title: Ecoli_P2_T3_kinetic1

description: Cells were in P2 phase (glucose exhaustion), the sampling was performed 3 min after rifampicin addition. It is the first kinetics out of 3 for this phase

source_name: E. coli in P2 phase, Sampling 3 minutes after rifampicin addition in kinetic 1


title: Foxp3-GFP+Treg_BACH2-RFP_LO_Male2_RNA-seq

status: Public on May 12 2020

type: SRA

city: Cambridge

first: Mohammed-Firas

last: Sadiyah

address: The Old Schools, Trinity Ln

country: United Kingdom

institute: University of Cambridge

library_source: transcriptomic

data_processing:
FastQ files underwent quality control with FastQC, adaptor trimming with Cutadapt and alignment to the NCBIM37 Mus musculus genome annotation with hisat2 using ClusterFlow pipelines
Differential gene expression analysis was performed using Cufflinks44 and differentially expressed genes were futher analysed using R
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values

molecule: total RNA

organism: Mus musculus

source_name: Treg cells

extract_protocol:
Single-cell suspensions were purified by total CD4+ T cell enrichment followed by FACS-sorting
stored in 40 µl RNAlater™ Stabilization Solution at -80 °C
Samples were processed using the QIAshredder Kit (Qiagen) according to the manufacturer’s protocol
RNA was extracted from samples using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s protocol
RNA Libraries were prepared using the SmartSeq2 protocol on an automated Hamilton NGS-STAR library preparation system and sequenced using a HiSeq 2500 System (Illumina)

tag: strain

tag: tissue

value: spleen

tag: age

value: post natal 12–13 weeks

tag: genotype

value: Foxp3EGFP-DTR Bach2tdRFP/+


title: Ecoli_P2_T1.5_kinetic1

type: RNA

city: Toulouse

first: Laurence

last: Girbal

address: 135 avenue de rangueil

country: France

institute: TBI

description: Cells were in P2 phase (glucose exhaustion), the sampling was performed 1.5 min after rifampicin addition. It is the first kinetics out of 3 for this phase

hyb_protocol: According to manufacturer instructions, 2 µg of labeled cDNA were hybridized onto E. coli K-12 gene expression arrays (Nimblegen, Roche) during 17 h at 42 °C.

scan_protocol: Arrays were later washed and scanned using MS200 Microarray Scanner (Nimblegen, Roche). Pictures were analyzed with DEVA 1.2.1 software.

data_processing: Raw probe intensities ( .pair files three replicates for each strain before and after transcription arrest by rifampicin addition) were processed and analyzed with R computing environment using the affy and limma package of Bioconductor. Twelve arrays (three reference T0 samples, and nine time points after addition of rifampicin) were used for P2 and P4 and eleven arrays (three reference T0 samples, and eight time points after addition of rifampicin) were used for P3. Only a normalization between arrays according to an invariant probeset intensities was performed. For each growth condition, a set of probes in the background for which the ranks were roughly invariant across all arrays was selected. The median value of the invariant probe set intensities was used as a scaling factor for normalization between the growth conditions. After normalization, the intensity of a transcript was calculated by a RMA-summarization procedure [Irizarry et al, 2003, Biostatistics 4(2): 249-264] within each condition.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli in P2 phase, Sampling 1.5 minute after rifampicin addition in kinetic 1

label_protocol: According to manufacturer instructions, 1 µg of cDNA was labeled using one color DNA labeling kit

growth_protocol: The laboratory strain E. coli K12 MG1655 was grown in bioreactors in M9 glucose (3g/l) at 37 °C. The pH was set to 7. All cultures were inoculated at OD 0.2 from overnight pre-cultures performed in similar conditions. Biomass was estimated from absorbance at 600 nm. Each culture was repeated three times to provide independent biological kinetics.

extract_protocol: After thawing and centrifugation steps, total RNA was extracted with TRIZOL® Reagent (Ambion) according to the manufacturer’s instructions. DNA contamination was eliminated with Turbo DNase kit (Ambion). Total RNA concentration and integrity were measured using a Nanodrop® spectrophotometer and Agilent BioAnalyzer, respectively.

treatment_protocol: At glucose exhaustion, during acetate consumption and during carbon starvation, samples were collected for the reference time point (T0) for the half-life determination procedure. Subsequently, rifampicin (500 µg.mL-1) was added to inhibit transcription initiation, and cells were harvested at different time points after this addition. Cultures were performed in independent biological triplicates. Samples were immediately frozen in liquid nitrogen upon collection.

tag: sampling time, repetition


title: Foxp3-GFP+Treg_cKO_Rep3_RNA-seq

value: post natal 18–21 weeks

value: Bach2fl/fl Foxp3EGFP-Cre-ERT2


title: Ecoli_P2_T0_kinetic1

description: Cells were in P2 phase (glucose exhaustion), the sampling was performed just before rifampicin addition. It is the first kinetics out of 3 for this phase

source_name: E. coli in P2 phase, Sampling before rifampicin addition in kinetic 1


title: Foxp3-GFP+Treg_cKO_Rep2_RNA-seq


title: wholeembryo_AWB_CEWAFLo1

city: Quebec

first: Valerie

middle: S

last: Langlois

state: QC

address: 490 rue de la Courrone

department: Centre Eau Terre Environnement

country: Canada

institute: Intitut national de la recherche scientifique (INRS)

description: Gene expression after exposure from fertilization to hatch

hyb_protocol: Agilent One-Color Low-Input Labeling kit

scan_protocol: SureScan Microarray Scanner, 5 uM

data_processing: R package limma

organism: Oryzias latipes

source_name: whole embryo, AWB, CEWAF Lo 1

growth_protocol: Medaka embryos were collected from a colony at Queen’s University and maintained according to a protocol approved by the Queen’s Animal Care Committee (Langlois-2015-1584).

extract_protocol: Qiagen Rneasy Micro Kit

treatment_protocol: Within 24 hours post-fertilization, eggs were assigned randomly to treatment groups. Each treatment included duplicate jars of at least 15 eggs (n = 30/treatment) exposed for up to 16 days by a static daily renewal protocol; fresh WAF and CEWAF solutions were made daily. Jars were constantly gently agitated on a New Brunswick Scientific Innova 2000 platform shaker (Eppendorf, Germany) at 60 rpm to ensure water movement and gas exchange. Newly-hatched fish were sampled < 24 h post-hatch at the same time each day.

value: whole embryo

tag: oil

value: AWB

tag: treatment

value: CEWAF Lo

tag: grouping


title: NAA100-E-L35-B_FPKM

city: Beijing

first: Lei

last: He

address: No. 17 Tsinghua east road

country: China

institute: China Agricultural University

data_processing:
The original image data was transfered into sequence data by base calling, which is defined as raw data or raw reads and saved as fastq files.
The dirty raw reads including reads with adaptors, reads in which unknown bases are more than 10% and low quality reads (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read) were removed to get the clean reads.
Clean reads were mapped to reference grapevine genome V2 using Bowtie. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level was calculated by using FPKM method.
Genome_build: http://genomes.cribi.unipd.it/DATA/V2/V2.1/
Supplementary_files_format_and_content: Results include length, excepted_count and FPKM and the description of gene for each sample were shown in xlsx table files.

organism: Vitis vinifera

source_name: grape berry

growth_protocol: Clusters of Vitis vinifera L. cv. Cabernet Sauvignon grapevines cultivated in Shanxi Academy of Agricultural Sciences Pomology Institute, Shanxi, China in 2015 were used for the study.

extract_protocol:
Three biological replicates for each sample were performed. A sub-sample of 50 berries were randomly selected from each biological replicate for RNA extraction. Total RNA was extracted from the frozen deseeded berries (whole pericarp) using a SpectrumTM Plant Total RNA Kit (Sigma-Aldrich, CA, USA).  RNA integrity and quality were assessed by analysis with the Aglient 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The 1000 mg/L ABA, 800 mg/L ABA and 100 mg/L NAA solutions containing 0.05% Tween 20 were applied at seven weeks after flowering (berry still hard and green, E-L 33 stage), with 0.05% Tween solution as the control. The spray of these solutions was performed at sunset to avoid the rapid evaporation of the solutions. After the first spray solution was absorbed, the second application were conducted ten hours later at the same day. A randomized block design was considered for this study, and each treatment or control was replicated in three plots of 50 vines. Each berry sample replicate included 500 berries collected from 50 vines. Sampling was performed at four E-L stages (E-L 34, E-L 35, E-L 36 and E-L 38) according to modified E-L system. Then, the samples were kept in dry ice and immediately transferred to laboratory. Before the extraction, samples were washed with distilled water to remove the unabsorbed ABA and NAA residues on berry surface.

tag: cultivar

value: Cabernet Sauvignon

tag: Stage


title: PK_B_12h

city: Yangzhou

first: jing

last: wang

address: 12 Wen-hui East Road

institute: Yangzhou university

data_processing:
Basecalls performed using Illumina Casava1.7 software
The raw sequencing reads are filtered by removing low quality reads, and clean reads were obtained. The clean reads was then mapped to the whole pig genome using HISAT2 software.
Expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) was used to evaluate the expression level of each gene and the fold-changes between different samples. The Pearson correlation coefficient (R2) was calculated to quantify the degree of correlation between repeated samples by using SPSS 19.0 software.
Genome_build: whole pig genome (https://www.ncbi.nlm.nih.gov/genome/?term=Sus+scrofa)
Supplementary_files_format_and_content: FPKM,expected number of Fragments Per Kilo base of transcript sequence per Millions base pairs sequenced,considers the effect of  sequencing depth and gene length for the reads count at the same time

organism: Sus scrofa

extract_protocol:
Total RNAs from the SVA- and mock-infected groups were extracted using RNA extraction kit (#DR104-1) and the RNA of 4μg per sample was used in the construction of cDNA library using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

tag: cell type

value: porcine kidney cells

value: mock-infected

tag: time point


title: PK_C_12h


title: Foxp3-GFP+Treg_cKO_Rep1_RNA-seq


title: NAA100-E-L35-A_FPKM


title: NAA100-E-L34-C_FPKM


title: NAA100-E-L34-A_FPKM


title: Foxp3-GFP+Treg_BACH2-RFP_LO_Male1_RNA-seq


title: PK_A_12h


title: NAA100-E-L35-C_FPKM


title: Foxp3-GFP+Treg_BACH2-RFP_LO_Female1_RNA-seq


title: Foxp3-GFP+Treg_BACH2-RFP_LO_Female2_RNA-seq


title: wholeembryo_AWB_WAFHi2

source_name: whole embryo, AWB, WAF Hi 2

label_protocol: Agilent One-Color Low-Input Labeling kit

value: WAF Hi


title: NAA100-E-L34-B_FPKM


title: Foxp3-GFP+Treg_BACH2-RFP_HI_Male2_RNA-seq


title: PK_B_6h


title: ABA1000-E-L38-C_FPKM


title: wholeembryo_AWB_WAFHi1

source_name: whole embryo, AWB, WAF Hi 1


title: wholeembryo_AWB_WAFLo3

source_name: whole embryo, AWB, WAF Lo 3

value: WAF Lo


title: wholeembryo_AWB_WAFLo2

source_name: whole embryo, AWB, WAF Lo 2


title: PK_A_6h


title: TP_C_12h

value: SVA-infected


title: Foxp3-GFP+Treg_BACH2-RFP_HI_Male1_RNA-seq


title: ABA1000-E-L38-A_FPKM


title: wholeembryo_AWB_WAFLo1

source_name: whole embryo, AWB, WAF Lo 1


title: wholeembryo_AWB_WAFHi3

source_name: whole embryo, AWB, WAF Hi 3


title: Foxp3-GFP+Treg_BACH2-RFP_HI_Female2_RNA-seq


title: ABA1000-E-L36-C_FPKM


title: PK_C_6h


title: Foxp3-GFP+Treg_BACH2-RFP_HI_Female1_RNA-seq


title: TP_A_12h


title: ABA1000-E-L36-A_FPKM


title: ABA1000-E-L36-B_FPKM


title: ABA1000-E-L35-C_FPKM


title: SK-N-BE(2)-C ALYREF antibody ChIP

city: Kensington

first: Zsuzsanna

last: Nagy

address: Lowy Cancer Research Centre, C25/9 High St

country: Australia

institute: Children's Cancer Institute

description: ChIPed DNA using ALYREF antibody

library_source: genomic

data_processing:
Reads from fastq files were first quality trimmed using TrimGalore (v0.4.5) using parameters (--phred33 --fastqc --illumina --paired --quality 20 --length 20)
Reads were aligned to the human reference genome (GRCh38) using bowtie2 (v2.1.0) using parameters (--local --no-unal -X 2000), resulting sam files were converted to bam files and sorted using samtools (v1.9)
Reads aligned to ENCODE blacklisted regions were removed using bedtools (v2.27.1).
Peaks were then called using MACS2 (v2.1.1) in paired end mode for with an FDR q-value threshold of 0.05 with parameters (-B -q 0.05 -f BAMPE --SPMR -g hs). Fold enrichment tracks were also generated using MACS2 (v2.1.1) and converted to the bigwig format using bedtools (v2.27.1).
HOMER (v4.10.3) was used to annotate peaks (promoters were considered to be -1000bp/+100bp from the transcription start site (TSS)) and then to perform de novo/known motif discovery on ALYREF peak regions using parameters (-size 200 -p 8)
Genome_build: GRCh38
Supplementary_files_format_and_content: annotated peak text file produced from MACS2 (v2.1.1) and then annotated using HOMER (v4.10.3)
Supplementary_files_format_and_content: bigWig file generated by converting MACS2 (v2.1.1) fold enrichment bedgraph file using bedtools (v2.27.1), scores represent fold enrichment values of ALYREF compared to genomic input

molecule: genomic DNA

organism: Homo sapiens

source_name: Neuroblastoma tumour derived

growth_protocol: SK-N-BE(2)-C cells were obtained from ATCC (CRL-2268) and cultured in DMEM with 10% FBS at 37°C & 5% CO2.

extract_protocol:
SK-N-BE(2)-C cells (1x10^7) were harvested and lysed, lysates were then clarified from sonicated nuclei and histone-DNA complexes were isolated using chromatin immunoprecipitation with a mouse anti-ALYREF antibody (11G5, ImmunoQuest) or control mouse IgG (Santa Cruz).
Sequencing libraries were created using an Illumina TruePrep DNA Library Prep Kit (TD501) following manufacturers instructions.

treatment_protocol: SK-N-BE(2)-C cells were routinely subcultered at 90% confluency to maintain an exponential growth phase.

value: Neuroblastoma

value: MYCN_amp, 17q gain

tag: anitbody

value: Mouse anti-ALYREF antibody (11G5, ImmunoQuest)


title: SK-N-BE(2)-C genomic input

description: Genomic input used for ChIP


title: ABA1000-E-L35-B_FPKM


title: TP_B_6h


title: TP_C_6h


title: mut batch 2

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

data_processing:
RNA-Seq reads were aligned to Ogataea parapolymorpha DL-1 reference using STAR version 2.5.3a in 2Pass mode
resulted sequence alignment map file (SAM) were filtered on ambigious alignments and sorted with samtools to sorted binary alignement file (BAM)
The sorted BAM file was processed with htseq-count from the HTSeq framework version 0.9.1 with -m union and -stranded reverse to calculate the transcript counts
The raw transcript counts were normalized on fragments per kilobase million (FPKM) by applying rpkm module from edgeR package
Genome_build: Ogataea parapolymorpha DL-1 GCF_000187245.1
Supplementary_files_format_and_content: Comma delimited file, normalized transcript counts

molecule: polyA RNA

organism: Ogataea parapolymorpha

source_name: mutant batch_0.37 S2

growth_protocol: O. parapolymorpha IMD010 was grown in batch bioreactors (initial volume 1.4 L) in synthetic medium (pmid: 1523884) with an initial glucose concentration of 7.5 g/L as carbon source and 0.15 g/L pluronic 6100 PE antifoam. Cultures were maintained at 30°C, stirred at 800 rpm, aerated at 0.5 vvm with compressed air and pH was kept constant at pH 5.0 by the automatic addition of 2M KOH.

extract_protocol:
Processing of samples and isolation of total RNA were performed essentially as described in pmid: 30147677. The resulting frozen biomass was gently thawed on ice and spun down at 4700 x g for 5 min at 0°C. Pellets were then resuspended in 5 ml/g dryweight in ice-cold AE buffer (50 mM sodium acetate and 10 mM EDTA, pH 5.0), followed by addition of 5 ml/g dryweight of acid-phenol:chloroform:isoamyalcohol (125:24:1, pH 4.5, Thermo Fisher Scientific) and 0.5 mL/g dryweight 10 % sodium dodecyl sulfate. The resulting mix was vortexed for 30 s and incubated for 5 min at 65 °C. After homogenizing for 30 sec by vortexing, 800 µL aliquots were distributed in RNase-free screw-cap tubes. After centrifugation (15 min at 10,000 x g), the aqueous phase was transferred to a new tube containing 0.4 mL of acid phenol/chloroform. The mix was vortexed for 30 seconds, centrifuged (15 min at 10,000 x g) and the aqueous phase was again transferred to a new tube. RNA was then ethanol precipitated and re-suspended in RNAse-free water. Prior to cDNA synthesis, purity, concentration and integrity of the RNA in the samples was assessed with the Nanodrop (Thermo Fisher Scientific), Qubit (Thermo Fisher Scientific) and Tapestation 220 with RNA Screen Tape (Agilent Technologies), respectively, according the manufacturers’ recommendations.
cDNA libraries were prepared using the TruSeq RNA V2 kit (Illumina)and sequenced on HISeq 2500 (Illumina) at Novogene (HK) Company Ltd (Hong Kong, China).

treatment_protocol: Cultures samples were directly quenched in liquid nitrogen under vigorous stirring.

tag: carbon source

value: Glucose

tag: specific growth rate (h-1)

value: Complex I mutant


title: TP_B_12h


title: TP_A_6h


title: ABA1000-E-L35-A_FPKM


title: mut batch 1

source_name: mutant batch_0.37 S1


title: Microarray genotyping [313605]

type: genomic

city: Stanford

first: Thomas

last: Quertermous

state: CA

address: 300 Pasteur Drive

department: Medicine Cardiology

country: USA

institute: Stanford University

description:
Sample 15
processed data file: SNP_table_9-15.txt
processed data file: Sample_9-15.txt
raw data file: Full_data_9-15.txt
raw data file: Paired_sample_table_9-15.txt

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays and incubate at 48C for overnight.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Genomic DNA extracted from human coronary artery smooth muscle cells was genotyped using Illumina Infinium Multi-Ethnic Global 8 Kit.

label: not applicable

label_protocol: 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37C. After incubation the amplified DNA was fragmented with fragmentation mix, precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

growth_protocol: Primary human coronary artery smooth muscle cells (HCASMCs) derived from normal human donor hearts were purchased from three different manufacturers, Lonza, PromoCell and Cell Applications (all tested negative for mycoplasma contamination) at passage 2 and were maintained in growth-supplemented smooth muscle basal media (Lonza # CC-3182) according to the manufacturer’s instructions. All experiments were performed on HCASMCs between passages 4 and 7.

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using proteinase K and repeated phenol-chloroform extraction.

treatment_protocol: Not applicable

value: Coronary artery smooth muscle cells

tag: passage

value: passage 4-7


title: Microarray genotyping [400Z012]

description:
Sample 13
processed data file: SNP_table_9-15.txt
processed data file: Sample_9-15.txt
raw data file: Full_data_9-15.txt
raw data file: Paired_sample_table_9-15.txt

source_name: human coronary artery smooth muscle cells


title: Microarray genotyping [9092401]

description:
Sample 14
processed data file: SNP_table_9-15.txt
processed data file: Sample_9-15.txt
raw data file: Full_data_9-15.txt
raw data file: Paired_sample_table_9-15.txt


title: wholeembryo_Dispersant_DispControl1

source_name: whole embryo, Dispersant, Disp Control

value: Dispersant Control

value: Dispersant


title: 121-1

city: Daejeon

first: Galam

last: Leem

address: 291 Daehakro Yusunggu

country: South Korea

institute: KAIST

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

source_name: Tumor-infiltrating CD8 T cells

growth_protocol: Cells were isolated from fresh tisuse with MACS tumor dissociation kit.

extract_protocol:
RNA was extracted from cells with TRIzol RNA isolation reagents.
Poly(A) RNA Selection + SMARTer stranded RNA-Seq kit HT
QuantSeq 3' mRNA-Seq Library Prep Kit FWD

treatment_protocol: Untreated

value: ovary

value: CD39- CD8 T cells

value: Untreated

tag: disease state

value: Metastatic ovarian cancer


title: 121-2

tag: tissue

value: CD137- CD39+ CD8 T cells


title: 121-3

value: CD137+ CD39+ CD8 T cells


title: ABA1000-E-L34-B_FPKM

value: Cabernet Sauvignon


title: 89-3


title: Microarray genotyping [9102101]

description:
Sample 12
processed data file: SNP_table_9-15.txt
processed data file: Sample_9-15.txt
raw data file: Full_data_9-15.txt
raw data file: Paired_sample_table_9-15.txt


title: 89-2


title: ABA1000-E-L34-A_FPKM


title: mut cs01 1

source_name: mutant chemostat_0.1 S1

growth_protocol: O. parapolymorpha IMD010 was grown in chemostat bioreactors (working volume 1.4 L) at a dilution rate of 0.1 h-1 in synthetic medium (pmid: 1523884) with 7.5 g/L glucose as carbon source and 0.15 g/L pluronic 6100 PE antifoam. Cultures were maintained at 30°C, stirred at 800 rpm, aerated at 0.5 vvm with compressed air and pH was kept constant at pH 5.0 by the automatic addition of 2M KOH.

tag: strain


title: 89-1


title: ABA1000-E-L34-C_FPKM


title: mut ret 2

source_name: mutant retentostat_0.001 S2

growth_protocol: O. parapolymorpha IMD010 was grown in retentostat bioreactors (working volume 1.4 L) at a dilution rate of 0.025 h-1 in synthetic medium (pmid: 1523884), except 1.5X trace elements concentration and 2X vitamins concentration, with 5 g/L glucose as carbon source and 0.15 g/L pluronic 6100 PE antifoam. Cultures were maintained at 30°C, stirred at 800 rpm, aerated at 0.5 vvm with compressed air and pH was kept constant at pH 5.0 by the automatic addition of 10% (w/v) NH4OH. Retentostat cultivation was preceded by chemostat cultivation at the same conditions, except that 10 g/L glucose was used as carbon source.

tag: genotype


title: mut cs01 2

source_name: mutant chemostat_0.1 S2


title: Microarray genotyping [1062201.3]

description:
Sample 11
processed data file: SNP_table_9-15.txt
processed data file: Sample_9-15.txt
raw data file: Full_data_9-15.txt
raw data file: Paired_sample_table_9-15.txt


title: Control-E-L38-C_FPKM

value: Control


title: 88-3


title: mut ret 1

source_name: mutant retentostat_0.001 S1

growth_protocol: O. parapolymorpha IMD010 was grown in retentostat bioreactors (working volume 1.4 L) at a dilution rate of 0.025 h-1 in synthetic medium (pmid: 1523884), except 1.5X trace elements concentration and 2X vitamins concentration was used, with 5 g/L glucose as carbon source and 0.15 g/L pluronic 6100 PE antifoam. Cultures were maintained at 30°C, stirred at 800 rpm, aerated at 0.5 vvm with compressed air and pH was kept constant at pH 5.0 by the automatic addition of 10% (w/v) NH4OH. Retentostat cultivation was preceded by chemostat cultivation at the same conditions, except that 10 g/L glucose was used as carbon source.


title: Control-E-L38-B_FPKM

source_name: grape berry


title: Microarray genotyping [397Z030]

description:
Sample 10
processed data file: SNP_table_9-15.txt
processed data file: Sample_9-15.txt
raw data file: Full_data_9-15.txt
raw data file: Paired_sample_table_9-15.txt


title: 88-2


title: Control-E-L38-A_FPKM


title: mut cs025 2

source_name: mutant chemostat_0.025 S2

growth_protocol: O. parapolymorpha IMD010 was grown in chemostat bioreactors (working volume 1.0 L) at a dilution rate of 0.025 h-1 in synthetic medium (pmid: 1523884) with 7.5 g/L glucose as carbon source and 0.15 g/L pluronic 6100 PE antifoam. Cultures were maintained at 30°C, stirred at 800 rpm, aerated at 0.5 vvm with compressed air and pH was kept constant at pH 5.0 by the automatic addition of 2M KOH.


title: wholeembryo_Water_NegControl4

source_name: whole embryo, Water, Neg Control

value: whole embryo

value: Negative Control

value: Water


title: 88-1


title: Microarray genotyping [3141]

description:
Sample 8
processed data file: SNP_table_1-8.txt
processed data file: Sample_1-8.txt
raw data file: Full_data_1-8.txt
raw data file: Paired_sample_table_1-8.txt


title: Microarray genotyping [1848]

description:
Sample 9
processed data file: SNP_table_9-15.txt
processed data file: Sample_9-15.txt
raw data file: Full_data_9-15.txt
raw data file: Paired_sample_table_9-15.txt


title: Microarray genotyping [1858]

description:
Sample 7
processed data file: SNP_table_1-8.txt
processed data file: Sample_1-8.txt
raw data file: Full_data_1-8.txt
raw data file: Paired_sample_table_1-8.txt


title: mut cs025 1

source_name: mutant chemostat_0.025 S1

value: Glucose


title: Control-E-L36-A_FPKM


title: Control-E-L36-B_FPKM


title: Control-E-L35-C_FPKM


title: Control-E-L35-B_FPKM


title: Control-E-L35-A_FPKM


title: Control-E-L36-C_FPKM


title: Control-E-L34-C_FPKM


title: Control-E-L34-B_FPKM


title: wt ret 2

source_name: wildtype retentostat_0.001 S2

growth_protocol: O. parapolymorpha CBS11895 was grown in retentostat bioreactors (working volume 1.4 L) at a dilution rate of 0.025 h-1 in synthetic medium (pmid: 1523884), except 1.5X trace elements concentration and 2X vitamins concentration, with 5 g/L glucose as carbon source and 0.15 g/L pluronic 6100 PE antifoam. Cultures were maintained at 30°C, stirred at 800 rpm, aerated at 0.5 vvm with compressed air and pH was kept constant at pH 5.0 by the automatic addition of 10% (w/v) NH4OH. Retentostat cultivation was preceded by chemostat cultivation at the same conditions, except that 10 g/L glucose was used as carbon source.

value: wildtype


title: wt cs0025 2

source_name: wildtype chemostat_0.025 S2

growth_protocol: O. parapolymorpha CBS11895 was grown in chemostat bioreactors (working volume 1.0 L) at a dilution rate of 0.025 h-1 in synthetic medium (pmid: 1523884) with 7.5 g/L glucose as carbon source and 0.15 g/L pluronic 6100 PE antifoam. Cultures were maintained at 30°C, stirred at 800 rpm, aerated at 0.5 vvm with compressed air and pH was kept constant at pH 5.0 by the automatic addition of 2M KOH.


title: wt ret 1

source_name: wildtype retentostat_0.001 S1

growth_protocol: O. parapolymorpha CBS11895 was grown in retentostat bioreactors (working volume 1.4 L) at a dilution rate of 0.025 h-1 in synthetic medium (pmid: 1523884), except 1.5X trace elements concentration and 2X vitamins concentration was used, with 5 g/L glucose as carbon source and 0.15 g/L pluronic 6100 PE antifoam. Cultures were maintained at 30°C, stirred at 800 rpm, aerated at 0.5 vvm with compressed air and pH was kept constant at pH 5.0 by the automatic addition of 10% (w/v) NH4OH. Retentostat cultivation was preceded by chemostat cultivation at the same conditions, except that 10 g/L glucose was used as carbon source.


title: H1703-ct-Group-1

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

source_name: human cancer cell line

growth_protocol: Cells were growth in RPMI with 10% FBS and 1% penicillin/streptomycin. For 72 hours, IFN-gamma treated group was treated with 20ng/ml human recombinant interferon-gamma and control group was untreated.

treatment_protocol: 20ng/ml IFN-gamma for 72 hours.

tag: cell line origin

value: lung cancer

tag: agent


title: A375-ct-Group-1

value: skin


title: 549-IFN-Group-2

value: IFN-gamma


title: A375-IFN-Group-2


title: A498-ct-Group-1

value: kidney


title: A498-IFN-Group-2

value: kideny


title: H1703-IFN-Group-2


title: Control-E-L34-A_FPKM

tag: treatment


title: 549-ct-Group-1


title: wt cs0025 1

source_name: wildtype chemostat_0.025 S1


title: KBM7_input

status: Public on May 11 2020

city: Wien

first: Georg

middle: E

last: Winter

state: Austria

address: Lazarettgasse 14, AKH BT25.3

country: Austria

institute: CeMM - Research Institute for Molecular Medicine of the Austrian Academy of Sciences

data_processing:
trimming: skewer v 0.1.126 -f sanger -t 8 -m any
alignment: bowtie v2.3.4 --very-sensitive, later filtering for MAPQ > 30 using sambamba v0.5.5
peak calling: macs v2.1.0 callpeak with narrow peak setting and KBM7_input.fastq.gz as control sample (using the --fix-bimodal --extsize 180 --bw 200 parameters)
SuperEnhancer calling: H3K27ac peaks (p < 1e-9) that don't overlap H3K4me3 peaks over RefSeq TSS (p < 1e-9) were used as input for ROSE with "-c $KBM7_input -s 12500 -t 0". 532 SEs were then assigned to the closest active (TT-seq RPKM > median) protein coding genes (RefSeq NM_*) located in the same TAD (Rao et al., Cell 2014).
Genome_build: hg38
Supplementary_files_format_and_content: bigWig generation: coverage files were generated from reads extended to 130bp using bedtools v2.20.1 (bamtobed | slop -s -l 0 -r 130 | genomeCoverageBed -bg). BigWig files with scores of [reads per basepair per million] were generated using bedGraphToBigWig

source_name: KBM7 chronic myeloid leukemia cell line

growth_protocol: KBM7 cells were grown in IMDM medium supplemented with 10% FBS and 1% Pen/Strep.

extract_protocol:
Standard DNA extraction from KBM7 cells using cell lysis. Probe sonicator 3 minutes total sonication time (1 sec on, 4 sec off, 60% amplitude) on ice.
Library construction using Rubicon ThruPLEX kit.

value: chronic myeloid leukemia cell line

tag: chip antibody


title: KBM7_H3K4me3

value: H3K4me3 (Millipore 07-473)


title: KBM7_H3K27ac

value: H3K27ac (Abcam ab4729)


title: DG_SZ_0858

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

data_processing:
Single-end/Peired-end reads were aligned with STAR 2.5.2b using options "“--outFilterMultimapNmax 10 --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 3 --twopassMode Basic" to the reference sequence (hg19 from UCSC)
Human reference was used for gene annotation and counting (GRCh37.87). Uniquely mapped reads were quantified using HTSeq python suite using protein coding genes by gene.
Genome_build: hg19
Supplementary_files_format_and_content: Input tables are included as tab separated files.

source_name: hippocampus

extract_protocol:
Total RNA was extracted and purified using a protocol combining Trizol and chloroform extraction, the GeneJET RNA Purification Kit, and a motorized mini-pestle vibrator for tissue homogenization. RNA purity and concentration were assessed on the Nanodrop spectrophotometer and Agilent2100 Bioanalyzer for RNA Integrity number (RIN) determination.
Total RNA was rRNA ribo-depleted, and strand-specific cDNA libraries were synthesized before sequencing on an Illumina HiSeq 2500 sequencer. Stranded, single-end 50-base-pair reads were generated for the preliminary CA3 cohort data. Stranded paired-end 100-base-pair reads were generated for additional cohorts. Libraries and sequencing were performed at the UTSW McDermott Sequencing Core and UTSW Genomics & Microarray Core.

tag: diagnosis

value: schizophrenia

value: DG

tag: gender

value: M

tag: age

tag: pmi

tag: rin

tag: drug

value: OFF

value: hippocampus


title: DG_SZ_0851


title: Ecoli_P3_T1.5_kinetic2

description: Cells were in P3 phase (acetate consumtion) the sampling was performed 1.5 min after rifampicin addition. It is the second kinetics out of 3 for this phase

source_name: E. coli in P3 phase, Sampling 1.5 minute after rifampicin addition in kinetic 2

tag: sampling time, repetition


title: DG_SZ_0849


title: Microarray genotyping [399Z015]

description:
Sample 3
processed data file: SNP_table_1-8.txt
processed data file: Sample_1-8.txt
raw data file: Full_data_1-8.txt
raw data file: Paired_sample_table_1-8.txt

source_name: human coronary artery smooth muscle cells

tag: cell type

value: Coronary artery smooth muscle cells

value: passage 4-7


title: Microarray genotyping [2102]

description:
Sample 2
processed data file: SNP_table_1-8.txt
processed data file: Sample_1-8.txt
raw data file: Full_data_1-8.txt
raw data file: Paired_sample_table_1-8.txt

tag: passage


title: Microarray genotyping [61646600]

description:
Sample 6
processed data file: SNP_table_1-8.txt
processed data file: Sample_1-8.txt
raw data file: Full_data_1-8.txt
raw data file: Paired_sample_table_1-8.txt


title: Microarray genotyping [289727]

description:
Sample 5
processed data file: SNP_table_1-8.txt
processed data file: Sample_1-8.txt
raw data file: Full_data_1-8.txt
raw data file: Paired_sample_table_1-8.txt


title: Microarray genotyping [2109]

description:
Sample 1
processed data file: SNP_table_1-8.txt
processed data file: Sample_1-8.txt
raw data file: Full_data_1-8.txt
raw data file: Paired_sample_table_1-8.txt


title: DG_SZ_0860


title: wholeembryo_Water_NegControl2

value: whole embryo

tag: oil

value: Negative Control

value: Water

tag: grouping


title: DG_SZ_0840

value: ON

tag: tissue


title: DG_SZ_0841

value: F


title: DG_SZ_0838


title: HTAPP-951-SMP-4652_TST-V3_channel1

first: Orr

last: Ashenberg

state: MA

address: 415 Main Street

department: Klarman Cell Observatory

institute: Broad Institute

description:
Single-cell or single nucleus RNA-Seq (10X). The count matrix is stored as an HDF5 file.
For each cell or nucleus (row): cell name, annotation, median number of reads per cell, median number of UMIs per cell, median number of genes per cell, median fraction of UMIs mapping to mitochondrial genes, fraction of cells called as empty droplets, and fraction of cells called as doublets.

data_processing:
3' RNAseq (10x kit V2 or V3 chemistry)
Demultiplexing is run using Cell Ranger mkfastq.
Cell Ranger count is run using the Cumulus cellranger_workflow.
Supplementary_files_format_and_content: Raw count matriece are in the HDF5 Feature Barcode Matrix Format used by 10x, and metadata files are comma-delimited text.

source_name: sarcoma

extract_protocol:
Dissociated individual cells or isolated individual nuclei from fresh, frozen, or cryopreserved tumor samples. In some fresh samples, CD45 cells were depleted by flow sorting.
3' RNAseq (10x kit V2 or V3 chemistry)

tag: sample type

value: HTAPP-951-SMP-4652 TST-V3


title: CY128_nuclei_channel1

source_name: melanoma

value: CY128 nuclei


title: DG_SZ_0847


title: HTAPP-316-SMP-991_NST_channel1

source_name: ovarian

value: HTAPP-316-SMP-991 NST


title: DG_SZ_0839


title: CY112_nuclei_channel2

value: CY112 nuclei


title: HTAPP-951-SMP-4652_CST-V3_channel1

value: HTAPP-951-SMP-4652 CST-V3


title: wholeembryo_Water_NegControl1

description: Gene expression after exposure from fertilization to hatch


title: wholeembryo_Dispersant_DispControl2

source_name: whole embryo, Dispersant, Disp Control

value: Dispersant Control

value: Dispersant


title: DG_SZ_0837

value: schizophrenia

value: DG

value: M


title: HTAPP-975-SMP-4771_TST-V3_channel1

value: HTAPP-975-SMP-4771 TST-V3


title: HTAPP-316-SMP-991_TST_channel1

value: HTAPP-316-SMP-991 TST


title: wholeembryo_Water_NegControl3

value: whole embryo


title: HTAPP-316-SMP-991_CST_channel1

value: HTAPP-316-SMP-991 CST


title: HTAPP-624-SMP-3212_fresh_channel1

value: HTAPP-624-SMP-3212 fresh


title: DG_CTL_0859

value: control

value: OFF

value: hippocampus


title: DG_SZ_0810

value: ON


title: HTAPP-951-SMP-4652_TST-V2_channel1

value: HTAPP-951-SMP-4652 TST-V2


title: HTAPP-727-SMP-3781_fresh-CD45neg-T1_channel1

value: HTAPP-727-SMP-3781 fresh-CD45neg-T1


title: Microarray genotyping [1238]

description:
Sample 4
processed data file: SNP_table_1-8.txt
processed data file: Sample_1-8.txt
raw data file: Full_data_1-8.txt
raw data file: Paired_sample_table_1-8.txt

value: Coronary artery smooth muscle cells

value: passage 4-7


title: CLL-pilot1_fresh_channel1

source_name: CLL

value: CLL-pilot1 fresh


title: ABA1000-E-L38-B_FPKM

source_name: grape berry

tag: cultivar

value: Cabernet Sauvignon

tag: Stage


title: wholeembryo_Dispersant_DispControl3

value: Dispersant Control

tag: treatment

value: Dispersant


title: HTAPP-443-SMP-5491_CST_channel1

source_name: glioma

value: HTAPP-443-SMP-5491 CST


title: DG_CTL_0852

value: DG

value: M


title: HTAPP-963-SMP-4741_TST_channel1

source_name: MBC

value: HTAPP-963-SMP-4741 TST


title: DG_CTL_0846

value: F


title: HTAPP-589-SMP-2851_TST_channel2

value: HTAPP-589-SMP-2851 TST


title: DG_CTL_0848

value: control

value: OFF


title: DG_CTL_0857

value: hippocampus


title: HTAPP-589-SMP-2851_CST_channel1

value: HTAPP-589-SMP-2851 CST


title: DG_CTL_0850


title: MGH125_fresh_channel1

value: MGH125 fresh


title: HTAPP-963-SMP-4741_CST_channel2

value: HTAPP-963-SMP-4741 CST


title: DG_CTL_0842


title: DG_CTL_0843


title: DG_SZ_0812

value: schizophrenia

value: ON


title: HTAPP-394-SMP-1561_CST_channel1

value: HTAPP-394-SMP-1561 CST


title: DG_CTL_0820


title: DG_CTL_0818


title: DG_CTL_0844


title: HTAPP-963-SMP-4741_fresh_channel1

value: HTAPP-963-SMP-4741 fresh


title: DG_CTL_0816


title: HTAPP-735-SMP-3841_fresh_channel2

value: HTAPP-735-SMP-3841 fresh


title: CA3_SZ_0873


title: HTAPP-285-SMP-751_fresh_channel1

value: HTAPP-285-SMP-751 fresh


title: HTAPP-StJude-SMP-PDX1_nuclei_channel1

source_name: neuroblastoma

value: HTAPP-StJude-SMP-PDX1 nuclei


title: DG_CTL_0845

value: DG

value: M


title: HTAPP-254-SMP-571_LD_channel1

value: HTAPP-254-SMP-571 LD


title: CA3_SZ_0868


title: CA3_SZ_0867

value: F


title: HTAPP-StJude-SMP-PDX1_cell_channel1

value: HTAPP-StJude-SMP-PDX1 cell


title: CA3_SZ_0869

value: OFF


title: HTAPP-244-SMP-451_CST_channel1

value: HTAPP-244-SMP-451 CST


title: CA3_SZ_0866

value: hippocampus


title: HTAPP-244-SMP-451_TST_channel1

value: HTAPP-244-SMP-451 TST


title: HTAPP-656-SMP-3481_fresh-T1_channel1

value: HTAPP-656-SMP-3481 fresh-T1


title: CA3_SZ_0865

value: schizophrenia


title: HTAPP-312-SMP-901_fresh-T1_channel1

value: HTAPP-312-SMP-901 fresh-T1


title: HTAPP-312-SMP-902_fresh-C4-T2_channel1

value: HTAPP-312-SMP-902 fresh-C4-T2


title: NSCLC17_fresh-cd45n_channel1

source_name: lung cancer

value: NSCLC17 fresh-cd45n


title: CA3_SZ_0862

value: ON


title: CA3_SZ_0863


title: NSCLC17_fresh-PDEC_channel1

value: NSCLC17 fresh-PDEC


title: CA3_SZ_0872


title: CA3_SZ_0861


title: CA3_CTL_0886

value: control


title: NSCLC14_fresh-PDEC_channel1

value: NSCLC14 fresh-PDEC


title: NSCLC14_fresh-LE_channel1

value: NSCLC14 fresh-LE


title: CA3_CTL_0885

value: M


title: HTAPP-394-SMP-1561_NST_channel2

value: HTAPP-394-SMP-1561 NST


title: HTAPP-656-SMP-3481_TST_channel1

value: HTAPP-656-SMP-3481 TST


title: CA3_SZ_0871

value: F

value: OFF


title: HTAPP-244-SMP-451_EZ_channel1

value: HTAPP-244-SMP-451 EZ


title: CA3_SZ_0870

value: hippocampus


title: CA3_CTL_0884


title: CA3_SZ_0864


title: NSCLC14_fresh-C4_channel1

value: NSCLC14 fresh-C4


title: CA3_CTL_0882


title: CA3_CTL_0883


title: HTAPP-244-SMP-451_NST_channel1

value: HTAPP-244-SMP-451 NST


title: centrocyte Ezh2(Y641F)fl/wt;Cγ1-cre 4

city: New York

first: Cem

last: Meydan

state: New York

address: 1305 York

department: Physiology & Biophysics

institute: Weill Cornell Medical College

description:
cells sorted: B220+, FAS+, CD38-, CXCR4-, CD86+
Ezh2-4_CC_d8

data_processing:
RNAseq fastq files were trimmed using Trim Galore and cutadapt to remove adapter sequences.
Trimmed fastq files were aligned using STAR (version 2.5.3a) to the mouse genome (mm10) using Gencode (version M12) transcriptome assembly.
Coding genes were quantified using subread featureCounts (v1.4.5-p1) to annotate uniquely mapped reads to Gencode annotation.
Genome_build: mm10
Supplementary_files_format_and_content: Gene counts

source_name: B-cells from spleen

extract_protocol:
Cells were sorted into Trizol reagent (Invitrogen) and RNA was extracted following the manufacturer instructions. RNA quality was evaluated using Agilent Technologies 2100 Bioanalyzer and samples that passed the quality control (RNA Integrity Number ≥8) were subjected to library preparation
Library preparation, sequencing and post-processing of the raw data was performed at the Epigenomics Core at Weill Cornell Medicine. Illumina TruSeq RNA sample kits were used for libarary preparation, according to the manufacturer.

treatment_protocol: Mice were immunized with sheep red blood cells (SRBC) 8 days before extraction of spleens

tag: genotype

tag: strain

value: 3 months

tag: littermate

value: litter 1


title: CA3_CTL_0881

tag: diagnosis

tag: gender

tag: age


title: centrocyte Ezh2(Y641F)fl/wt;Cγ1-cre 2

description:
cells sorted: B220+, FAS+, CD38-, CXCR4-, CD86+
Ezh2-2_CC_d8


title: CA3_CTL_0880

tag: pmi

tag: rin

tag: drug


title: centrocyte Ezh2(Y641F)fl/wt;Cγ1-cre 3

description:
cells sorted: B220+, FAS+, CD38-, CXCR4-, CD86+
Ezh2-3_CC_d8


title: centrocyte Cγ1-cre 4

description:
cells sorted: B220+, FAS+, CD38-, CXCR4-, CD86+
Cont-4_CC_d8


title: centrocyte Ezh2(Y641F)fl/wt;Cγ1-cre 1

description:
cells sorted: B220+, FAS+, CD38-, CXCR4-, CD86+
Ezh2-1_CC_d8


title: CA3_CTL_0879


title: centrocyte Cγ1-cre 3

description:
cells sorted: B220+, FAS+, CD38-, CXCR4-, CD86+
Cont-3_CC_d8


title: centrocyte Cγ1-cre 2

description:
cells sorted: B220+, FAS+, CD38-, CXCR4-, CD86+
Cont-2_CC_d8


title: CA3_CTL_0878


title: CA3_CTL_0877


title: centrocyte Cγ1-cre 1

description:
cells sorted: B220+, FAS+, CD38-, CXCR4-, CD86+
Cont-1_CC_d8


title: centroblast Ezh2(Y641F)fl/wt;Cγ1-cre 4

description:
cells sorted: B220+, FAS+, CD38-, CXCR4+, CD86-
Ezh2-4_CB_d8


title: centroblast Ezh2(Y641F)fl/wt;Cγ1-cre 2

description:
cells sorted: B220+, FAS+, CD38-, CXCR4+, CD86-
Ezh2-2_CB_d8


title: centroblast Ezh2(Y641F)fl/wt;Cγ1-cre 1

description:
cells sorted: B220+, FAS+, CD38-, CXCR4+, CD86-
Ezh2-1_CB_d8


title: CA1_SZ_0856

value: schizophrenia


title: CA3_CTL_0875


title: centroblast Cγ1-cre 4

description:
cells sorted: B220+, FAS+, CD38-, CXCR4+, CD86-
Cont-4_CB_d8


title: CA3_CTL_0874


title: CA1_SZ_0835


title: CA1_SZ_0831


title: centroblast Cγ1-cre 2

description:
cells sorted: B220+, FAS+, CD38-, CXCR4+, CD86-
Cont-2_CB_d8


title: CA1_SZ_0833


title: CA1_SZ_0855


title: CA1_SZ_0825


title: centroblast Cγ1-cre 3

description:
cells sorted: B220+, FAS+, CD38-, CXCR4+, CD86-
Cont-3_CB_d8


title: SATB1-SE_4C-seq_MED14-dTAG_2h_dTAG7_C

data_processing:
Reads were kept if the nucleotides 1-16 had a hamming distance of at most 2 with the read primer nucleotides 1 to 16 and if the restriction enzyme cut site (nt 17-20) had also at most a hamming distance of 2. The read primer was removed from the raw reads and output.
Duplicate reads were collapsed and the restriction enzyme recognition site was added again at the beginning of a collapsed read.
The collapsed reads were then mapped with bowtie (v. 1.2.3) to the human genome (hg19) with parameters -n 2 -e 70 -m 1 -k 1 --best -l 200. This output only unique mapping reads with at most 2 mismatches.
The genome was insilico digested with the respective two restriction enzymes used for each 4C-experiment. Only reads are kept that either mapped to nonblind fragments or so called halfblind fragments. Nonblind fragments had both restriction enzyme cut sites present, one at each end. Halfblind fragments had only the first restriction enzyme present at both ends.
Then, bamtools merge (version 2.5.1) was used to merge all nonblind and halfblind files from the three biological replicates.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig generation: bamCoverage (version 3.2.1) with options --normalizeUsing CPM --binSize 500 --smoothLength 6500 was used to create the final bigwig files.

extract_protocol:
Chromatin contacts for 4C libraries were generated as previously described (PMID: 22961246).
Viewpoint fragments were amplified using indicated primers. Sequencing-compatible overhangs were introduced by a second PCR reaction.

treatment_protocol: 15mio cells were treated for 2h with 500nM dTAG7 or DMSO and then fixed with 1% MeOH-free PFA for 10min at room temperature.

tag: cell line

tag: cell type

value: chronic myeloid leukemia cell line

tag: genotype/variation

value: 2h 500nM dTAG7

tag: viewpoint annotation

tag: restriction enzymes

value: NlaIII - DpnII

tag: viewpoint forward primer

value: GTGGACTGAGGGGGTACATG

tag: viewpoint reverse primer

value: GTTAGAACCAGGTACTGCCA


title: SATB1-SE_4C-seq_MED14-dTAG_2h_dTAG7_B

tag: treatment


title: SATB1-SE_4C-seq_MED14-dTAG_2h_dTAG7_A


title: SATB1-SE_4C-seq_MED14-dTAG_2h_DMSO_C

value: 2h DMSO


title: DG_SZ_0814

value: DG

value: M

value: ON

tag: tissue


title: CA3_CTL_0876

value: control

value: OFF


title: CA1_SZ_0824

value: hippocampus


title: SATB1-SE_4C-seq_MED14-dTAG_2h_DMSO_B


title: CA1_SZ_0813


title: CA1_SZ_0821

value: F


title: CA1_SZ_0811


title: centroblast Ezh2(Y641F)fl/wt;Cγ1-cre 3

description:
cells sorted: B220+, FAS+, CD38-, CXCR4+, CD86-
Ezh2-3_CB_d8

tag: genotype

tag: strain


title: SATB1-SE_4C-seq_MED14-dTAG_2h_DMSO_A


title: MYB-SE_4C-seq_MED14-dTAG_2h_dTAG7_C

value: NlaIII - CviQI

value: ACAGCCTTTTGATTGACATG

value: ATGGGTTATTTTCGTCTCG


title: CA1_SZ_0809

tag: diagnosis

value: schizophrenia


title: MYB-SE_4C-seq_MED14-dTAG_2h_dTAG7_B

value: chronic myeloid leukemia cell line


title: CA1_CTL_0853

tag: gender


title: centroblast Cγ1-cre 1

description:
cells sorted: B220+, FAS+, CD38-, CXCR4+, CD86-
Cont-1_CB_d8

tag: age

value: 3 months

tag: littermate

value: litter 1


title: CA1_SZ_0826

tag: pmi

tag: rin


title: CA1_CTL_0836

tag: drug


title: CA1_SZ_0822


title: MYB-SE_4C-seq_MED14-dTAG_2h_DMSO_C

tag: cell line

tag: cell type


title: MYB-SE_4C-seq_MED14-dTAG_2h_DMSO_A

tag: genotype/variation

tag: viewpoint annotation


title: MYB-SE_4C-seq_MED14-dTAG_2h_DMSO_B

tag: restriction enzymes

tag: viewpoint forward primer


title: MYB-SE_4C-seq_MED14-dTAG_2h_dTAG7_A

tag: treatment

value: 2h 500nM dTAG7

tag: viewpoint reverse primer


title: CA1_CTL_0834

tag: tissue


title: mouse LSK, LCE410

first: Luyi

last: Tian

address: 415 main st Cambridge

institute: Broad institute

description: index sorted hematopoietic stem and progenitor cells from Dach1 reporter mice, FACS value in FACS_annotation.csv

data_processing:
gene counting matrix generated using scPipe 1.3.0
reads were aligned using Rsubread 1.29.6
Genome_build: ENSEMBL Homo_sapiens.GRCh38.88
Supplementary_files_format_and_content: gene counting matrix, rows repsent genes and each column is a well

source_name: hematopoietic stem and progenitor cells

growth_protocol: All mice were bred and maintained under specific pathogen-free conditions at WEHI, according to institutional guidelines. C57BL/6 (CD45.2), C57BL/6 Pep3b (CD45.1), Cas9-Tg or Dach1-GFP mice aged between 8-16 weeks were used.

extract_protocol:
marrow cells from either C57BL/6 mice or Dach1-GFP mice were harvested, made into a single cell suspension, incubated with red cell removal buffer (NH4Cl), followed by incubation with anti-CD117-APC, then incubation with anti-APC magnetic beads, followed by purification on a LS column (Miltenyit biotech). This enriched fraction was then stained with a cocktail of antibodies including anti-Sca1, anti-Il7Ra-biotin, anti-CD16/32, anti-CD135-PE, anti-CD150, anti-CD48. Cells were sorted either in bulk or using the single cell mode of a BD Fusion cell sorter.
For CEL-seq2, Single cells were flow sorted into chilled 384-well PCR plates containing 1.2ul of primer/ERCC mix using a BD FACSAria III flow cytometer. Sorted plates were sealed and immediately frozen upside down at -80C. Then these plates, together with the mRNA mixture plates, were taken from -80C and processed using an adapted Cel-Seq2 protocol with the following variations. We pooled the samples after the first strand synthesis and the second strand synthesis was performed using NEBNext Second Strand Synthesis module. NucleoMag NGS Clean-up and Size select magnetic beads were used for all DNA purification and size selection steps.

treatment_protocol: A targeting vector was constructed in which sequence encoding a biotin tag was inserted immediately prior to the stop codon in exon 12 of the Dach1 gene, along with an IRES-GFP-frt-flanked neomycin resistance cassette following the stop codon. This targeting vector was linearized and electroporated into C57BL/6 embryonic stem cells. Transfected cells were selected in G418 and resistant clones picked and expanded. Clones in which the targeting vector had recombined with the endogenous Dach1 locus were identified by southern blot analysis and a targeted ES cell clone was injected into Balb/c blastocysts to generate chimeric mice. Male chimeras were mated with C57BL/6 females to yield mice heterozygous for the targeted Dach1 allele (Dach1T); these were then bred with mice expressing Flpe recombinase to excise the neomycin resistance cassette generating mice carrying the Dach1bio-GFP locus.

value: bone marrow

value: hematopoietic stem and progenitor cells

tag: cellular barcode

value: 8bp as in cell_barcode.csv

tag: umi position

value: 6bp after the cell barcode

tag: barcode position

value: R1 first eight base


title: CA1_CTL_0832

tag: diagnosis

value: control

tag: gender

tag: age


title: CA1_CTL_0830

value: M

tag: pmi

tag: rin

value: OFF


title: mouse LSK, LCE409


title: mouse LSK, LCE408


title: CA1_CTL_0828

tag: drug

value: hippocampus


title: CA1_CTL_0823

value: F


title: CA1_CTL_0827


title: CA1_CTL_0829


title: CA1_CTL_0819


title: CA1_CTL_0815


title: CA1_CTL_0817


title: CA1_CTL_0854


title: Day 40 - 9

first: Siyuan

last: Zhang

address: 6001 Forest Park Rd

department: Department of Pathology

data_processing:
Base calling was performed using Real Time Analysis (RTA) v1.17.21.3 (Illumina)
RTA output was demultiplexed and converted to FastQ with Bcl2FastQ conversion software v1.8.4 (Illumina)
Reads were trimmed and aligned to homo sapiens and mus musculus reference genomes. Only reads that aligned uniquely to the human reference genome were kept for further analysis.
Normalization was performed using cuffnorm from the cufflinks data analysis pipeline.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include normalized FKPM values for each sample

growth_protocol: MDA-MB-231-tdTomato cells were routinely cultured in DMEM/F-12 supplemented with 10% fetal bovine serum and pen/strep

extract_protocol:
Total RNA was isoalted using the Acturus PicoPure RNA isolation kit (Life Technologies) according to the manufacturer's instructions
Sequencing libraries were constructed using the Ovation Single Cell RNA-Seq System (NuGEN).

tag: cell type

value: breast cancer cells were injected into the carotid artery of Rag1-/- mice

tag: timepoint

tag: cell line


title: Day 40 - 7


title: Day 40 - 8


title: mouse LSK, LCE407


title: Day 40 - 6


title: Day 40 - 5


title: Day 40 - 3


title: 1074083.HDD.Liver.Tumor.BALBc.mm10

city: Tarrytown

first: Alexandra

last: Eichten

state: NY

address: 777 old saw mill river road

institute: Regeneron Pharmaceuticals Inc.

description: male

data_processing:
The Cell Ranger Suite version 2.0 was used to perform sample de-multiplexing, barcode processing and single cell gene UMI (unique molecular index)
Genome_build: mm10 for mouse cells and B37 for human cells
Supplementary_files_format_and_content: tab-delimited text files include UMI values for samples/cells

source_name: HDD Liver+Tumor

growth_protocol: HDD with 50 μg of plasmids encoding mKras (G12D), Cas9 and sgTrp53 or mKras (G12D), Cas9 and sgRNA (empty vector) was used to induce liver tumors in CB.17/SCID, C57Bl6 and Balb/c mice; 1x10^6 HT-29 human colon carcinoma cells were grown intrahepatically in male CB.17/SCID mice.

extract_protocol:
Tissues (tumor bearing liver (tumor and adjacent normal), adjacent normal, liver tumors and naïve liver) were minced, enzymatically digested for 13 minutes using 2.5 mg/ml collagenase Type II, 2.5 mg/ml collagenase Type IV (Gibco), and 0.5 mg/ml DNase (Sigma) in PBS / 1% BSA at 37°C, treated with DMEM containing 10% FBS and filtered (70-µm nylon filter; Falcon). Single cell suspensions were subjected to 1X PharMLyse for 5 (tumor) or 10 (tumor bearing liver, adjacent normal tissue, naïve liver tissue) minutes, washed and subjected to dead cell removal kit (130-090-101, Miltenyi). The remaining cells were used for single cell sequencing.
Single cell suspensions from HT-29 tumor bearing livers underwent a depletion step using the following FITC conjugated Abs: single cell suspensions were incubated with anti-CD44 (338804, Biolegend) and anti-EpCam (324204, Biolegend) antibodies using 10 µl anti-FITC-beads for 1x10^6 total cells. The remaining cells were used for single cell sequencing.
Cellular suspensions (~6000 cells) were loaded on a Chromium Single Cell Instrument (10X Genomics) to generate single cell GEMs. Single-cell RNAseq libraries were prepared using version 1 Chromium Single cell 3’ Library, Gel beads & Mutiplex kit (10X Genomics).

treatment_protocol: no treatments

tag: strain

value: BALB/c

value: Liver+Tumor

value: adult

tag: genotype

value: WT


title: 1072369.HDD.Liver.Tumor.C57Bl6.mm10

description: male


title: 1074079.Normal.Liver.C57Bl6.mm10

description: male

source_name: Normal Liver

value: Normal Liver


title: 1074078.Normal.Liver.C57Bl6.mm10

description: male


title: 1074081.Normal.Liver.SCID.mm10

description: male

value: SCID


title: 1073082.HDD.Liver.Tumor.C57Bl6.mm10

description: male


title: 1074077.HDD.Liver.Tumor.C57Bl6.mm10

description: male


title: 1074082.HDD.Liver.Tumor.BALBc.mm10

description: male


title: 1074080.Normal.Liver.SCID.mm10

description: male


title: 1072368.HDD.Liver.Tumor.C57Bl6.mm10

description: male


title: 1072367.HDD.Liver.Tumor.BALBc.mm10

description: male


title: Day 40 - 1


title: Day 40 - 2


title: Day 7 - 3


title: 1072364.HDD.Liver.Tumor.SCID.mm10

description: male


title: 1072366.HDD.Liver.Tumor.BALBc.mm10

description: male


title: 1049461.HDD.Liver.SCID.mm10

description: male

source_name: HDD Liver

value: Liver


title: Day 7 - 2


title: Day 7 - 1


title: 1049462.HDD.Tumor.SCID.mm10

description: male

source_name: HDD Tumor

value: Tumor


title: 1049460.HDD.Tumor.BALBc.mm10

description: male

value: BALBc


title: Day 40 - 4


title: 1049459.HDD.Liver.BALBc.mm10

description: male


title: 1048341.HDD.Liver.Tumor.C57Bl6.mm10

description: male


title: 1048243.HDD.Liver.Tumor.BALBc.mm10

description: male


title: 1072363.HDD.Liver.Tumor.SCID.mm10

description: male


title: CLL-pilot1_TST_channel1

description:
Single-cell or single nucleus RNA-Seq (10X). The count matrix is stored as an HDF5 file.
For each cell or nucleus (row): cell name, annotation, median number of reads per cell, median number of UMIs per cell, median number of genes per cell, median fraction of UMIs mapping to mitochondrial genes, fraction of cells called as empty droplets, and fraction of cells called as doublets.

tag: sample type

value: CLL-pilot1 TST


title: 1048242.HDD.Tumor.BALBc.mm10

description: male


title: Hep YFV Asibi_3

city: Lyon

first: magali

last: roche

address: 8 avenue Rockfeller

institute: university lyon 1

data_processing:
base calling:
FastQ file generation using bcl2fastq v2.17.1.14 - no mismatch in index
Trimming using cutadapt v1.3 - parameters:
alignment using TopHat v2.06 with default parameters
Gene and spikes raw counts and normalization using Cufflink v2.0.2
Genome_build: Homo sapiens hg19, RefSeq annotation from UCSC
Supplementary_files_format_and_content: FPKMs

source_name: Hep YFV Asibi

extract_protocol:
RNA was harvested using QIAgen protocols. TruSeq RNA Library Prep Kit v2 (Illumina, San Diego, CA, USA) was used with 100 ng of total RNA for the construction of sequencing libraries.
ERCC spikes (ERCC RNA Spike-In Mix, Ref: 4456740 Thermofisher Scientific, Waltham, MA, USA) were added into RNA samples before library preparation to evaluate reproducibility and to normalize RNA-seq data. RNA libraries were prepared for sequencing using standard Illumina protocols
TruSeq stranded polyA library

value: hepatocytes

tag: model

value: monocellular model

tag: infection

value: wild-type

tag: time

value: 24h post infection


title: Hep YFV 17D_2

source_name: Hep YFV 17D

value: vaccine


title: Hep YFV 17D_1


title: Hep YFV 17D_3


title: Hep YFV 17D_4


title: Hep YFV Asibi_4


title: Hep YFV Asibi_2


title: Hep Control_3

source_name: Hep Control

value: control


title: Input centrocyte Ezh2(Y641F)fl/wt;Cγ1-cre 3

data_processing:
Ezh2 mutation causes global enrichment of H3K27me3 marks across the genome and relative normalization methods such as total sum scaling would fail to show the global increase, therefore Drosophila spike-ins were utilized to normalize the total amounts across samples.
Fastq files were trimmed and separated into the Drosophila and mouse cells using BBsplit with mm10 and dm6 reference genomes, only the reads unambiguously mapping to one of the genomes were taken.
The split reads were aligned using bwa mem to mm10 and dm6. Duplicate marking and removal was done by Picard.
Reads were normalized by comparing the IP vs input to get RPKM values and using the Drosophila spike-in read counts in a local regression model using the Comp-ChIP-seq method.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized and scaled bigwigs

source_name: germinal center B-cells from spleen

extract_protocol:
Cells were sorted into PBS and fixed with 1% formaldehyde. MicroChIP was performed using TrueMicroChip kit (Diagenode) according to manufacturer instructions with following modifications. For each replicate, ~20,000 cells were pooled together with 1 million Drosophila Kc167 cells and processed using Covaris E220E sonicator at peak power 140, duty factor 5, 5 cycles/burst, 20 min per sample. The sonicated samples were then cleared by 10 min centrifugation and mixed with 20 µg antibody (anti-H3K27me3, Cell Signaling 9733), and incubated overnight with rotation at 4ºC. Complexes were pulled down using Protein A Dynabeads (ThermoFisher Scientific), washed and de-crosslinked with kit buffers, and DNA was isolated using standard phenol-chloroform procedure.
Libraries were prepared using MicroPlex Library preparation kit (Diagenode), with 8 cycles of amplification

tag: spike-in

value: Drosophila

value: 3-4 months

tag: littermate

value: mixed litters


title: Input centrocyte Ezh2(Y641F)fl/wt;Cγ1-cre 2


title: Hep Control_4


title: Input centrocyte Ezh2(Y641F)fl/wt;Cγ1-cre 1


title: Hep YFV Asibi_1


title: 1048239.HDD.Liver.C57Bl6.mm10

description: male

tag: tissue

value: adult


title: 1048240.HDD.Tumor.C57Bl6.mm10

description: male

value: WT


title: Input centrocyte Cγ1-cre 3


title: Input centrocyte Cγ1-cre 1


title: Hep Control_1


title: 1048241.HDD.Liver.BALBc.mm10

description: male


title: Input centrocyte Cγ1-cre 2


title: Input centroblast Ezh2(Y641F)fl/wt;Cγ1-cre 3


title: Hep/Kup YFV 17D_4

source_name: Hep/Kup YFV 17D

value: hepatocytes + kupffer cells

value: pluricellular model


title: Hep/Kup YFV 17D_2


title: Hep Control_2


title: Hep/Kup YFV Asibi_2

source_name: Hep/Kup YFV Asibi


title: Hep/Kup YFV Asibi_4


title: Input centroblast Cγ1-cre 2


title: Hep/Kup YFV Asibi_3


title: Hep/Kup Control_4

source_name: Hep/Kup Control


title: Input centroblast Cγ1-cre 3


title: H3K27me3 ChIP centrocyte Ezh2(Y641F)fl/wt;Cγ1-cre 3

description: cells sorted: B220+, FAS+, CD38-, CXCR4-, CD86+


title: Hep/Kup YFV Asibi_1


title: Input centroblast Ezh2(Y641F)fl/wt;Cγ1-cre 2


title: Hep/Kup Control_3


title: Input centroblast Cγ1-cre 1


title: Input centroblast Ezh2(Y641F)fl/wt;Cγ1-cre 1


title: Hep/Kup YFV 17D_3


title: H3K27me3 ChIP centrocyte Ezh2(Y641F)fl/wt;Cγ1-cre 2


title: Hep/Kup Control_1


title: H3K27me3 ChIP centroblast Ezh2(Y641F)fl/wt;Cγ1-cre 3

description: cells sorted: B220+, FAS+, CD38-, CXCR4+, CD86-


title: H3K27me3 ChIP centrocyte Ezh2(Y641F)fl/wt;Cγ1-cre 1


title: H3K27me3 ChIP centrocyte Cγ1-cre 1


title: H3K27me3 ChIP centrocyte Cγ1-cre 2


title: H3K27me3 ChIP centrocyte Cγ1-cre 3


title: Hep/Kup Control_2


title: H3K27me3 ChIP centroblast Ezh2(Y641F)fl/wt;Cγ1-cre 1


title: Hep/Kup YFV 17D_1


title: ATAC-Seq TexInt_rep3

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

data_processing:
fastq files were aligned to GRCm38/mm10 reference  genome using bowtie2
Samtools/bedtools were used to process and filter mitochondrial reads and to remove duplicates.Peak calling was performed using MACS v2 (FDR q-value 0.01).
differential expression analysis was run using DESeq 2 package and data normalized
Differentially  accessible regions were identified following DESeq2 normalization using an FDR cut-off < 0.05 or 0.01 or otherwise indicated
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text file with normalized counts

source_name: CD8 T cells

growth_protocol: At D30 p.i. with Cl13, CD8 T cells were isolated from spleens of infected recipients

extract_protocol:
Lysates were centrifuge (750xg,  10min, 4oC) and nuclei were resuspended in 50μl of transposition reaction mix (TD  buffer [25μl], Tn5 Transposase [2.5μl], nuclease-free water [22.5μl]; (Illumina)) and  incubated for 30min at 37oC.
Transposed DNA fragments were purified using a  Qiagen Reaction MiniElute Kit, barcoded with NEXTERA dual indexes (Illumina)  and amplified by PCR for 11 cycles using NEBNext High Fidelity 2x PCR Master  Mix (New England Biolabs). PCR products were purified using a PCR Purification  Kit (Qiagen) and amplified fragments size was verified on a 2200 TapeStation  (Agilent Technologies) using High Sensitivity D1000 ScreenTapes (Agilent  Technologies). Libraries were quantified by qPCR using a KAPA Library Quant Kit  (KAPA Biosystems).

treatment_protocol: Sorted cells (2.5-to-5x104) were washed  twice in cold PBS and resuspended in 50μl of cold lysis buffer (10nM Tris-HCl, pH  7.4, 10mM NaCl, 3mM MgCl2, 0.1% Tween).

tag: background strain

tag: treatment

value: LCMV Clone 13 infection


title: ATAC-Seq Tex Term_rep1


title: ATAC-Seq Tex Term_rep2


title: ATAC-Seq Tex Term_rep3


title: H3K27me3 ChIP centroblast Cγ1-cre 3

tag: age


title: H3K27me3 ChIP centroblast Ezh2(Y641F)fl/wt;Cγ1-cre 2


title: H3K27me3 ChIP centroblast Cγ1-cre 1


title: ATAC-Seq TexInt_rep1


title: ATAC-Seq TexProg2_rep3


title: ATAC-Seq TexProg1_rep2


title: ATAC-Seq TexProg2_rep1


title: ATAC-Seq TexProg1_rep1


title: RNA-Seq Tex Term_rep3

description:
TexTerm_rep3
Tterm3_S2

data_processing:
Raw FASTQ files from RNAseq paired-end sequencing were aligned to the  GRCm38/mm10 reference genome using Kallisto
Low count transcripts were removed and trimmed using the TMM normalization method
Genes with differential  expression across samples (DEGs) were assessed using the R package Limma
Differential genes were calculated using a FDR cutoff of 0.01 and Log2 fold change of 1 otherwise indicated
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text file with normalized counts

growth_protocol: At D30 post infection. with Cl13, CD8 T cells were isolated from spleens of infected recipients

extract_protocol:
mRNA was extracted using RNeasy Plus Micro kit  (Qiagen) following manufacturer’s protocol and eluted in 14μl of RNAse free water.  mRNA quality was assessed on a 2200 TapeStation (Agilent Technologies) using  High Sensitivity RNA ScreenTape (Agilent Technologies).mRNA from each  biological replicate (5ng/sample) was converted into cDNA and amplified (9 cycles)  using the SMART-Seq V4 Ultra Low Input RNA Kit (Takara Bio).
10ng of cDNA  was used to prepare DNA libraries using Nextera XT DNA Library Prep Kit  (Illumina). Barcoded samples were pooled, diluted at 1.8pM, loaded onto a TG  NextSeq 500/550 High Output Kit v2 (150 cycles, 400M reads, Illumina) and  paired-end sequencing was performed on a NextSeq 550 (Illumina)

treatment_protocol: Sorted cells were centrifuged, resuspended in 350μl of RLT buffer (RNeasy Plus  Micro kit, Qiagen) in DNA LoBind tubes (Eppendorf), vortexed for 30s, flash-frozen  on dry ice and stored at -80oC

value: LCMV Clone13 infection


title: RNA-Seq Tex Term_rep2

description:
TexTerm_rep2
Tterm2_S8


title: ATAC-Seq TexInt_rep2


title: RNA-Seq TexInt_rep3

description:
TexInt_rep3
LateT3_S3


title: RNA-Seq TexProg2_rep1

description:
TexProg2_rep1
EarlyT1_S14


title: RNA-Seq TexProg2_rep3

description:
TexProg2_rep3
EarlyT3_S9


title: RNA-Seq TexProg2_rep2

description:
TexProg2_rep2
EarlyT2_S11


title: H3K27me3 ChIP centroblast Cγ1-cre 2


title: RNA-Seq TexInt_rep1

description:
TexInt_rep1
LateT1_S16


title: RNA-Seq TexProg1_rep3

description:
TexProg1_rep3
Ly108hi3_S6


title: ATAC-Seq TexProg2_rep2


title: RNA-Seq TexProg1_rep2

description:
TexProg1_rep2
Ly108hi2_S13


title: RNA-Seq TexInt_rep2

description:
TexInt_rep2
LateT2_S18


title: RNA-Seq TexProg1_rep1

description:
TexProg1_rep1
Ly108hi1_S15


title: Rad21_degron_IAA_GRO_rep3

city: Boston

first: Frederick

middle: W

last: Alt

address: 1 Blackfan Circle

department: PCMM

institute: Boston Children's Hospital

description: aligned to AJ851868/mm20 hybrid genome

data_processing:
Library strategy: Gro-Seq
Reads were aligned using bowtie 2.2.8 with --non-deterministic flag
reads were quantified for specific loci using samtools version 1.8
bigwig files were produced using RseqQ package
Genome_build: AJ851868/mm9 hybrid genome
Supplementary_files_format_and_content: bigwig files contain peak information for samples

source_name: v-Abl transformed pro-B cell line

extract_protocol:
Briefly, 10 million cells were permeabilized with permeabilization buffer (10 mM Tris-HCl, pH 7.4, 300 mM sucrose, 10 mM KCl, 5 mM MgCl2, 1 mM EGTA, 0.05% Tween-20, 0.1% NP40 substitute, 0.5 mM DTT, one tablet of protease inhibitors per 50 ml and 4 units Rnase inhibitor per ml) and resuspended in 100 ul storage buffer (10 mM Tris-HCl, pHHH 8.0, 25% (vol/vol) glycerol, 5 mM MgCl2, 0.1 mM EDTA and 5 mM DTT). Permeabilized cells were subjected to nuclear run-on (2xRun-on mix: 5 mM Tris-Cl, PH 8.0, 2.5 mM MgCl2, 0.5 mM DTT, 150 mM KCl, 0.5 mM ATP, 0.5 mM CTP, 0.5 mM GTP, 0.5 mM BrUTP, 10 units of RNase inhibitor, 1% sarkosyl) at 37o for 5 min, followed by Trizol-based RNA extraction.
Illumina adapters were ligated to RNA followed by cDNA generation with reverse transcriptase.  Libraries were PCR-amplified with Illumina primers and subjected to sequencing.

value: Rad21degron, Emu-Bcl2, RAG2 deficient

value: 500 uM IAA 6h, 3 uM STI-571 with 500uM IAA treated for 4 days


title: Rad21_degron_NT_GRO_rep3

description: aligned to AJ851868/mm19 hybrid genome

value: 3 uM STI-571 treated for 4 days


title: DBA 15 liver

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

country: Germany

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

description: Hepatic gene expression of DBA mice on HFD.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters  to obtain background subtracted and spatially detrended Processed Signal intensities. Data was filtered using 0.1 quantile cutoff to eliminate low level signals.

source_name: liver

label_protocol: Cy3-labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit from Agilent according to the manufacturer's instructions, followed by RNeasy column purification.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from murine tissue using TRIzol™ reagent (Invitrogen, Germany). From parental NZO, B6, C3H, 129/Ola and DBA mice (6 weeks of age), samples of liver were aliquoted for RNA extraction. The procedure was carried out according to manufacturer’s instructions. RNA quality was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Germany) and the manufacturer’s instructions were followed to measure RNA integrity (RIN). Samples with RIN values >8 were subsequently selected for microarray analysis.

treatment_protocol: Mice were fed a high fat diet (45%, fat, Research Diets)

tag: gender

value: male

value: HFD

value: liver


title: Rad21_degron_IAA_GRO_rep2

description: aligned to AJ851868/mm18 hybrid genome


title: 129/ola m9 liver

description: Hepatic gene expression of 129/Ola mice on HFD.


title: 129/ola m4 liver


title: 129/ola m5 liver


title: RNA-Seq Tex Term_rep1

description:
TexTerm_rep1
Tterm1_S12


title: Heart tissue_Normal diet_rep3

city: Suzhou

first: Tianqing

last: Peng

state: Jiangsu

address: No.199 Ren'ai Road

department: IBMS

institute: Soochow University

description: Gene expression after 4 months of normal diet feeding

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 min at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2505C) using one color scan setting for 8x60K  array slides (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0 (Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: Heart tissue_Normal diet_4 months

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng RNA using the One-Color Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by purification using RNeasy Mini Kit (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted and purifed from   heart tissues using the mirVana™ RNA Isolation Kit   and QIAGEN RNeasy® Mini Kit, respectively, following   the manufacturers’ instructions.

treatment_protocol: Male C57BL/6 mice at age of 4 weeks were maintained on either a high fat diet (60% kcal from fat, HFD) or standard chow diet (normal diet, ND) for 4 months. Mice were sacrificed by the end of the 4th months with hearts harvested and subjected to micro-array analysis

tag: Sex

value: standard chow diet (normal diet, ND)

value: heart


title: Rad21_degron_NT_GRO_rep2

description: aligned to AJ851868/mm17 hybrid genome


title: Heart tissue_Normal diet_rep1


title: Heart tissue_High fat diet_rep2

description: Gene expression after 4 months of high fat diet feeding

source_name: Heart tissue_High fat diet_4 months

value: high fat diet (60% kcal from fat, HFD)


title: 129/ola m7 liver


title: Heart tissue_Normal diet_rep2


title: DBA 8 liver


title: Heart tissue_High fat diet_rep3


title: NZO 11 liver

description: Hepatic gene expression of NZO mice on HFD.

value: NZO/HiBomDife


title: Rad21_degron_IAA_GRO_rep1

description: aligned to AJ851868/mm16 hybrid genome


title: DBA 5 liver


title: NZO 7 liver


title: CTCF_degron_IAA_GRO_rep3

description: aligned to AJ851868/mm14 hybrid genome

value: CTCFdegron, Emu-Bcl2, RAG2 deficient


title: Rad21_degron_NT_GRO_rep1

description: aligned to AJ851868/mm15 hybrid genome


title: NZO 9 liver


title: DBA 9 liver


title: B6 11 liver

description: Hepatic gene expression of B6 mice on HFD.


title: NZO 3 liver


title: B6 10 liver


title: B6 15 liver


title: CTCF_degron_IAA_GRO_rep2

description: aligned to AJ851868/mm12 hybrid genome


title: CTCFChIP_HCT116spikingin_parental_input_rep2_3

description: aligned to AJ851868/mm9 hybrid genome

data_processing:
Reads were aligned using bowtie 2.2.8 with --non-deterministic flag
reads were quantified for specific loci using samtools version 1.8
bigwig files were produced using RseqQ package
Genome_build: AJ851868/mm9 hybrid genome,hg19
Supplementary_files_format_and_content: bigwig files contain peak information for samples

extract_protocol:
Crosslinked cells were treated with cell lysis buffer (5mM PIPES pH 8, 85mM KCl, 0.5% NP-40) and nuclei lysis buffer (50mM TrisCl pH 8.1, 10mM EDTA, 1% SDS) and subjected to sonication. IP was performed using  Rad21 antibody(Abcam, #ab992) or CTCF antibody (Millipore, #07-729). IP and Input DNA were de-crosslinked at 65o overnight and purified via Qiagen PCR purification columns.
ChIP-Seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (NEB, #E7645)

value: Emu-Bcl2, RAG2 deficient

tag: antibody


title: CTCFChIP_HCT116spikingin_CTCFdegron_IAA_input_rep2_3

description: aligned to AJ851868/mm9 hybrid genome


title: Parental_GRO_rep2

description: aligned to AJ851868/mm11 hybrid genome


title: Rad21ChIP_HCT116spikingin_CTCFdegron_IAA_rep3

description: aligned to AJ851868/mm9 hybrid genome

value: Rad21 antibody (Abcam, #ab992)


title: B6 9 liver


title: Rad21ChIP_HCT116spikingin_parental_rep3

description: aligned to AJ851868/mm9 hybrid genome


title: CD4+_Input

city: Bellinzona

first: Samuele

last: Notarbartolo

address: Via Vela 6

country: Switzerland

institute: Institute for Research in Biomedicine

data_processing:
Data processing was run on the Fish the ChIPs automated pipline (Barozzi, I., Termanini, A., Minucci, S. & Natoli, G. Fish the ChIPs: a pipeline for automated genomic annotation of ChIP-Seq data. Biol Direct 6, 51 2011).
Alignment: Bowtie
Peak calling: MACS 1.4
Genome_build: Homo sapiens (hg19)
Supplementary_files_format_and_content: Processed data included in the submission are: Excel files (.merge.xlsx) containing peaks genomic coordinates, MACS p-value, FDR and fold enrichment; tiled data files (.tdf) files for ChIP-seq data graphical visualization in the Integrative Genome Viewer software

source_name: primary CD4+ T lymphocytes

growth_protocol: Blood from healthy donors was obtained from the Swiss Blood Donation Centres of Basel and Lugano and was used in compliance with the Federal Office of Public Health (authorization n. A000197/2 to F.S.). PBMCs were isolated from buffy-coat by Ficoll-Paque Plus (GE Healthcare Life Sciences) gradient and samples were enriched for CD4+ T cells by positive selection with magnetic microbeads (Miltenyi Biotec) to an average purity of 97.5%.

extract_protocol:
ChIP was performed as previously described (Blecher-Gonen, R. et al. Nat. Protoc. 8, 539-554. 2013). Briefly, 50 x 10^6 cells were fixed in 1% formaldehyde (Sigma-Aldrich) for exactly 10 min at RT under rotation. Crosslinking reaction was quenched by the addition of 125 mM Tris-HCl pH 7.6 for 5 min at RT. Cells were washed 3 times with ice-cold PBS. The cell pellet was then resuspended in RIPA buffer (without Triton X-100) supplemented with protease inhibitors (Halt™ Protease Inhibitor Cocktail, Thermo Scientific) and frozen at -80°C. Chromatin was sheared with a Bioruptor® Plus bath sonicator (Diagenode) applying the following settings: 5 x 10 cycles 30 sec ON and 60 sec OFF, high intensity, at 4°C. Every 10 cycles samples were mixed and briefly spun down. The shearing of DNA into 200-300 bp fragments was evaluated by electrophoresis on a 1.5% agarose gel. Prior to IP, 1% Triton X-100 was added to the sample and an aliquot was stored at -20°C as input control. Antibody-bound Protein G dynabeads™ (Life Technologies) were added to each sample (10 μg ETS-1 antibody per sample) and immunoprecipitation was performed overnight at 4°C on a rotating wheel. The day after, dynabeads were thoroughly washed: 6 times with RIPA buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% 1% Na-Deoxycholate), then twice with RIPA-500 buffer (10 mM Tris-HCl pH 8.0, 500 mM NaCl, 1 mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% 1% Na-Deoxycholate), twice with LiCl wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Na-Deoxycholate), and once with TE buffer. ChIP DNA was eluted with direct elution buffer (10 mM Tris-HCl pH 8.0, 300 mM NaCl, 5 mM EDTA, 0.5% SDS) and subjected to RNAse A and proteinase K treatment before overnight de-crosslinking at 65°C. Finally, de-crosslinked DNA was purified with SPRI magnetic beads and eluted in 10 mM Tris-Cl pH 8.0. ChIP DNA was quantified by picogreen on a Qubit 2.0 device.
ChIP-seq libraries were prepared as previously described (Blecher-Gonen, R. et al. Nat. Protoc. 8, 539-554. 2013).

treatment_protocol: CD4+ T cells were processed directly after isolation without any additional treatment.

tag: subject status

value: healthy donor

value: peripheral blood

tag: cell type

value: ex-vivo magnetic sorted CD4+ T cells

tag: activation state

value: resting


title: Rad21ChIP_HCT116spikingin_parental_rep2

description: aligned to AJ851868/mm9 hybrid genome

tag: genotype


title: RNA 40%-360-1

city: Münster

first: Sara

middle: A

last: Wickström

address: Röntgenstraße 20

department: Cell & Tissue Dynamics

institute: Max Planck Institute for Molecular Biomedicine

data_processing:
kallisto (version 0.45.0) was used to map reads
featureCounts (version v1.6.2) was used to estimate gene counts
DEseq2 (version 1.22.2) was used to calculate pairwise differential gene expression
genome build; GRCh38
processed data files format and content; normalized_annotated_counts_all.results.tsv containing annotated DEseq2 results

source_name: normal human epidermal keratinocyte

growth_protocol: Human epidermal stem/progenitor cells (EPCs) isolated from pooled neonatal human foreskin biopsies were purchased from CellnTec (HPEKp) and grown in suppliers cell culture medium (CnT-Prime; CellnTec). Cells were used in passages 2.

extract_protocol:
For RNA-Seq total RNA was isolated using the NucleoSpin RNA Plus kit (Macherey&Nagel). After quantification and quality control using Agilent 2200 TapeStation, total RNA amounts were adjusted and libraries were prepared using the TruSeq Stranded Total RNA kit with Ribo-zero gold rRNA depletion (Illumina).
For RNA sequencing libraries were prepared using the TruSeq Stranded Total RNA kit with Ribo-zero gold rRNA depletion (Illumina)

treatment_protocol: 400,000 cells were plated on fibronectin-coated (20 µg/ml) elastic silicone chambers 16 hours prior to initiating 40% cyclic uniaxial stretch at 0.1Hz in a custom-build uniaxial stretcher. 3 h before initiation of cyclic stretch, culture medium was replaced by medium containing 1.8 mM Ca2+.Cells were stretched for indicated amount of time.

value: skin

value: normal human epidermal keratinocyte

tag: passage

value: Passage 2


title: RNA 40%-360-2


title: RNA 40%-360-3


title: CTCFChIP_CTCFdegron_IAA_rep3

description: aligned to AJ851868/mm9 hybrid genome

value: CTCF antibody (Millipore, #07-729)

value: 500 uM IAA 6h, 3 uM STI-571 with 500uM IAA treated for 4 days


title: C3H m5 liver

description: Hepatic gene expression of C3H mice on HFD.

value: male

tag: strain

value: HFD

value: liver


title: RNA 40%-30-3


title: RNA 40%-30-2


title: C3H m1 liver


title: Heart tissue_High fat diet_rep1

value: high fat diet (60% kcal from fat, HFD)

value: heart


title: C3H m3 liver


title: CTCFChIP_CTCFdegron_IAA_rep2

description: aligned to AJ851868/mm9 hybrid genome

value: CTCFdegron, Emu-Bcl2, RAG2 deficient


title: CTCFChIP_parental_NT_rep3

description: aligned to AJ851868/mm9 hybrid genome

value: Emu-Bcl2, RAG2 deficient

value: 3 uM STI-571 treated for 4 days


title: RNA 40%-30-1


title: RNA 0%-3


title: Parental_GRO_rep3

description: aligned to AJ851868/mm13 hybrid genome


title: CTCFChIP_parental_NT_rep2

description: aligned to AJ851868/mm9 hybrid genome


title: RNA 0%-2


title: CD4+_ETS1_ChIP

value: healthy donor

tag: chip antibody

value: Ets-1 (C-20); Santa Cruz Biotechnology, sc-350X, L1012


title: C3H m2 liver


title: Rad21ChIP_HCT116spikingin_Rad21degron_IAA_input_rep2

description: aligned to AJ851868/mm9 hybrid genome

value: Rad21degron, Emu-Bcl2, RAG2 deficient


title: RNA 0%-1


title: Rad21ChIP_HCT116spikingin_Rad21degron_IAA_rep2

description: aligned to AJ851868/mm9 hybrid genome

value: Rad21 antibody (Abcam, #ab992)


title: Rad21ChIP_HCT116spikingin_CTCFdegron_IAA_rep2

description: aligned to AJ851868/mm9 hybrid genome


title: Rad21ChIP_HCT116spikingin_Rad21degron_NT_input_rep2

description: aligned to AJ851868/mm9 hybrid genome


title: JH4_parental_IAA_pool_offtarget

description: aligned to AJ851868/mm9 hybrid genome

data_processing:
Library strategy: Linear-amplification PCR-mediated HTGTS
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the indicated reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9, mm9_DFL16.1-RSS-U-inversion, mm9_DFL16.1-RSS-D-inversion, mm9_DFL16.1-inversion, mm9_DQ52-inversion, mm9_DH-cluster-inversion, mm9_DQ52-replace-DFL16.1,  mm9_DQ52inv-replace-DFL16.1, mm9_DFL16.1-replace-DQ52, mm9_DFL16.1inv-replace-DQ52, mm9_DFL16.1JH4
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

source_name: v- Abl transformed pro-B cell line

extract_protocol:
DNA was lysed overnight at 56degC in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, precipitated by isopropanol and dissolved in buffer containing 10mM Tris-HCl pH7.5, 0.1mM EDTA
LAM-HTGTS V(D)J-Seq libraries were prepared using linear-amplification PCR-mediated HTGTS.

treatment_protocol: 3 uM STI-571 treated for 4 days

value: v- Abl transformed pro-B cell line

value: WT, Emu-Bcl2, RAG2 deficient

tag: treatment protocol

value: RAG2 nucleofected,  500 uM IAA 6h, 3 uM STI-571 with 500uM IAA treated for 4 days

tag: growth protocol


title: Rad21ChIP_HCT116spikingin_Rad21degron_NT_rep2

description: aligned to AJ851868/mm9 hybrid genome


title: 3C_iEm_IGCR1deleted_Rad21degron_IAA_rep2

description: aligned to AJ851868/mm9 hybrid genome

data_processing:
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to inditated reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: AJ851868/mm9 hybrid genome
Supplementary_files_format_and_content: bedgraph files

extract_protocol:
DNA was lysed overnight at 56degC in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, precipitated by isopropanol and dissolved in buffer containing 10mM Tris-HCl pH7.5, 0.1mM EDTA
3C-HTGTS libraries were prepared using linear-amplification PCR-mediated HTGTS.
Linear-amplificate PCR-mediated HTGTS

value: IGCR1deleted, Rad21degron, Emu-Bcl2, RAG2 deficient


title: JH4_CTCFdegron_IAA_pool_offtarget

description: aligned to AJ851868/mm9 hybrid genome


title: JH4_CTCFdegron_IAA_rep5_offtarget

description: aligned to AJ851868/mm9 hybrid genome


title: 3C_iEm_IGCR1deleted_Rad21degron_IAA_rep1

description: aligned to AJ851868/mm9 hybrid genome

value: 500 uM IAA 6h, 3 uM STI-571 with 500uM IAA treated for 4 days


title: 3C_iEm_IGCR1deleted_Rad21degron_NT_rep2

description: aligned to AJ851868/mm9 hybrid genome

value: IGCR1deleted,Rad21degron, Emu-Bcl2, RAG2 deficient


title: 3C_iEm_IGCR1deleted_Rad21degron_NT_rep1

description: aligned to AJ851868/mm9 hybrid genome


title: JH4_CTCFdegron_IAA_rep4_offtarget

description: aligned to AJ851868/mm9 hybrid genome


title: H3K27ac_HiChIP_MED14-dTAG_2h_dTAG7_A

data_processing:
conversion and demultiplexing: Illumina2bam
FASTQ files were in silico digested by looking for the restriction enzyme religations sites GATCGATC. Only the 5 prime part of a read is kept after removing the remainder of a read when cut at the restriction site. All non cut reads are kept.
All filtered reads are then mapped to human genome assembly hg19 with bowtie2 (version 2.2.3) using options --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder
The human genome was insilico digested with MboI enzyme and mapped reads are assigned to the insilico digested genome fragments. Read pairs are tagged as valid if they had the correct orientation and are on different fragments.
Genome_build: hg19
Supplementary_files_format_and_content: hic generation: .hic files were generated with the 'pre' tool from juicer tools (version 1.8.9).

extract_protocol:
Chromatin contacts were generated and pulldown performed as previously described (PMID: 27643841).
Library construction using Illumina Tn5.

tag: cell line

value: chronic myeloid leukemia cell line

tag: genotype/variation

value: 2h 500nM dTAG7

value: H3K27ac (Abcam ab4729)


title: JH4_CTCFdegron_IAA_rep1_offtarget

description: aligned to AJ851868/mm9 hybrid genome

tag: tissue


title: H3K27ac_HiChIP_MED14-dTAG_2h_dTAG7_B

tag: treatment


title: H3K27ac_HiChIP_MED14-dTAG_2h_DMSO_A

value: 2h DMSO


title: PRO-seq_MJ-17-76_MED14-dTAG_2h_dTAG7_C

description: cross-compare only to MJ-17-76 samples

data_processing:
library strategy: PROT-seq
conversion and demultiplexing: Illumina2bam
FASTQ conversion: bamtools v2.3.0 convert -format fastq
trimming: cutadapt v1.9.1 -a "TGGAATTCTCGGGTGCCAAGG" --minimum-length=10
reverse_complement: fastx_reverse_complement v0.0.14
alignment: 'bowtie v2.2.9 --very-sensitive' to a fused index of hg38_dm6_rDNA-U13369; later filtered with 'samtools v1.7 view -q 20'
spike-in_counting: number of reads aligning to dm6 were counted with "samtools view | awk '$3 ~ /dm6_/ {++dm6_count}'" and normalization factor alpha=1e6/dm6_count (see PMID: 25437568)
signal_trimming_to_3prime_base: only 3' base (Pol II active center) was retained in BED files with "bedtools v2.26.0 bamtobed | awk '($6 == "+") {print $1,$3-1,$3,$4,$5,$6}; ($6 == "-") {print $1,$2,$2+1,$4,$5,$6}'"
Genome_build: hg38
Supplementary_files_format_and_content: bigWig generation: spike-in normalized, strand-specific signal tracks were computed with 'bedtools v2.26.0 genomeCoverageBed -bg -strand -scale $alpha' followed by UCSC 'bedGraphToBigWig v4'

extract_protocol:
PRO-seq libraries were generated as previously described (PMID: 27442863), with 4 parallel run-on reactions per sample. Total RNA was merged after the first RNA precipitation step.
Library construction by PCR amplification with custom primers.

treatment_protocol: 60mio cells were treated for 0.5-2h with 500nM dTAG7, 500nM NVP2, or DMSO and 5% Drosophila S2 cells added for cross-normalization before extracting nuclei on ice.

tag: experiment id

tag: molecule subtype

value: nuclear RNA


title: H3K27ac_HiChIP_MED14-dTAG_2h_DMSO_B


title: 3C_JH4_CTCFdegron_IAA_rep1

description: aligned to AJ851868/mm9 hybrid genome

value: CTCFdegron, Emu-Bcl2, RAG2 deficient


title: PRO-seq_MJ-17-76_MED14-dTAG_2h_dTAG7_D

description: cross-compare only to MJ-17-76 samples


title: PRO-seq_MJ-17-76_MED14-dTAG_2h_DMSO_D

description: cross-compare only to MJ-17-76 samples


title: 3C_JH4_parental_rep1

description: aligned to AJ851868/mm9 hybrid genome

value: Emu-Bcl2, RAG2 deficient

value: 3 uM STI-571 treated for 4 days


title: PRO-seq_MJ-17-76_MED14-dTAG_2h_DMSO_C

description: cross-compare only to MJ-17-76 samples


title: 3C_iEm_Rad21degron_IAA_rep3

description: aligned to AJ851868/mm9 hybrid genome


title: PRO-seq_MJ-19-30_MED14-dTAG_2h_dTAG7_30min_NVP2_B

description: cross-compare only to MJ-19-30 samples

value: 2h 500nM dTAG7 and last 30min 500nM NVP2


title: JH4_parental_IAA_rep3_offtarget

description: aligned to AJ851868/mm9 hybrid genome


title: JH4_parental_IAA_rep4_offtarget

description: aligned to AJ851868/mm9 hybrid genome


title: PRO-seq_MJ-19-30_MED14-dTAG_2h_dTAG7_30min_NVP2_A

description: cross-compare only to MJ-19-30 samples


title: JH4_CTCFdegron_IAA_rep6_offtarget

description: aligned to AJ851868/mm9 hybrid genome


title: 3C_iEm_Rad21degron_NT_rep3

description: aligned to AJ851868/mm9 hybrid genome

value: Rad21degron, Emu-Bcl2, RAG2 deficient


title: JH4_CTCFdegron_IAA_rep3_offtarget

description: aligned to AJ851868/mm9 hybrid genome


title: PRO-seq_MJ-19-30_MED14-dTAG_30min_NVP2_A

description: cross-compare only to MJ-19-30 samples

value: 30min 500nM NVP2


title: JH4_CTCFdegron_IAA_rep2_offtarget

description: aligned to AJ851868/mm9 hybrid genome

value: v- Abl transformed pro-B cell line


title: JH4_parental_IAA_rep2_offtarget

description: aligned to AJ851868/mm9 hybrid genome

value: WT, Emu-Bcl2, RAG2 deficient


title: PRO-seq_MJ-19-30_MED14-dTAG_30min_NVP2_B

description: cross-compare only to MJ-19-30 samples


title: PRO-seq_MJ-19-30_MED14-dTAG_2h_DMSO_B

description: cross-compare only to MJ-19-30 samples


title: 3C_VH81X_Rad21degron_NT_rep3

description: aligned to AJ851868/mm9 hybrid genome


title: JH4_BMProB_rep6

description: aligned to AJ851868/mm9 hybrid genome

source_name: 129SV mouse BM pro-B cell

value: 129SV mouse BM pro-B cell

value: Wild-type

value: Sorted pro-B cells by FACS (B220+CD43+IgM-)


title: PRO-seq_MJ-19-14_MED14-dTAG_1h_dTAG7_B

description: cross-compare only to MJ-19-14 samples

value: 1h 500nM dTAG7


title: 3C_VH81X_Rad21degron_IAA_rep3

description: aligned to AJ851868/mm9 hybrid genome

value: 500 uM IAA 6h, 3 uM STI-571 with 500uM IAA treated for 4 days


title: PRO-seq_MJ-19-14_MED14-dTAG_1h_DMSO_B

description: cross-compare only to MJ-19-14 samples

value: chronic myeloid leukemia cell line

value: 1h DMSO


title: 3C_DQ52JH1_CTCFdegron_IAA_rep1

description: aligned to AJ851868/mm9 hybrid genome


title: PRO-seq_MJ-19-14_MED14-dTAG_1h_dTAG7_A

description: cross-compare only to MJ-19-14 samples


title: 3C_DQ52JH1_BMProB_rep1

description: aligned to AJ851868/mm9 hybrid genome

growth_protocol: opti-MEM medium with 10% FBS

value: 2ng/ml IL-7 and 2ng/ml SCF for 4 days


title: 3C_DQ52JH1_parental_rep1

description: aligned to AJ851868/mm9 hybrid genome


title: PRO-seq_MJ-19-30_MED14-dTAG_2h_dTAG7_B

description: cross-compare only to MJ-19-30 samples

value: 2h 500nM dTAG7

value: nuclear RNA


title: PRO-seq_MJ-19-30_MED14-dTAG_2h_DMSO_A

description: cross-compare only to MJ-19-30 samples

value: 2h DMSO


title: JH4_CTCFdegron_NT_b_rep6

description: aligned to AJ851868/mm9 hybrid genome

value: CTCFdegron, Emu-Bcl2, RAG2 deficient

value: RAG2 nucleofected, 3 uM STI-571 treated for 4 days


title: w303a_200U_20min

first: Hyelim

last: Jo

address: 335 Gwahangno, Yuseong-Gu

department: Biological science

data_processing:
Alignment: bowtie2 (Index; Saccer3)
Sorting and converting to bam files: samtools
Visualization: HOMER
Converting to BigWig files: bedGraphToBigWig
Genome_build: Saccer3
Supplementary_files_format_and_content: BigWig files of the processed ChIP-seq&ATAC-seq raw files and Wig files of the MNase-seq

organism: Saccharomyces cerevisiae

growth_protocol: Yeast strains were grown at 30℃ in  YP medium containing 2% glucose.

extract_protocol:
The amplified library was purified with a Qiagen PCR purification kit.
ChIP-seq libraries for ChIP-seq were prepared 10ng of input DNA or 1 to  10 ng of eluted ChIP DNA using NEXT-flex ChIP-seq kit(Bioo Scientific,5143). ATAC-seq libraries were prepared customized adapter primer. The libraries for MNase-seq were prepared using ase-seq were prepared alsing and TruSeq Nano DNA LT Library Prer Kit(Illumina, FC-121-4001/4002). 100ng of Mononucleosome

treatment_protocol: spheroplasted with 50 mg/ml zymolyase 20T, and then incubated with transposase. Transposition reactions and PCR amplifications were performed.

tag: background genotype

value: wild type(w303a)


title: chd1_200U_20min

tag: antibody