

address: 876 Newell Dr, 321 Bartram Hall

institute: University of Florida

description: Gene expression data from wdr-23 worms with control RNAi

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

scan_protocol: GeneChips were scanned using the GeneChip 7G scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Caenorhabditis elegans

source_name: C. elegans wdr-23(tm1718) with control RNAi

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (3’IVT Expression Kit, Affymetrix).

growth_protocol: Worms were grown from the syncrohonized L1 larval stage until the majority were at the L4 larval stage.

extract_protocol: Each replicate contained 200-500 worms that were washed in liquid NGM buffer containing 1% lysogeny broth and total RNA was extracted with an Ambion RNAqueous®-Micro Kit (Austin, TX) according to manufactuer's recommendation.

treatment_protocol: Worms were fed HT115 bacteria containing dsRNA expression plasmids.  Media was standard NGM agar with 0.2% lactose and 50 ug/ml carbenicillin.

value: whole animal

value: wdr-23(tm1718) with control RNAi

value: L4 larval stage


title: Nuclear_RNA_LSD1_WT_mES_rep2

description: Nuclear RNA


title: E14.5_KO1_scRNA-Seq


title: wdr-23 mutant control RNAi, biological rep3


title: UCH1_H3K27ac_DMSO_1

description: H3K27ac IP


title: UCH1_H3K27ac_DMSO_2

description: H3K27ac IP


title: Nuclear_RNA_LSD1_WT_mES_rep1

description: Nuclear RNA


title: wdr-23 mutant control RNAi, biological rep4


title: E14.5_WT1_scRNA-Seq


title: wdr-23 mutant control RNAi, biological rep1


title: wdr-23 mutant skn-1 RNAi, biological rep3

description: Gene expression data from wdr-23 worms with skn-1 RNAi

source_name: C. elegans wdr-23(tm1718) with skn-1 RNAi

value: wdr-23(tm1718) with skn-1 RNAi


title: E14.5_WT2_scRNA-Seq


title: UCH1_H3K9ac_KDOBA67_2

description: H3K9ac IP

value: chordoma


title: Nuclear_RNA_LSD1_GT_mES_rep2

description: Nuclear RNA


title: UCH1_H3K9ac_KDOBA67_1

description: H3K9ac IP


title: Nuclear_RNA_KDM5C_WT_mES_rep1

description: Nuclear RNA

value: 129S1/SvImJ + C57BL/6J


title: UCH1_H3K9ac_KDOBA67_3

description: H3K9ac IP


title: Nuclear_RNA_LSD1_GT_mES_rep1

description: Nuclear RNA


title: BPI-10

city: Chapel Hill

first: Samir

last: Kelada

state: NC

address: 120 Mason Farm Road GMB 5007

institute: University of North Carolina at Chapel Hill

data_processing:
Quality control with FastQC and MultiQC
Reads aligned to genome with STAR version 2.6.0
Alignments quantified with Salmon version 0.9.1
Genome_build: mm10/GRCm38 Gencode version M18
Supplementary_files_format_and_content: Unnormalized counts from Salmon quant.sf files using R/tximport (1.14.0) i.e. txi$counts

source_name: whole lung (right middle lobe)

growth_protocol: Mice were housed on alpha-dri bedding. Genotypes were mixed within cages

extract_protocol:
RNA was isolated using QIAGEN RNAeasy kit according to manufacturers protocol
2ug of RNA per sample was provided for library preparation. Libraries were prepared by the University of North Carolina High Throughput Sequencing Facility using the KAPA Stranded  mRNA library prep kit (Roche).
Samples were sequenced on an Illunina HS4000; 50bp single end reads; 20 million reads/sample

treatment_protocol: No treatment.

tag: strain background

tag: condition

value: naïve

value: Female

value: 12 weeks


title: BPI-6

tag: genotype

value: Male


title: UCH1_H3K9ac_DMSO_3

description: H3K9ac IP


title: BPI-5

value: KO


title: Nuclear_RNA_KDM5C_WT_mES_rep2

description: Nuclear RNA


title: BPI-9


title: UCH1_H3K9ac_DMSO_1

description: H3K9ac IP

value: DMSO


title: BPI-3


title: BPI-8


title: wdr-23 mutant skn-1 RNAi, biological rep1


title: placentome_cortisol_140d_ replicate 2

first: Maureen

last: Keller-Wood

address: 1225 Center Dr

department: Pharmacodynamics

description: Gene expression at 140 days gestation

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >8.3 pmol Cy3/µg cRNA) was  fragmented and hybridized to Agilent Sheep Oligo Microarrays (G4813A) by the ICBR facility at the University of Florida according to Agilent's methodology.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2505B) using one color (green) scan setting for 8x15k array slides, by the ICBR facility at University of Florida.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.1.1.1 (Agilent) using default parameters (protocol GE1-v5_10 and Grid: 019921_D_F_20100112)  background detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data were normalized to the chip median and log transformed.

organism: Ovis aries

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng RNA using the One-Color Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Continuous infusions of cortisol to the ewe were begun at approximately day 115 of gestation

extract_protocol: RNA was extracted with Trizol (Life Technologies, Carlsbad, CA), and purified through Qiagen Rneasy+ kits with on-column DNase digestion (QIAGEN, Valencia, CA) according to manufacturers' protocols.Total RNA concentration was measured by Nanodrop ND-1000 and RNA quality was monitored by Agilent Bioanalyzer

treatment_protocol: Ewes were infused with 1mg/kg/day cortisol or vehicle from approximately day 115 to 140 d of pregnancy (n=7, cortisol; n=77control). Placentomes (n=7 control, n=5 cortisol) were  collected and RNA extracted.

value: placentome

tag: treatment group

value: cortisol


title: placentome_cortisol_140d_ replicate 4

description: Gene expression at 140 days gestation


title: placentome_cortisol_140d_ replicate 3

description: Gene expression at 140 days gestation


title: wdr-23 mutant skn-1 RNAi, biological rep2


title: Nuclear_RNA_KDM5C_KO_mES_rep2

description: Nuclear RNA


title: N2 control RNAi, biological rep3

description: Gene expression data from wildtype

source_name: C. elegans N2 with control RNAi

value: N2 with control RNAi


title: placentome_cortisol_140d_ replicate 1

description: Gene expression at 140 days gestation


title: N2 control RNAi, biological rep2

description: Gene expression data from wildtype


title: placentome_control_140d_ replicate 7

description: Gene expression at 140 days gestation

value: control


title: UCH1_input_ac_DMSO_2

description: Input for H3K27ac and H3K9ac


title: Input_LSD1_GT_mES_rep2

description: Lsd1-GT mES

data_processing:
Full length reads were mapped to mm9 using Bowtie (v1.1.2)
PCR-duplicates were removed.
For conversion to bigwig files, reads were extended to a total length of 180 bases from the first sequenced base. Libraries were normalized to 1 million reads.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files represent genome coverage after normalizing to 1 million reads.

extract_protocol:
Sonicated chromatin was immunoprecipitated overnight with antibodies immobilized on Dynabeads Protein G.
Illumina TruSeq DNA Library Prep
ChIP-DNA was deproteinized, treated with Rnase-A, 3' end-repaired with T4 DNA polymerase and T4 Polynucleotide Kinase, 3' dA-tailed, ligated to adaptors, size selected and PCR amplified. Libraries were pooled and 280-600 bp were gel purified for sequencing.

treatment_protocol: Cells were crosslinked on plates for 30min at 37C. Cells were washed and lysed. Nuclei were sonicated on ice with a micro-tip of Branson Sonifier S-450 for 30 cycles (20 sec ON and 40 sec OFF)


title: BPI-7


title: N2 control RNAi, biological rep1

description: Gene expression data from wildtype


title: UCH1_input_ac_DMSO_3

description: Input for H3K27ac and H3K9ac


title: Nuclear_RNA_KDM5C_KO_mES_rep1

description: Nuclear RNA


title: UCH1_H3K9ac_DMSO_2

description: H3K9ac IP


title: KDM5C_KDM5C_WT_mES_rep2

description: KDM5c WT mES


title: KDM5C_KDM5C_WT_mES_rep1

description: KDM5c WT mES


title: BPI-4

value: WT


title: placentome_cortisol_140d_ replicate 5

description: Gene expression at 140 days gestation


title: HDAC1_SCBT_LSD1_WT_mES_rep1

description: Lsd1-WT mES

value: Santa Cruz sc-6298


title: Failed Ventricle 4 CAGE-Seq

city: Chicago

first: Anthony

middle: Martin

last: Gacita

address: 303 E Superior St. Lurie 7-240

department: Center for Genetic Medicine

institute: Northwestern Univeristy Feinberg School of Medicine

description:
CAGE-seq from Failed Left Ventricle Tissue
Promoter_Table_All_Info.txt
Enhancer_Table_All_Info.txt
TRID74_CAGE-seq

data_processing:
RNA-Seq (CAGE)
Reads were aligned to hg19 using STAR (v2.5.2)
CAGEr was used to find CAGE-tag transcriptional start sites
CAGEfightR was used to cluster singals and do downstream analysis
See publication for detailed data processing steps
Genome_build: hg19
Supplementary_files_format_and_content: Promoter_Table_All_Info.txt contains all of the information for promoter clusters
Supplementary_files_format_and_content: Enhancer_Table_All_Info.txt contains all of the information for enhancer clusters
RNA-Seq
Reads were trimmed with trimmomatic
Reads were aligned to hg19 using STAR (v2.5.2)
HT-seq Count was used to assign reads to transcripts.
EdgeR was used to normalize counts calculate differential expression.
Differentially expressed genes were filtered for an FDR p-value < 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: RNA_Seq_Differential_Genes.txt contains statistics for differential gene expression as outputted by EdgeR.

source_name: Human Left Ventrice Tissue

extract_protocol:
RNA was extracted from tissue using TRIzol and the Aurum Total RNA Mini Kit (Bio-Rad, Hercules, CA; 7326820).
nAnT-iCAGE (DNAFORM)

tag: phenotype

value: Heart Failure


title: HDAC1_SCBT_LSD1_GT_mES_rep1

description: Lsd1-GT mES


title: HDAC1_Bethyl_LSD1_WT_mES_rep1

description: Lsd1-WT mES

value: Bethyl A300-713A


title: Failed Ventricle 3 CAGE-Seq

description:
CAGE-seq from Failed Left Ventricle Tissue
Promoter_Table_All_Info.txt
Enhancer_Table_All_Info.txt
TRID60_CAGE-seq


title: Input_LSD1_WT_mES_rep2

description: Lsd1-WT mES


title: UCH1_input_ac_KDOBA67_2

description: Input for H3K27ac and H3K9ac


title: UCH1_input_ac_KDOBA67_3

description: Input for H3K27ac and H3K9ac


title: Input_LSD1_WT_mES_rep1

description: Lsd1-WT mES


title: BPI-2


title: UCH1_input_ac_KDOBA67_1

description: Input for H3K27ac and H3K9ac


title: placentome_control_140d_ replicate 3

description: Gene expression at 140 days gestation


title: HDAC1_Bethyl_LSD1_GT_mES_rep1

description: Lsd1-GT mES


title: A2ARKO2

city: New York

first: Zhi

last: Li

address: 435 East 30th St, 9th Floor  New York, NY 10016

institute: NYU School of Medicine

description: transcriptome

data_processing:
Alignment with Star
Quantification with HT-seq
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Phenotype confirmed global A2AR KO on C57BL/6 background

growth_protocol: Adenosine A2A receptor knockout (A2ARKO) mice, bred on a C57BL/6 background (referred to here as wild type, WT) were bred and raised in the same facility (Science Building Animal Facility, NYU Langone Medical Center), receiving the same food and care.

extract_protocol: RNA was extracted from pooled chondrocytes harvested from entire litters of either WT of A2ARKO animals. RNA was extracted from trypsinized primary cells using QUIAGEN’s RNeasy Mini Kit (cat. No. 74104) according to manufacturer’s instructions. Three (3) litters of WT and A2ARKO were processed and submitted for RNA sequencing, namely WT1-3 and A2ARKO1-3. Isolated RNA was submitted to and processed by the Genome Technology Center (GTC) at NYU Langone Health using Illumina HiSeq 4000 to acquire chondrocytes transcriptome.

value: Primary chondrocytes

tag: genotype/variation

value: A2AR KO


title: BPI-1


title: HTLV-1-infected cell line_KK-1

type: genomic

city: Saga

first: Tatsuro

last: Watanabe

state: Saga

address: 5-1-1 Nabeshima, Saga

country: Japan

institute: Saga University

description:
KK-1
Cell line, T-cells

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 or HumanMethylationEPIC Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).

data_processing:
Genome Studio software (V2011.1 Methylation module 1.9.0) was used. Beta values were obtained after background correction and normalization to internal controls.
The GSE136189_GPL13534_beta_and_raw_data.txt and GSE136189_GPL23976_beta_and_raw_data.txt files include normalized Beta values, unmethylated signal intensities, methylated signal intensitites, and detection p-values.

label: Cy5 and Cy3

source_name: T-cell 34

label_protocol: Standard Illumina Protocol.

growth_protocol: RPMI-1640 containing 10% FBS and Pen/Str was used for T-cell lines.

extract_protocol: Genomic DNA samples were isolated using QIAamp DNA Kit (Qiagen).

value: T cells


title: TCDD59

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

institute: Michigan State University

description: nuclear RNA

data_processing:
Following sequencing quality control, CellRanger v3.0.2 (10X Genomics) was used to align reads to a custom reference genome which included introns and exons to consider pre-mRNA and mature mRNA present in the nuclei.
Raw counts were further analysed using Seurat v3.1.1. Each sample was filtered for (i) genes expressed in at least 3 nuclei, (ii) nuclei which express at least 100 genes, and (iii) ≤1% mitochondrial genes.
Additional quality control was performed using the scater package (v1.10.1). The DoubletFinder v2.0.2 package excluded putative doublets from subsequent analyses.
Clustering of nuclei was performed using Seurat integration tools at a resolution of 0.2
Genome_build: mm10 release 93
Supplementary_files_format_and_content: Processed data files for individual sample are CellRanger filtered_feature_bc_matrix outputs which includes barcodes (barcodes.tsv.gz),  features (features.tsv.gz), and the matrix (matrix.mtx.gz).
Supplementary_files_format_and_content: RData file represents the full processed Seurat R data object generated using Seurat v3.1.

source_name: Liver

extract_protocol:
Nuclei were isolated from frozen liver samples (~200mg) as previously described (dx.doi.org/10.17504/protocols.io.3fkgjkw). Briefly, livers were diced in EZ Lysis Buffer (Sigma-Aldrich), homogenized using a disposable dounce homogenizer, and incubated on ice for 5 minutes. The homogenate was filtered using a 70 μm cell strainer, transferred to microcentrifuge tube, and centrifuged at 500 x g and 4°C for 5 minutes. The supernatant was removed and fresh EZ lysis buffer was added for an additional 5 minutes on ice following by centrifugation at 500 x g and 4°C for 5 minutes. The nuclei pellet was washed twice in nuclei wash and resuspend buffer (1X PBS, 1% BSA, 0.2 U/μL RNAse inhibitor) with 5 minute incubations on ice. Following the washes, the nuclei pellet was resuspended in nuclei wash and resuspend buffer containing DAPI (10 μg/mL). The resuspended nuclei were filtered with 40 μm strainer and immediately underwent fluorescence activated cell sorting (FACS) using a BD FACSAria IIu (BD Biosciences, San Jose, CA) with 70 μm nozzle.
Libraries were prepared using the 10X Genomics Chromium Single Cell 3’ v3 kit (10X Genomics)

treatment_protocol: Mice were orally gavaged with sesame oil vehicle control or 30 µg/kg TCDD every 4 days for 28 days.

value: day

value: degree celsius

value: percent

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad

tag: vendor

value: Accustandard

value: sesame oil

value: oral gavage

tag: dose

value: microgram per kilogram

tag: batch


title: H3K4me3_LSD1_WT_mES_rep2

description: Lsd1-WT mES

tag: strain

tag: chip antibody

value: Millipore 04-745


title: H3K4me3_LSD1_WT_mES_rep1

description: Lsd1-WT mES


title: Healthy Ventricle 3 CAGE-Seq

description:
CAGE-seq from Healthy Left Ventricle Tissue
Promoter_Table_All_Info.txt
Enhancer_Table_All_Info.txt
LV7_CAGE-seq

value: Healthy


title: Input_LSD1_GT_mES_rep1

description: Lsd1-GT mES


title: UCH1_input_ac_DMSO_1

description: Input for H3K27ac and H3K9ac

source_name: UCH1 chordoma cells

tag: cell line

tag: cell type

value: chordoma

tag: treatment

value: DMSO


title: Healthy Ventricle 2 CAGE-Seq

description:
CAGE-seq from Healthy Left Ventricle Tissue
Promoter_Table_All_Info.txt
Enhancer_Table_All_Info.txt
LV6_CAGE-seq


title: TCDD51

description: nuclear RNA

tag: Sex

value: Male

value: 10X Genomics Chromium Single Cell 3’ v3 kit


title: H3K4me3_LSD1_GT_mES_rep2

description: Lsd1-GT mES

tag: strain of origin


title: HTLV-1-infected cell line_ST-1

description:
ST-1
Cell line, T-cells

source_name: T-cell 32

value: T cells


title: placentome_control_140d_ replicate 5

description: Gene expression at 140 days gestation

tag: tissue

value: placentome

value: control


title: HTLV-1-infected cell line_ATN-1

description:
ATN-1
Cell line, T-cells

source_name: T-cell 31


title: WT2

description: transcriptome

tag: strain background

value: Primary chondrocytes

value: WT


title: VEH62

description: nuclear RNA

value: day

value: degree celsius

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Aquavive water (Innovive)

value: Harlan Teklad 22/5 Rodent Diet 8940


title: VEH64

description: nuclear RNA

value: Harlan Teklad

value: Accustandard

value: sesame oil

value: oral gavage

value: microgram per kilogram


title: placentome_control_140d_ replicate 4

description: Gene expression at 140 days gestation

tag: treatment group


title: placentome_control_140d_ replicate 6

description: Gene expression at 140 days gestation


title: WT1

description: transcriptome


title: Healthy Ventricle 1 CAGE-Seq

description:
CAGE-seq from Healthy Left Ventricle Tissue
Promoter_Table_All_Info.txt
Enhancer_Table_All_Info.txt
LV5_CAGE-seq

tag: phenotype

value: Healthy


title: Failed Ventricle 2 CAGE-Seq

description:
CAGE-seq from Failed Left Ventricle Tissue
Promoter_Table_All_Info.txt
Enhancer_Table_All_Info.txt
TRID53_CAGE-seq

value: Heart Failure


title: A2ARKO3

description: transcriptome

tag: genotype/variation

value: A2AR KO


title: i32-UCH1-DMSO-1-48h-r1_S20

data_processing:
Analysis of the data was performed using CGAT tools and pipelines (https://github.com/cgat-developers)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using hisat2 v2.1.0 with parameters --score-min L,0.0,-0.2
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files of read counts for each sample

source_name: Chordoma cell line

extract_protocol:
RNA from cells was harvested using Trizol reagent. Libraries were constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®
RNA libraries were prepared for sequencing using standard NEB protocols

value: DMSO

tag: donor

tag: time


title: HTLV-1-infected cell line_KOB

description:
KOB
Cell line, T-cells

source_name: T-cell 33

value: KOB

value: T cells


title: A2ARKO1

description: transcriptome

value: Primary chondrocytes


title: T-cells_(CD3+/CD4+/CD7-/CADM1+)_acute ATL_3

description:
A3_N
Clinical specimen, T-cells

source_name: T-cell 28

tag: diagnosis

value: Acute ATL

tag: gender

value: Male

tag: age

tag: wbc (/ul)

tag: lym (%)

value: Unmeasurable

tag: abn. lym (%)

tag: sil-2r (u/ml)


title: i31-UCH1-ISRIB-KDO-3-48h-r1_S19

tag: treatment

tag: cell line


title: T-cells_(CD3+/CD4+/CD7-/CADM1+)_acute ATL_2

description:
A2_N
Clinical specimen, T-cells

source_name: T-cell 27

tag: cell type

value: Female


title: WT3

description: transcriptome

tag: tissue

value: WT


title: T-cells_(CD3+/CD4+/CD7-/CADM1+)_acute ATL_1

description:
A1_N
Clinical specimen, T-cells

source_name: T-cell 26


title: H3K4me3_LSD1_GT_mES_rep1

description: Lsd1-GT mES

source_name: mouse embryonic stem cells

tag: strain

tag: strain of origin

tag: chip antibody

value: Millipore 04-745


title: placentome_control_140d_ replicate 2

description: Gene expression at 140 days gestation

value: placentome

tag: treatment group

value: control


title: placentome_control_140d_ replicate 1

description: Gene expression at 140 days gestation


title: Failed Ventricle 1 CAGE-Seq

description:
CAGE-seq from Failed Left Ventricle Tissue
Promoter_Table_All_Info.txt
Enhancer_Table_All_Info.txt
TRID33_CAGE-seq

tag: phenotype


title: i34-UCH1-DMSO-3-48h-r1_S22

tag: donor

tag: time


title: H3K4me2_LSD1_GT_mES_rep2

description: Lsd1-GT mES

value: Millipore 05-790


title: Con MII rep 2

city: beijing

first: Qian

last: Zhou

state: china

address: Chao Yang Qu,  Zhong Guo Ke Xue Yuan Da Xue

institute: institute of zoology, Chinese academy of sciences

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2
The read counts were summed by Htseq software and gene differential analysis was performed by edgeR R package
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values of gene for each Sample

source_name: mouse oocyte

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: wildtype

tag: Stage

value: MII

value: oocyte


title: H3K4me1_LSD1_WT_mES_rep2

description: Lsd1-WT mES

value: Millipore 07-436


title: i33-UCH1-DMSO-2-48h-r1_S21

value: DMSO


title: i28-UCH1-KDO-3-48h-r1_S16


title: HTLV-1-infected cell line_MT-2

description:
MT-2
Cell line, T-cells

source_name: T-cell 30


title: H3K4me2_LSD1_WT_mES_rep1

description: Lsd1-WT mES


title: HTLV-1-infected cell line_MT-1

description:
MT-1
Cell line, T-cells

source_name: T-cell 29


title: BAF250aGKO MII rep 2


title: BAF250aGKO MII rep 1


title: H3K4me1_LSD1_WT_mES_rep1

description: Lsd1-WT mES

value: Abcam ab8895


title: BAF250aGKO GV rep 2

value: GV


title: BAF250aGKO GV rep 1


title: i30-UCH1-ISRIB-KDO-2-48h-r1_S18


title: H3K4me2_LSD1_GT_mES_rep1

description: Lsd1-GT mES


title: H3K4me2_LSD1_WT_mES_rep2

description: Lsd1-WT mES


title: H3K4me2_KDM5C_WT_mES_rep1

description: KDM5c WT mES

value: 129S1/SvImJ + C57BL/6J


title: T-cells_(CD3+/CD4+/CD7dimly+/CADM1+)_chronic ATL_4

description:
C4_D
Clinical specimen, T-cells

source_name: T-cell 24

tag: diagnosis

value: Chronic ATL

value: T cells

tag: gender

tag: age

tag: wbc (/ul)


title: Con MII rep 1


title: i29-UCH1-ISRIB-KDO-1-48h-r1_S17

tag: treatment


title: i27-UCH1-KDO-2-48h-r1_S15

tag: cell line


title: T-cells_(CD3+/CD4+/CD7-/CADM1+)_chronic ATL_4

description:
C4_N
Clinical specimen, T-cells

source_name: T-cell 25

tag: cell type

tag: lym (%)

tag: abn. lym (%)

tag: sil-2r (u/ml)


title: T-cells_(CD3+/CD4+/CD7+/CADM1-)_chronic ATL_4

description:
C4_P
Clinical specimen, T-cells

source_name: T-cell 23


title: T-cells_(CD3+/CD4+/CD7-/CADM1+)_chronic ATL_3

description:
C3_N
Clinical specimen, T-cells

source_name: T-cell 22

value: Male


title: Con GV rep 1

tag: strain

tag: tissue


title: i26-UCH1-KDO-1-48h-r1_S14


title: i25-UCH1-ISRIB-3-48h-r1_S13

value: ISRIB+DMSO


title: T-cells_(CD3+/CD4+/CD7dimly+/CADM1+)_chronic ATL_3

description:
C3_D
Clinical specimen, T-cells

source_name: T-cell 21


title: Con GV rep 2


title: i24-UCH1-ISRIB-2-48h-r1_S12


title: H3K4me1_LSD1_GT_mES_rep1

description: Lsd1-GT mES

tag: strain of origin

tag: chip antibody


title: H3K4me1_LSD1_GT_mES_rep2

description: Lsd1-GT mES


title: H3K27ac_LSD1_WT_mES_rep2

description: Lsd1-WT mES

value: Active Motif 39135


title: T-cells_(CD3+/CD4+/CD7+/CADM1-)_chronic ATL_3

description:
C3_P
Clinical specimen, T-cells

source_name: T-cell 20


title: H3K27ac_LSD1_WT_mES_rep1

description: Lsd1-WT mES


title: T-cells_(CD3+/CD4+/CD7-/CADM1+)_chronic ATL_2

description:
C2_N
Clinical specimen, T-cells

source_name: T-cell 19

value: Female


title: WGBS_Tumor_Lo_6

city: Vienna

first: Hana

last: Imrichova

address: Lazarettgasse 14, AKH BT 25.3

country: Austria

institute: CeMM, Vienna

data_processing:
Bisulfite alignment of the WGBS reads to the mm10/GRCm38 assembly of the mouse reference genome and methylation calling was performed using gemBS (version 3.3.0) (https://doi.org/10.1093/bioinformatics/bty690) with the following parameters: sampling_rate = 4, non_stranded = False, remove_individual_bams = True, mapq_threshold = 10, qual_threshold = 13, reference_bias = 2, left_trim = 5, right_trim = 0, keep_improper_pairs = True, keep_duplicates = False, haploid = False, conversion = auto, remove_individual_bcfs = True, contig_pool_limit = 100000000, phred_threshold = 10.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: *bed: Bed files include CpG methylation calls for each sample.

source_name: CD8+ T cells

growth_protocol: TILs were isolated from Yumm1.7 melanoma tumors 18 days after engraftment based on mitotracker staining.

extract_protocol: None provided

value: CD8+ intratumoral T cells (in vivo FACS purified cells)


title: H3K27ac_LSD1_GT_mES_rep1

description: Lsd1-GT mES


title: H3K27ac_KDM5C_WT_mES_rep1

description: KDM5c WT mES


title: WGBS_Tumor_Hi_4


title: H3K27ac_LSD1_GT_mES_rep2

description: Lsd1-GT mES


title: ATAC_Tumor_Lo_2

data_processing:
Conversion and demultiplexing: IlluminaBasecallsToMultiplexSam to generate one bam file per lane from the data on the Illumina machine, IlluminaSamDemux to demultiplex the bam file into multiple samples (https://github.com/DanieleBarreca/picard).
Trimming: Trimmomatic (version 0.32).
Alignment: Bowtie2 (version 2.2.4) with the ‘very-sensitive-local’ parameter, later duplicate reads were removed using sambamba markdup (version 0.5.5) and only primary alignments with mapping quality >30 were retained.
Peak calling: Peaks were called using MACS2 (version 2.1.1.20160309) on each individual sample using the function callpeak with narrow peak setting (using the --nomodel --extsize 147 --p 1e-09 parameters). Peaks overlapping with blacklisted regions (downloaded from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/) were discarded.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: bigWig generation: Coverage files were generated from reads extended to 130bp using bedtools (version 2.26.0), using the following command: bamtobed | slop -s -l 0 -r 130 | genomeCoverageBed -bg. bigWig files containing counts of reads per basepair per million were created by the UCSC Genome Browser’s bedGraphToBigWig tool.

growth_protocol: TILs were isolated from Yumm1.7 melanoma tumors 18 days after engraftment based on mitotracker staining. In vitro-generated CD8 T cells were activated from OT-1 splenocytes.

extract_protocol: DNA were collected by Qiagen MinElute kit.

treatment_protocol: In vitro-generated CD8 T cells were treated with Oligomycin A and Mdivi-1 for 6 hours followed by the collection of MDR/MG-Hi and -Lo population.