title: RRC8

first: Tetsushi

last: Iida

address: 1-1-1 Yayoi

department: Research Center for Biological Visualization

institute: The Institute for Quantitative Biosciences (IQB), The University of Tokyo

description:
RRC_Mt009
Pooled linkage analysis. Mutant clones from ascospores of backcrossed yeast strains were cultured in YPD at 30 Cerecius overnight. Prepared genomic DNA was shared by Covaris S220 and purified. Sequencing libraries were prepared by KAPA  kit and TruSeqHT-compatible adaptors.

data_processing:
Library strategy: Whole genome sequencing
To identify causative rcc-mutations, FASTQ files were analyzed with the webtool Mudi (version2, http://naoii.nig.ac.jp/mudi_top.html)
Genome_build: Saccharomyces_cerevisiae.EF4.68
Supplementary_files_format_and_content: tsv files were generated by the webtool "mudi". Mutations called by the analysis were listed.

organism: Saccharomyces cerevisiae BY4741

source_name: Stationary phase yeast cells

growth_protocol: Yeast mutant clones were separately cultured in 1 ml of 1% Bacto Yeast Extract (BD), 2% Bacto Peptone and 2% Glucose (Wako) (YPD) at 30｡C with shaking in plate shaker.

extract_protocol:
Cells for each mutant group were harvested together by centrifugation at 3,000 g at room temperature, washed twice with water and suspended in 500 µl 0.2 M Tris-HCl pH8.0, 2.5% 2-ME. After 30 minutes incubation at 30°C, cells were resuspended in 500 µl 40 mM NaPhosphate pH6.8, 1 M sorbitol and 2% Zymolyase 100T (Nacali tesque, 07665-55) and incubated at 37°C for 1 hour. The resulting spheroplasts were harvested by centrifugation at 9,000 g at room temperature and resuspended in 500 µl of pre-warmed 50 mM Tris-HCl pH7.5, 0.2 M NaCl, 0.1 M EDTA and 5% SDS. After 30 minutes incubation at 65°C, the cell lysate was extracted twice with phenol/chloroform/isoamylalcohol (pH 8.0) and combined with1 ml of ethanol. The precipitated DNA was picked up, rinsed with 70% ethanol, dried and dissolved in 250 µl 10 mM Tris-HCl pH8.0, 1 mM EDTA and 0.4mg/ml RNase A (Nippon gene, 313-01461) and incubated at 37°C for 2 hours. The DNA was purified by phenol/chloroform/isoamylalcohol (pH 8.0) extraction and ethanol precipitated without salt and dissolved in 150 µl 10 mM Tris-HCl pH8.0, 1 mM EDTA.
For NGS sequencing, 2 µg DNA in 100 µl TE buffer was sheared at 4°C with a Covaris S220 ultrasonicator (Covaris) using a microtube AFA fiber (Covaris, 520045) with the following settings: peak power 140, duty factor 10, cycle/burst 200, duration 45 s. The resulting 400~500 bp DNA fragments were separated on an 1.5% agarose gel and purified with a NucleoSpin Gel and PCR Clean-up kit. Genomic DNA libraries for NGS sequencing were prepared with 100 ng gel-purified DNA and TruSeqHT (Illumina) compatible adaptors and amplified by 3 PCR cycles (98°C 15s, 50°C 30 s and 72°C 1 minute) using a KAPA library preparation kit (KAPA biosystems, KK8201). After purification of the PCR reactions with 1 volume AMpureXP beads (Beckman Coulter, A63881), equimolar mixtures of the libraries were sequenced on a MiSeq system (Illumina). Reactions for 200 bp, paired-end runs were prepared with the MiSeq Reagent Kit v3 (Illumina, MS-102-3003).

tag: strain name

tag: mating type

value: MATa and MAT alpha mixture

tag: growth phase

value: stationary


title: 13_HC_Auto_068_239

status: Public on Jan 03 2019

type: SRA

city: Columbus

first: Benjamin

middle: T.

last: Kopp

state: Ohio

address: 700 Children’s Drive

department: Section of Pediatric Pulmonology

country: USA

institute: Nationwide Children’s Hospital

library_source: transcriptomic

data_processing:
Each sample was aligned to the GRCh38.p9 assembly of the Homo Sapiens reference from NCBI (http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.35/) using version 2.5.2b of the RNA-Seq aligner STAR
Features were identified from the GFF file that came with the assembly from NCBI.
Feature coverage counts were calculated using version 0.6.1p1 of HTSeq -count
Differentially expressed features were calculated using DESeq2
Genome_build: human NCBI GRCh38.p9
Supplementary_files_format_and_content: Excel spreadsheet containing normalized read counts for each sample (columns U - CB) and differential expression data (columns F - T) for each feature

molecule: total RNA

organism: Homo sapiens

source_name: whole blood

extract_protocol:
rRNA was removed from 1000ng with TruSeq Stranded Total RNA with Ribo-Zero Globin Complete kit (Illumina, CA)
libraries were constructed from first strand cDNA using TruSeq Stranded Total RNA with Ribo-Zero Globin Complete kit (Illumina, CA)

tag: diagnosis

value: healthy control

tag: tissue

value: whole blood

tag: patient id


title: L005N

type: genomic

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 1-5-45 Yushima

department: Department of Molecular Oncology

country: Japan

institute: Tokyo Medical and Dental University

description: DNA methylation profile of human liver cancer #L005, non-tumorous tissue

hyb_protocol: Standard Illumina protocol

scan_protocol: iScan with standard recommended Illumina scanner setting

data_processing: GenomeStudio software

label: Unmethylated: Cy5, Methylated: Cy3

molecule: genomic DNA

source_name: Human liver cancer #L005, non-tumorous tissue

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted from tissue specimens by using QIAamp DNA Mini Kit (QIAGEN). The integrity of the obtained DNA was confirmed by using 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Tissue samples were stored in RNAlater (Thermo Fisher Scientific) at -80°C immediately after dissected.

value: Liver cancer, non-tumorous tissue


title: BM1a

city: Gothenburg

first: Jana

last: Biermann

address: Medicinaregatan 1F

country: Sweden

institute: University of Gothenburg

hyb_protocol: Hybridization probes were denatured, preannealed, and cohybridized to arrays pretreated with the Universal Microarray Hybridization Kit. Following hybridization, slides were washed at room temperature and dried by centrifugation.

scan_protocol: Images and raw signal intensities were acquired using an Agilent G2505B DNA microarray scanner and GenePix Pro 6.0.1.22 image analysis software

data_processing: Pin-based LOWESS normalized, spot intensities representing the tumor (cy3) and reference (cy5) channels were background-corrected by subtracting the median background from the median foreground signal intensities. BASE database used.

source_name: Human breast tumor

label_protocol: Tumor and reference genomic DNA were differentially labeled using a random labeling kit with Cy3-dCTP and Cy5-dCTP, respectively

extract_protocol: Genomic DNA was isolated from fresh-frozen tissue specimens using the Wizard Genomic DNA extraction kit, including proteinase K treatment followed by phenol chloroform purification

tag: gender

value: female

value: Human breast tumor

source_name: Normal female genomic DNA

value: Normal female genomic DNA


title: DL4184 phenol-chloroform based method biological repeat 2

city: Edinburgh

first: Benura

last: Azeroglu

address: Alexander Crum Brown Road

country: United Kingdom

institute: University of Edinburgh

library_source: genomic

data_processing:
Library strategy: Nextera XT
Alignment: reads were mapped to a bespoke reference sequence (DL4201_in_lab_reference_genome) using the default parameters of software BWA (Li H, Durbin R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics. 2010;26(5):589-595).
Data extraction: Depth of coverage was extracted from each de-duplicated alignment file (in .bam) format using SAMtools software (Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16)).
Normalisation: An in-lab R script was used to normalise (based on the total depth) the library size for individual depth of coverage data.
Genome_build: DL4201_in_lab_reference_genome.fasta (GSE107972)
Supplementary_files_format_and_content: Each of the CSV files contains the coordinates of nucleotides of the reference genome (DL4201_in_lab_reference_genome.fasta (GSE107972)) starting from an arbitrary position at the origin of replication of E. coli and covering the circular genome in column 1 under the header "position". Subsequent eight columns contain the depth of coverage data from individual strains under the headers of the corresponding strain names and biological replicates (A for biological replicate 1 or B for biological replicate 2).

organism: Escherichia coli

source_name: Bacterial Cell Lysates

growth_protocol: Cells were grown in LB media supplemented with 0.2% arabinose at 37°C to and OD600nm of 0.2-0.25

extract_protocol:
DNA from samples denoted as phenol-chloroform based method (samples 1-8) was extracted using  phenol-chloroform DNA extraction.
DNA from samples denoted as IN (sample 9-24)  was isolated using the MinElute PCR purification kit (Qiagen).
Samples for phenol-chloroform based method (sample 1-8) were processed following Illumina's protocol from the Nextera XT  library preparation kit, whilst rest of the samples (samples 9-24) were processed following NEB’s protocol from the NEBNext® ChIP-Seq library preparation kit.

treatment_protocol:
Samples denoted as phenol-chloroform based method (samples 1-8) were treated with a series of enzymes.
Samples denoted as IN (sample 9-16) were treated with 1% formaldehyde  to capture protein DNA interactions for 10 min at 22.5C with and quenched using glycine to a final concentration of 0.5M
Samples denoted as IN and sonication based method (sample 9-24) underwent a round of sonication to shear the chromatin using a Diagenode Bioruptor at 30 s intervals for 10 min at high amplitude at 5 °C.

tag: strain

tag: genotype/variation

value: BW27784 lacZ:XXX mhpR:XXX proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ::pal246 cynX::GmR  lacIq  lacZX-

tag: treatment

value: phenol-chloroform


title: DL4184 phenol-chloroform based method biological repeat 1


title: RRC7

description:
RRC_Mt008
Pooled linkage analysis. Mutant clones from ascospores of backcrossed yeast strains were cultured in YPD at 30 Cerecius overnight. Prepared genomic DNA was shared by Covaris S220 and purified. Sequencing libraries were prepared by KAPA  kit and TruSeqHT-compatible adaptors.


title: 12_Orkambi_007_V2

value: CF


title: 11_Orkambi_006_Base


title: 15_Orkambi_009_V2


title: 10_HC_Auto_066_237


title: L001N

description: DNA methylation profile of human liver cancer #L001, non-tumorous tissue

source_name: Human liver cancer #L001, non-tumorous tissue


title: BS1a


title: RRC4

description:
RRC_Mt006
Pooled linkage analysis. Parental yeast strains YTT66 and YTT67 were cultured in YPD at 30 Cerecius overnight. Prepared genomic DNA was shared by Covaris S220 and purified. Sequencing libraries were prepared by KAPA  kit and TruSeqHT-compatible adaptors.


title: BS1b


title: L001T

description: DNA methylation profile of human liver cancer #L001, tumorous tissue

source_name: Human liver cancer #L001, tumorous tissue

value: Liver cancer, tumorous tissue


title: RRC6

description:
RRC_Mt007
Pooled linkage analysis. Mutant clones from ascospores of backcrossed yeast strains were cultured in YPD at 30 Cerecius overnight. Prepared genomic DNA was shared by Covaris S220 and purified. Sequencing libraries were prepared by KAPA  kit and TruSeqHT-compatible adaptors.


title: LSC 3

city: Cambridge

first: Guangan

last: Hu

state: MA

address: 500 Main Street

department: Koch Institute

institute: MIT

data_processing:
Illumina software used for basecalling.
Sequences were trimed with 8 bases in 5-prime and aligned to the human genome using Tophat2
Raw counts of each gene for each sample were calculated by Rsem program
Raw counts of each sample normaized with TMM in calcNormFactors() of edgeR, values log2-transformed
Differentially expressed genes between paired samples before and after treatment were performed using the program edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample

source_name: CD123+ leukemic stem cells

growth_protocol: Bulk human leukemia cells and LSCs were sorted by flow cytometry based on expression of GFP, CD33 and CD123

extract_protocol:
Qiagen RNeasy Micro Kit
SMARTer Universal Low Input RNA Kit

tag: patient

value: donor 3

tag: cell type

value: CD123+ leukemic stem cells


title: 1052_p3_H

city: Stockholm

first: Eva

last: Hedlund

address: Svante Arrhenius v. 16C

department: Department of Biochemistry and Biophysics

institute: Stockholm University

data_processing:
Illumina Casava1.7 software was used for basecalling
Adapters were trimmed with cutadapt -m 3
Single-end alignment to mm10 genome was performed with STAR 2.5.2b with default parameters
Read counts per gene were counted with featureCounts tool (version 1.5.3) from Subread package
Genome_build: mm10
Supplementary_files_format_and_content: Table with read counts for each gene in each experiment

molecule: polyA RNA

organism: Mus musculus

source_name: Growth plate cartilage

growth_protocol: Mice on mixed-background were used in the study. All animal work was approved by the Ethical Committee on Animal Experiments (Stockholm North Committee / Norra Djurförsöksetiska Nämd) and conducted in accordance with The Swedish Animal Agency´s Provisions and Guidelines for Animal Experimentation.

extract_protocol:
Directly after sacrifice, mice bones were embedded in OCT and snap-frozen in a hexane bath pre-cooled with dry ice. Sections of 10 microns were prepared on slides and stored at -80C. The sections were stained for visualization. LCM laser capture was used to select cells from the resting, the hypertrophic and the proliferative zones. Cells are directly picked after dissociation and deposited into lysis buffer. No RNA extraction is conducted. The cell lysis is proceed directly to library preparation.
Libraries for RNA-seq were prepared by using SMART-seq2 combined with Tn5 tagmentation

value: Growth plate cartilage

tag: zone

value: Hypertrophic zone

tag: timepoint

tag: animal

tag: fixation

value: Ethanol


title: 1048_p2_H


title: 1046_p2_H


title: LSC 2

value: donor 2


title: 1041_p2_P

value: Proliferative zone


title: Vehicle-treated (control) cells, rep4

city: Sheridan

first: Kenneth

middle: L

last: Jones

state: Wyoming

address: 1309 Coffeen Avenue STE 10090

institute: Bioinformatic Solutions LLC

description:
A673_vehicle_rep4
PolyA RNA
processed data file: FPKM.txt

data_processing:
Quality trim to a minimum of Q15.
Map to the GRCh38 genome using GSNAP version 2014-12-17 using the commandline /vol2/home/analysiscore/bin/gsnap_20141217_250/gsnap -d GRCh38_nonRedundant -v GRCh38_nonRedundant.snp142 --use-splicing=GRCh38_nonRedundant.ensembl.splicesites --max-mismatches=0.06 -i2 -n2 -Q --gunzip --force-xs-dir --nofails -B5 -t12 --read-group-id=$j --read-group-name=$j --read-group-library=$j --read-group-platform=illumina -A sam ./Illumina_data/${j}_filtered.fastq.gz > ./Illumina_data/$j.sam
Sort and index using SAMTOOLS.
Split forward and reverse reads using SAMTOOLS.
Call FPKM using CUFFLINKS, applying anti-sense reads to sense genes, and sense reads to anti-sense genes.
Genome_build: GRCh38
Supplementary_files_format_and_content: FPKM.txt: Tab-delimited text file containing FPKM values.

growth_protocol: Cells were grown in DMEM with 10% Fetal bovine serum, 1% Pen/Strep, 10mM Hepes, 1X MEM non-essential amino acids, and 1mM Sodium Pyruvate.

extract_protocol:
Total RNA was isolated using TRIzol extraction, and further purified using the Qiagen MinElute column kit.
Illumina directional mRNA prep.
HiSeq4000 using 1x151bp format.

treatment_protocol: Cells were treated with 2 micromolar JIB-04 (or vehicle) for 36 hours.

tag: cell line

value: Ewing's Sarcoma Cell line

value: Vehicle control


title: JIB-04-treated cells, rep2

description:
A673_JIB-04_rep2
PolyA RNA
processed data file: FPKM.txt


title: 1045_p3_P


title: JIB-04-treated cells, rep1

description:
A673_JIB-04_rep1
PolyA RNA
processed data file: FPKM.txt


title: RRC2_rrn10

description:
RRC_Mt003
Pooled linkage analysis. Mutant clones from ascospores of backcrossed yeast strains were cultured in YPD at 30 Celsius overnight. Prepared genomic DNA was sheared by Covaris S220 and purified. Sequencing libraries were prepared by KAPA kit and TruSeqHT-compatible adaptors.

data_processing:
Library strategy: Whole genome sequencing
ChIP-seq: The paired-end reads were merged to a set of single reads.
Low quality 15 bases were trimmed from the 3'-end of each read with Seqtk (https://github.com/lh3/seqtk).
Reads were mapped to the S. cerevisiae reference genome EF4.68 by means of bowtie-1.0.0 using the single-read mapping mode: “bowtie -S --best -k 1 -n 3 EF4.68.index Sample_trim.fastq > Sample_trim.sam”.
Mapped reads were counted by samtools-0.1.19.
The pileup data was generated by means of MACS2 (http://liulab.dfci.harvard.edu/MACS/).
ChIP-seq profile data were normalized by the number of mapped reads as fragment per million reads (fpm).
Whole genome sequencing: To identify causative rcc-mutations, FASTQ files were analyzed with the webtool Mudi (version2, http://naoii.nig.ac.jp/mudi_top.html).
Genome_build: Saccharomyces_cerevisiae.EF4.68
Supplementary_files_format_and_content: BedGraph files were generated by macs2 and normalized by mapped read number as fragment count per million (fpm).
Supplementary_files_format_and_content: *.tsv: Tab-delimited text files were generated by the webtool "mudi". Mutations called by the analysis were listed.

tag: strain name

value: MATa and MAT alpha mixture

value: stationary


title: JIB-04-treated cells, rep4

description:
A673_JIB-04_rep4
PolyA RNA
processed data file: FPKM.txt


title: Vehicle-treated (control) cells, rep3

description:
A673_vehicle_rep3
PolyA RNA
processed data file: FPKM.txt


title: RRC3_rrn5

description:
RRC_Mt004
Pooled linkage analysis. Mutant clones from ascospores of backcrossed yeast strains were cultured in YPD at 30 Celsius overnight. Prepared genomic DNA was sheared by Covaris S220 and purified. Sequencing libraries were prepared by KAPA kit and TruSeqHT-compatible adaptors.

tag: mating type


title: Vehicle-treated (control) cells, rep2

description:
A673_vehicle_rep2
PolyA RNA
processed data file: FPKM.txt


title: Vehicle-treated (control) cells, rep1

description:
A673_vehicle_rep1
PolyA RNA
processed data file: FPKM.txt


title: bulk leukemia 2

source_name: bulk leukemia cells

value: bulk leukemia cells


title: YTT66_YTT67

description:
RRC_Mt001
Pooled linkage analysis. Parental yeast strains YTT66 and YTT67 were cultured in YPD at 30 Celsius overnight. Prepared genomic DNA was sheared by Covaris S220 and purified. Sequencing libraries were prepared by KAPA kit and TruSeqHT-compatible adaptors.

value: YTT66 and YTT67

tag: growth phase


title: LSC 1

value: donor 1


title: 1039_p2_P


title: 1038_p2_R

value: Resting zone


title: 1037_p3_R


title: UAF30-MN3HA_RDN1-15_IP1

description:
UAF_ChIP015
Replicate sample_1. Parental yeast strain with normal rDNA copy, YPD culture cross-linked by 1% formaldehyde at 30degree Celsius for 30 minutes. 2x10^9 cells were lysed by YTZ-beads, and the extracts were sheared by Covaris S220 to 100bp average. After pelleting, soluble fractions were used for INPUT samples. After reverse-crosslinking and DNA purification, sequencing libraries were prepared by KAPA Hyperprep kit and TruSeqHT-compatible adaptors.

data_processing:
ChIP-seq: The paired-end reads were merged to a set of single reads.
Low quality 15 bases were trimmed from the 3'-end of each read with Seqtk (https://github.com/lh3/seqtk).
Reads were mapped to the S. cerevisiae reference genome EF4.68 by means of bowtie-1.0.0 using the single-read mapping mode: “bowtie -S --best -k 1 -n 3 EF4.68.index Sample_trim.fastq > Sample_trim.sam”.
Mapped reads were counted by samtools-0.1.19.
The pileup data was generated by means of MACS2 (http://liulab.dfci.harvard.edu/MACS/).
ChIP-seq profile data were normalized by the number of mapped reads as fragment per million reads (fpm).
Whole genome sequencing: To identify causative rcc-mutations, FASTQ files were analyzed with the webtool Mudi (version2, http://naoii.nig.ac.jp/mudi_top.html).
Genome_build: Saccharomyces_cerevisiae.EF4.68
Supplementary_files_format_and_content: BedGraph files were generated by macs2 and normalized by mapped read number as fragment count per million (fpm).
Supplementary_files_format_and_content: *.tsv: Tab-delimited text files were generated by the webtool "mudi". Mutations called by the analysis were listed.

source_name: MAT a exponentially growing yeast cells

extract_protocol:
Exponentially growing yeast cells in YPD media at 30°C were fixed with 1% formaldehyde (Wako, 064-00406) for 30 minutes at 30°C, followed by an additional 5 min with glycine added to a final concentration of 125 mM. Fixed cells were washed with PBS, pelleted by centrifugation at 20,000 g in a 2 ml screw-capped tube at 4°C and stored at -80°C. Cells were lysed with 1.5 ml yttrium stabilized zirconia grinding beads with a diameter of 0.5 mm (Nikkato, YTZ-0.5) for 45 seconds twice at 4 °C and 2,500 rpm on a horizontal tube-holder attached to a micro tube mixer (Eyla, CM-1000). Cell lysate was recovered in 800 µl of lysis buffer (50 mM Hepes-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton-X100, 0.1% Na-deoxicholate, 1 mM PMSF and 1x Complete protease inhibitor cocktail (Roche, 11873580001)). The lysate (850 µl) was sonicated at 4°C in a 1ml milliTube with an AFA Fiber (Covaris, 520130) using a Covaris S220 as follows: 3 cycles of peak power 200, duty factor 20, cycle/burst 200 and duration 5 minutes. The sheared DNA fragments (with an average length of 200 bp) were separated from the cell-debris by centrifugation at 20,000g, 5 minutes at 4°C, and the pellet was re-extracted with 375 µl of lysis buffer to completely collect the chromatin. From the collected chromatin (1115 µl) 50 µl samples were kept as controls for input and DNA content and a 15 µl sample to check proteins. The remainder (1 ml) was incubated with 10 µg anti-HA F-7 antibody at 4°C overnight on a rotation mixer. Subsequently, a 100 µl Dynabeads Protein G (Thermo Fisher, 10004D) suspension, masked with 5 mg BSA/ml, was incubated with the IP mixture for 1 hour at 4°C. The beads were washed rigorously with 1 ml lysis buffer (twice), 1ml lysis buffer with 500 mM NaCl (twice), 1ml wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate, 1 mM EDTA) (twice) and 1 ml of TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). The material captured on the beads was eluted by 10 minutes long incubations at 65°C with 50 µl, and 2 x 100 µl TES (10 mM Tris-HCl pH8.0, 1 mM EDTA, 1% SDS), after which the eluates were combined. The recovered material and input extract (50 µl combined with 200 µl TES) were incubated with 2 mg/ml Proteinase K (Merck Millipore, 124568) at 56 °C overnight to reverse the crosslinking and to digest the protein. After phenol/chloroform/isoamylalcohol (pH 8.0) extraction and ethanol precipitation with Ethachinmate (Nippongene, 312-01791), the precipitates were dissolved in 50 µl of TE containing 200 µg/ml RNase A and incubated at 37°C for 1 hour. The DNA sample was purified using 2 volumes (100 µl) of AMpureXP and eluted with 20 µl 5 mM Tris-HCl pH8.5.
Sequencing libraries for NGS sequencing were prepared with a Kapa Hyper Prep kit (Kapa Biosystems, KK8502) with 250 ng input DNA, or 1~5 ng ChIP DNA and Illumina TruSeq HT compatible adaptors according to the manufacturer’s protocol. The adaptor-ligated libraries were amplified by 6 cycles of PCR (98°C 15s, 60°C 30 s and 72°C 40 s) in the case of the input-library and by 11 cycles in the case of the ChIP sample using the Kapa kit and primer set TruHTAmp5Fw/TruHTAmp7Rv. Library purification was performed by double size-selection using 0.5 volume of AMpureXP beads (Beckman Coulter, A63881) per PCR reaction in each step: 25 µl of AMpureXP beads was added to 50 µl of PCR reaction to remove long library, after removal of 1st beads, and another 25 µl of AMpureXP beads was added to the supernatant and the library DNA was recovered from the 2nd bead fractions with 12.5 µl 5 mM Tris-HCl pH8.5. Equimolar mixtures of the libraries were prepared for paired-end sequencing (75 bp) with a MiSeq Reagent Kit v3 (Illumina, MS-102-3001) and sequenced on a MiSeq (Illumina).

value: MATa

value: exponential

tag: chip antibody

value: HA probe F-7 (Santa Cruz Biotechnology, sc-7392, lot C0317)


title: UAF30-MN3HA_RDN1-15_IP2

description:
UAF_ChIP016
Replicate sample_2. Parental yeast strain with normal rDNA copy, YPD culture cross-linked by 1% formaldehyde at 30degree Celsius for 30 minutes. 2x10^9 cells were lysed by YTZ-beads, and the extracts were sheared by Covaris S220 to 100bp average. After pelleting, soluble fractions were used for INPUT samples. After reverse-crosslinking and DNA purification, sequencing libraries were prepared by KAPA Hyperprep kit and TruSeqHT-compatible adaptors.

growth_protocol: Exponentially growing yeast cells in YPD media at 30°C were fixed with 1% formaldehyde (Wako, 064-00406) for 30 minutes at 30°C, followed by an additional 5 min with glycine added to a final concentration of 125 mM. Fixed cells were washed with PBS, pelleted by centrifugation at 20,000 g in a 2 ml screw-capped tube at 4°C and stored at -80°C.


title: JIB-04-treated cells, rep3

description:
A673_JIB-04_rep3
PolyA RNA
processed data file: FPKM.txt


title: bulk leukemia 1


title: 30_Orkambi_014_Base

tag: diagnosis

value: CF

tag: tissue

value: whole blood


title: BT-28_WT-Tag_RNA-seq

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

data_processing:
Basecalls performed using CASAVA
fastq files werer mapped with internal pipeline that employs Tophat2 and STAR
reads were counted using an internal pipeline and converted to FPKM using mm9
Genome_build: mm9
Supplementary_files_format_and_content: matrix txt file with FPKM for each gene symbol  for each sample

source_name: Mouse brainstem tumor

extract_protocol:
1 ml of Trizol (Invitrogen, 15596-018) was added to 2 x 106 dissociated neurosphere cells.  2 ul of 1:20 diluted ERCC spike in (Ambion Cat #4456740, Lot # 1412017) was added directly to the Trizol.  For tumor tissue, a piece of snap frozen tissue was mechanically dissociated in Trizol.   RNA was extracted following the standard Trizol protocol except the final 70% EtOH wash was repeated three times.
Libraries were prepared from total RNA with the TruSeq Stranded Total RNA Library Prep Kit (Illumina.)

tag: full genotype

value: Nestin-creERT2; H3f3aLSL-WT-Tag/+; LSL-PDGFRαV544ins; Trp53flox/flox

tag: gender

value: female


title: BT-29_WT-Tag_RNA-seq


title: BT-27_WT-Tag_RNA-seq

value: male


title: 1033_p2_R

value: Growth plate cartilage

value: Ethanol


title: BT-26_WT-Tag_RNA-seq


title: BT-24_K27M-Tag_RNA-seq

value: Nestin-creERT2; H3f3aLSL-K27M-Tag/+; LSL-PDGFRαV544ins; Trp53flox/flox


title: 1029_p28_H

value: Hypertrophic zone


title: UAF30-MN3HA_RDN1-150_IP2

description:
UAF_ChIP012
Replicate sample_2. Parental yeast strain with normal rDNA copy, YPD culture cross-linked by 1% formaldehyde at 30degree Celsius for 30 minutes. 2x10^9 cells were lysed by YTZ-beads, and the extracts were sheared by Covaris S220 to 100bp average. After pelleting, soluble fractions were used for INPUT samples. After reverse-crosslinking and DNA purification, sequencing libraries were prepared by KAPA Hyperprep kit and TruSeqHT-compatible adaptors.


title: UAF30-MN3HA_RDN1-15_INPUT1

description:
UAF_ChIP013
Replicate sample_1. Parental yeast strain with normal rDNA copy, YPD culture cross-linked by 1% formaldehyde at 30degree Celsius for 30 minutes. 2x10^9 cells were lysed by YTZ-beads, and the extracts were sheared by Covaris S220 to 100bp average. After pelleting, soluble fractions were used for INPUT samples. After reverse-crosslinking and DNA purification, sequencing libraries were prepared by KAPA Hyperprep kit and TruSeqHT-compatible adaptors.


title: 1031_p2_R


title: 1028_p28_P

value: Proliferative zone


title: UAF30-MN3HA_RDN1-150_IP1

description:
UAF_ChIP011
Replicate sample_1. Parental yeast strain with normal rDNA copy, YPD culture cross-linked by 1% formaldehyde at 30degree Celsius for 30 minutes. 2x10^9 cells were lysed by YTZ-beads, and the extracts were sheared by Covaris S220 to 100bp average. After pelleting, soluble fractions were used for INPUT samples. After reverse-crosslinking and DNA purification, sequencing libraries were prepared by KAPA Hyperprep kit and TruSeqHT-compatible adaptors.


title: 1030_p28_H


title: BT-23_K27M-Tag_RNA-seq


title: BT-22_K27M-Tag_RNA-seq


title: bulk leukemia 3

value: donor 3

value: bulk leukemia cells


title: UAF30-MN3HA_RDN1-15_INPUT2

description:
UAF_ChIP014
Replicate sample_2. Parental yeast strain with normal rDNA copy, YPD culture cross-linked by 1% formaldehyde at 30degree Celsius for 30 minutes. 2x10^9 cells were lysed by YTZ-beads, and the extracts were sheared by Covaris S220 to 100bp average. After pelleting, soluble fractions were used for INPUT samples. After reverse-crosslinking and DNA purification, sequencing libraries were prepared by KAPA Hyperprep kit and TruSeqHT-compatible adaptors.


title: UAF30-MN3HA_RDN1-150_INPUT2

description:
UAF_ChIP010
Replicate sample_2. Parental yeast strain with normal rDNA copy, YPD culture cross-linked by 1% formaldehyde at 30degree Celsius for 30 minutes. 2x10^9 cells were lysed by YTZ-beads, and the extracts were sheared by Covaris S220 to 100bp average. After pelleting, soluble fractions were used for INPUT samples. After reverse-crosslinking and DNA purification, sequencing libraries were prepared by KAPA Hyperprep kit and TruSeqHT-compatible adaptors.


title: BT-25_K27M-Tag_RNA-seq


title: UAF30-MN3HA_RDN1-150_INPUT1

description:
UAF_ChIP009
Replicate sample_1. Parental yeast strain with normal rDNA copy, YPD culture cross-linked by 1% formaldehyde at 30degree Celsius for 30 minutes. 2x10^9 cells were lysed by YTZ-beads, and the extracts were sheared by Covaris S220 to 100bp average. After pelleting, soluble fractions were used for INPUT samples. After reverse-crosslinking and DNA purification, sequencing libraries were prepared by KAPA Hyperprep kit and TruSeqHT-compatible adaptors.


title: 1026_p28_R


title: 1027_p28_P


title: WT_RDN1-15_IP1

description:
UAF_ChIP007
Replicate sample_1. Parental yeast strain with normal rDNA copy, YPD culture cross-linked by 1% formaldehyde at 30degree Celsius for 30 minutes. 2x10^9 cells were lysed by YTZ-beads, and the extracts were sheared by Covaris S220 to 100bp average. After pelleting, soluble fractions were used for INPUT samples. After reverse-crosslinking and DNA purification, sequencing libraries were prepared by KAPA Hyperprep kit and TruSeqHT-compatible adaptors.


title: skin, AD

type: RNA

city: Seoul

first: Kwang Hoon

last: Lee

address: 50-1, Yonsei-ro, Seodaemun-gu

department: Dermatology

country: South Korea

institute: Yonsei University College of Medicine

description: Gene expression data from atopic dermatitis induced NC/Nga mouse skin

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

label: biotin

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: Six-week old female NC/Nga mice were raised in specific-pathogen free condition.

extract_protocol: Total RNA were extracted using QIAGEN RNeasy mini kit following the manufacturer's instructions.

treatment_protocol: Induction of atopic dermatitis with Dermatophagoides farinae body extract ointment twice a week for 6 weeks. Treatment of recombinant ZAG twice a week for 6 weeks.

value: Female

tag: age

value: 13 week-old

value: NC/Nga dorsal skin

value: control


title: 1019_p28_H

value: Xylene


title: skin, AD-ZAG

description: Gene expression data from atopic dermatitis induced NC/Nga mouse skin topically treated with recombinant ZAG

tag: treatment

value: ZAG


title: WT_RDN1-15_INPUT2

description:
UAF_ChIP006
Replicate sample_2. Parental yeast strain with normal rDNA copy, YPD culture cross-linked by 1% formaldehyde at 30degree Celsius for 30 minutes. 2x10^9 cells were lysed by YTZ-beads, and the extracts were sheared by Covaris S220 to 100bp average. After pelleting, soluble fractions were used for INPUT samples. After reverse-crosslinking and DNA purification, sequencing libraries were prepared by KAPA Hyperprep kit and TruSeqHT-compatible adaptors.

value: MATa

value: exponential


title: BT-18_K27M-Tag_RNA-seq


title: WT_RDN1-15_INPUT1

description:
UAF_ChIP005
Replicate sample_1. Parental yeast strain with normal rDNA copy, YPD culture cross-linked by 1% formaldehyde at 30degree Celsius for 30 minutes. 2x10^9 cells were lysed by YTZ-beads, and the extracts were sheared by Covaris S220 to 100bp average. After pelleting, soluble fractions were used for INPUT samples. After reverse-crosslinking and DNA purification, sequencing libraries were prepared by KAPA Hyperprep kit and TruSeqHT-compatible adaptors.


title: WT_RDN1-15_IP2

description:
UAF_ChIP008
Replicate sample_2. Parental yeast strain with normal rDNA copy, YPD culture cross-linked by 1% formaldehyde at 30degree Celsius for 30 minutes. 2x10^9 cells were lysed by YTZ-beads, and the extracts were sheared by Covaris S220 to 100bp average. After pelleting, soluble fractions were used for INPUT samples. After reverse-crosslinking and DNA purification, sequencing libraries were prepared by KAPA Hyperprep kit and TruSeqHT-compatible adaptors.

value: HA probe F-7 (Santa Cruz Biotechnology, sc-7392, lot C0317)


title: BT-17_K27M-Tag_RNA-seq

value: female


title: BT-16_K27M-Tag_RNA-seq

value: male


title: BT-19_K27M-Tag_RNA-seq


title: WT_RDN1-150_INPUT2

description:
UAF_ChIP002
Replicate sample_2. Parental yeast strain with normal rDNA copy, YPD culture cross-linked by 1% formaldehyde at 30degree Celsius for 30 minutes. 2x10^9 cells were lysed by YTZ-beads, and the extracts were sheared by Covaris S220 to 100bp average. After pelleting, soluble fractions were used for INPUT samples. After reverse-crosslinking and DNA purification, sequencing libraries were prepared by KAPA Hyperprep kit and TruSeqHT-compatible adaptors.


title: 1015_p28_P

value: Growth plate cartilage


title: BT-14_K27M-Tag_RNA-seq

value: Nestin-creERT2; H3f3aLSL-K27M-Tag/+; LSL-PDGFRαV544ins; Trp53flox/flox


title: WT_RDN1-150_INPUT1

description:
UAF_ChIP001
Replicate sample_1. Parental yeast strain with normal rDNA copy, YPD culture cross-linked by 1% formaldehyde at 30degree Celsius for 30 minutes. 2x10^9 cells were lysed by YTZ-beads, and the extracts were sheared by Covaris S220 to 100bp average. After pelleting, soluble fractions were used for INPUT samples. After reverse-crosslinking and DNA purification, sequencing libraries were prepared by KAPA Hyperprep kit and TruSeqHT-compatible adaptors.


title: BT-21_K27M-Tag_RNA-seq


title: 1025_p28_P


title: BT-20_K27M-Tag_RNA-seq


title: 1013_p28_R

value: Resting zone


title: 1011_p28_H

value: Hypertrophic zone


title: BT-12_K27M-Tag_RNA-seq


title: KAT8-KO

city: hangzhou

first: Wanwan

last: Huai

address: yuhangtang road

country: China

institute: zhejiang university

data_processing:
Raw data were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Hisat2(version:2.0.4)was used to map the cleaned reads to the mouse GRCm38.p4 (mm10) reference genome with two mismatches.
FPKM value of each gene was calculated using cufflinks
Read counts of each gene were obtained by htseq-count.
Differentially expressed genes were identified using the DESeq R package functions estimateSizeFactors and nbinomTest.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: KAT8-KO_peritoneal macrophage

growth_protocol: Peritoneal macrophages were harvested from mice 3 days after thioglycollate (Merck) injection.

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Total RNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA), and RNA integrity was determined using an Agilent 2100 system and an RNA 6000 Nano kit (Agilent Technologies, Santa Clara, CA, USA).
Paired-end libraries were synthesized by using the TruSeq® RNA Sample Preparation Kit (Illumina, USA) following TruSeq® RNA Sample Preparation Guide.

treatment_protocol: VSV(1 MOI) for 8 hours

tag: strain background

tag: genotype/variation

tag: stimulation

value: VSV (1 MOI ) 8h

value: peritoneal macrophage


title: 1010_p28_R

tag: zone

tag: timepoint


title: WT

source_name: WT_peritoneal macrophage

tag: cell type


title: 1009_p28_P

value: Proliferative zone

tag: animal

tag: fixation


title: 1018_p28_P


title: BT-11_WT-Tag_RNA-seq

value: Nestin-creERT2; H3f3aLSL-WT-Tag/+; LSL-PDGFRαV544ins; Trp53flox/flox


title: 1008_p28_H


title: 1017_p28_R


title: BT-15_K27M-Tag_RNA-seq


title: 1016_p28_H


title: DL4257 sonication based method biological repeat 1

data_processing:
Alignment: reads were mapped to a bespoke reference sequence (DL4201_in_lab_reference_genome) using the default parameters of software BWA (Li H, Durbin R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics. 2010;26(5):589-595).
Data extraction: Depth of coverage was extracted from each de-duplicated alignment file (in .bam) format using SAMtools software (Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16)).
Normalisation: An in-lab R script was used to normalise (based on the total depth) the library size for individual depth of coverage data.
Genome_build: DL4201_in_lab_reference_genome.fasta (GSE107972)
Supplementary_files_format_and_content: Each of the CSV files contains the coordinates of nucleotides of the reference genome (DL4201_in_lab_reference_genome.fasta (GSE107972)) starting from an arbitrary position at the origin of replication of E. coli and covering the circular genome in column 1 under the header "position". Subsequent eight columns contain the depth of coverage data from individual strains under the headers of the corresponding strain names and biological replicates (A for biological replicate 1 or B for biological replicate 2).

tag: strain

value: BW27784 [delta]ruvAB lacZ:XXX mhpR:XXX proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ+ cynX::GmR  lacIq  lacZX-

value: round of sonication to shear the chromatin using a Diagenode Bioruptor at 30 s intervals for 10 min at high amplitude at 5 C.


title: WT_RDN1-150_IP1

description:
UAF_ChIP003
Replicate sample_1. Parental yeast strain with normal rDNA copy, YPD culture cross-linked by 1% formaldehyde at 30degree Celsius for 30 minutes. 2x10^9 cells were lysed by YTZ-beads, and the extracts were sheared by Covaris S220 to 100bp average. After pelleting, soluble fractions were used for INPUT samples. After reverse-crosslinking and DNA purification, sequencing libraries were prepared by KAPA Hyperprep kit and TruSeqHT-compatible adaptors.

tag: strain name

tag: mating type

tag: growth phase


title: WT_RDN1-150_IP2

description:
UAF_ChIP004
Replicate sample_2. Parental yeast strain with normal rDNA copy, YPD culture cross-linked by 1% formaldehyde at 30degree Celsius for 30 minutes. 2x10^9 cells were lysed by YTZ-beads, and the extracts were sheared by Covaris S220 to 100bp average. After pelleting, soluble fractions were used for INPUT samples. After reverse-crosslinking and DNA purification, sequencing libraries were prepared by KAPA Hyperprep kit and TruSeqHT-compatible adaptors.

tag: chip antibody


title: BT-9_WT-Tag_RNA-seq

tag: full genotype


title: BT-10_WT-Tag_RNA-seq

tag: gender


title: BT-8_WT-Tag_RNA-seq


title: BT-13_K27M-Tag_RNA-seq


title: 1006_p28_H

tag: tissue

value: Xylene


title: DL4243 sonication based method biological repeat 1

value: BW27784 [delta]ruvAB lacZ:XXX mhpR:XXX proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ::pal246 cynX::GmR  lacIq  lacZX-

tag: treatment


title: 1004_p28_P

value: Ethanol


title: 1005_p28_R


title: DL4257 sonication based method biological repeat 2


title: DL4184 sonication based method biological repeat 2

value: BW27784 lacZ:XXX mhpR:XXX proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ::pal246 cynX::GmR  lacIq  lacZX-


title: BT-6_K27M-Tag_RNA-seq


title: DL4201 sonication based method biological repeat 2

value: BW27784 lacZ:XXX mhpR:XXX proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ+ cynX::GmR  lacIq  lacZX-


title: DL4201 sonication based method biological repeat 1


title: BT-5_K27M-Tag_RNA-seq

value: female


title: BT-1_K27M-Tag_RNA-seq

value: male


title: BT-2_K27M-Tag_RNA-seq


title: DL4184 sonication based method biological repeat 1


title: 1001_p28_R

value: Growth plate cartilage


title: DL4243 sonication based method biological repeat 2


title: 1007_p28_P


title: DL4257 IN biological repeat 2

value: 1% formaldehyde  to capture protein DNA interactions for 10 min at 22.5C with and quenched using glycine to a final concentration of 0.5M


title: DL4201 IN biological repeat 2


title: DL4257 IN biological repeat 1


title: DL4243 IN biological repeat 2


title: DL4243 IN biological repeat 1


title: 12-D-FC

city: Fujisawa-city

first: Shuhei

last: Yao

state: Kanagawa

institute: Takeda pharmaceutical company LTD.

data_processing:
RNA-seq data were processed using Array Studio 8.0.0.78 (OmicSoft Corp., Cary, NC, U.S.A) as follows.
FASTQ files were mapped using mouse.mm10 as the reference library, and then gene annotations were added to the read count values with ensembl.R76.
After checking the mapping rate was over 85%, the read counts of all samples were exported.
RPKM files were provided by Beijing Genomics Institute (Hong Kong, China)
Genome_build: mm10

source_name: Prefrontal Cortex

extract_protocol:
The medial prefrontal cortex (mPFC) was dissected from 1 mm-thick coronal brain slices with a 1.5 mm-diameter tissue puncher. Total RNA were extracted from four mPFC samples from wild type (WT) mice, three mPFC samples from D1-RNB mice, and three mPFC samples from D2-RNB mice using the miRNeasy Mini Kit (QIAGEN, Hilden, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Prefrontal Cortex

tag: age

value: 3 month old

tag: genotype

value: WT


title: DL4201 IN biological repeat 1

tag: genotype/variation


title: 72-I-FC


title: 70-D-FC


title: 73-I-FC


title: 69-D-FC


title: DL4184 IN biological repeat 2


title: DL4184 IN biological repeat 1


title: 1003_p28_H

tag: zone

value: Hypertrophic zone


title: 3-I-FC


title: 4-D-FC


title: 2-I-FC


title: CD4 T cell wildtype rep2

city: New York

first: Yuheng

last: Lu

state: NY

address: 417 East 68th Street

institute: Memorial Sloan Kettering Cancer Center

data_processing:
The preprocessing, alignment, peak calling and quantification steps for the PolyA-Seq libraries were performed in the same way as the iCLIP libraries.
Internally primed peaks were removed as previously described.
Read counts were fitted using the DEXSeq model in order to identify cell-specific differences in 3’UTR isoform usage.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig format, containing the read coverage profiles on all chromosomes

source_name: CD4 T cell

extract_protocol:
polyadenylated RNA from cells activated for 48 hours (0, 24, and 48 hours for CD4 T cells) was selected by using Sera-Mag oligo-(dT)14 (GE Healthcare), and reverse-transcribed to cDNA using RT primer (RT_1).
The complementary (2nd) strand of cDNA was synthesized using the Klenow fragment (exo-, NEB) and extension primer (Ext_primer_1). Barcoded libraries, amplified by PCR from the double-stranded cDNA pool, were submitted for high throughput sequencing.

value: CD4 T cell

value: wild type

value: 48h after stimulation


title: CD4 T cell miR-155 KO rep3

value: miR-155 KO


title: 1546_p28_H

tag: timepoint


title: 5-D-FC


title: CD4 T cell wildtype rep1

tag: cell type


title: 1-I-FC


title: CD4 T cell wildtype rep3


title: CD4 T cell miR-155 KO rep2


title: DL4201 biological repeat 2 RecA Input

data_processing:
Alignment: reads were mapped to bespoke reference sequence (DL4201_in_lab_reference_genome) using the default parameters of software Bowtie 2 (Langmead, B. and Salzberg, S.L. (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods, 9, 357-359).
Count data was extracted from each de-duplicated alignment file (in .bam format) using HTSeq software (Anders S, Pyl PT, Huber W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31(2)) where features were defined as non-overlapping bins of 1 Kb covering the whole length of E. coli genome.
Normalisation: Counts were normalised by applying a single, sample-specific scaling factor.  To calculate this scaling factor, we implemented the median of ratios normalisation of DESeq software (Anders, S. and Huber, W. (2010) Differential expression analysis for sequence count data. Genome Biol, 11, R106) using R.
Genome_build: DL4201_in_lab_reference_genome.fasta (GSE107972)
Supplementary_files_format_and_content: csv

extract_protocol:
Cells were collected by centrifugation and washed three times in ice-cold 1X PBS. The pellet was then re-suspended in 250 μl ChIP buffer (200 mM Tris-HCl (pH 8.0), 600 mM NaCl 4% Triton X, Complete protease inhibitor cocktail EDTA-free (Roche)). Sonication of crosslinked samples was performed using the Diagenode Bioruptor® at 30s intervals for 10 min at high amplitude. After sonication, 350 μl of ChIP buffer was added to each sample, the samples were mixed by gentle pipetting and 100 μl of each lysate was removed and stored as ‘input’. Immunoprecipitation was performed overnight at 4°C using 1/100 anti-RecA antibody (Abcam, ab63797). IP samples were then incubated with Protein G Dynabeads® (Life Technologies) for 2 h at room temperature. All samples were washed 3 times with 1 X PBS + 0.02% Tween-20 before re-suspending the Protein G dynabeads in 200 μl of TE buffer (10 mM Tris (pH 7.4), 1 mM EDTA) + 1% SDS. 100 μl of TE buffer was added to the input samples and all samples were then incubated at 65°C for 10 h to reverse formaldehyde crosslinks. DNA was isolated using the MinElute PCR purification kit (Qiagen). DNA was eluted in 50 μl of TE buffer using a 2-step elution. Samples were stored at -20°C.
RecA binding to the chromosome of two E. coli strains was analyzed by RecA-ChIP.  Two biological repeats were carried out for each of the two strains. One strain experienced an induced DNA double strand break (DL4184) and one did not (DL4201).  Both strains were recombination proficient.

treatment_protocol: Protein DNA interactions were crosslinked for 10 min at 22.5C with 1% formaldehyde and quenched using glycine to a final concentration of 0.5M

value: BW27784 lacZ::XXX mhpR::XXX proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ+ cynX::GmR  lacIq  lacZX-


title: DL4201 biological repeat 1 RecA ChIP


title: DL4201 biological repeat 1 RecA Input


title: DL4201 biological repeat 2 RecA ChIP


title: 1545_p28_P

value: Proliferative zone

tag: animal


title: DL4184 biological repeat 2 RecA Input

value: BW27784 lacZ::XXX mhpR::XXX proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ::pal246 cynX::GmR  lacIq  lacZX-


title: DL4184 biological repeat 1 RecA Input


title: NSH-C_K27M-Tag_RNA-seq

source_name: Mouse e15.5 hindbrain neurosphere

tag: experiment id

value: Nestin-cre; H3f3aLSL-K27M-Tag/+

tag: growth protocol

value: Grown under neural precursor cell conditions


title: 1543_p28_H

tag: fixation

value: Ethanol


title: NSH-F_WT-Tag_RNA-seq

value: Nestin-cre; H3f3aLSL-WT-Tag/+

value: male


title: 1542_p28_P

value: Growth plate cartilage


title: CD4 T cell miR-155 KO rep1

tag: strain


title: DL4184 biological repeat 2 RecA ChIP


title: DL4184 biological repeat 1 RecA ChIP


title: NSF-C_K27M-Tag_RNA-seq

source_name: Mouse e15.5 forebrain neurosphere

value: female


title: NSF-F_WT-Tag_RNA-seq


title: 1540_p28_H


title: NSH-B_K27M-Tag_RNA-seq


title: 1541_p28_R

value: Resting zone


title: 1539_p28_P


title: NSH-E_WT-Tag_RNA-seq


title: NSF-B_K27M-Tag_RNA-seq


title: 1538_p28_R


title: 1537_p28_H


title: NSF-E_WT-Tag_RNA-seq


title: 1544_p28_R


title: Mammary tumor initiation treated with Saline, biological rep5

city: Bethesda

first: Anand

last: Merchant

address: 41 Center Dr

institute: NIH

description: Primary Tumor

data_processing: Normalization was performed using the software nSolver version 2.070 (NanoStrings Technologies). The gene expression intensities represent values after normalization to geometric means of control probes. Significant transcripts were selected using a t-test with p < 0.05.

source_name: Primary Tumor

label_protocol: Five hundred ng of total RNA was used. The assays were performed according to the manufacturer’s instructions (NanoStrings Technologies, Seattle, WA)

growth_protocol: Balb/C  nude  mice were supplemented with Sulforaphane (SFN) for 2 weeks before cell inoculation (daily i.p. injection of 50mg SFN/kg).Then, animals were  inoculated  subcutaneously  with 50,000  MDA-MB-231 D3H1 Luci  cells  into  the  4th  mammary  gland and SFN treatment was kept for more 3 weeks (total of 5 weeks). Mouse mammary primary tumor were resected 30 days after the cell injection.

extract_protocol: All tissue samples were snap frozen in liquid  nitrogen. RNAs were extracted using TRIzol reagent according to the manufacturer's recommendations (Invitrogen, Carlsbad, CA)

treatment_protocol: BalbC/nude mice were supplemented with SFN before and after cell inoculation (daily i.p. injection of 50mg SFN/kg for 2 and 3 weeks respectively)

tag: sample identification

tag: host

value: mouse

value: Mammary Primary Tumor Initiation. Tissue removed less then 20 days post cell injectiom

value: Daily i.p. injection of 0.9% Saline


title: 1536_p28_P


title: 1535_p28_R


title: NSH-D_WT-Tag_RNA-seq

tag: full genotype


title: Mammary tumor initiation treated with Saline, biological rep6

description: Primary Tumor

hyb_protocol: The assays were performed according to the manufacturer’s instructions (NanoStrings Technologies, Seattle, WA)


title: Mammary tumor initiation treated with Saline, biological rep2

description: Primary Tumor

scan_protocol: The assays were performed according to the manufacturer’s instructions (NanoStrings Technologies, Seattle, WA)


title: Mammary tumor initiation treated with Saline, biological rep3

description: Primary Tumor


title: Mammary tumor initiation treated with Saline, biological rep4

description: Primary Tumor


title: NSF-A_K27M-Tag_RNA-seq

tag: gender


title: Mammary tumor initiation treated with Saline, biological rep1

description: Primary Tumor

tag: tissue


title: Mammary tumor initiation treated with SFN, biological rep6

description: Primary Tumor

tag: treatment

value: Daily i.p. injection of 50mg SFN/kg


title: 1534_p28_H

value: Hypertrophic zone


title: 1533_p28_P


title: 1532_p28_R


title: Mammary tumor initiation treated with SFN, biological rep5

description: Primary Tumor


title: Mammary tumor initiation treated with SFN, biological rep3

description: Primary Tumor


title: BT-7_WT-Tag_RNA-seq

value: Nestin-creERT2; H3f3aLSL-WT-Tag/+; LSL-PDGFRαV544ins; Trp53flox/flox


title: 1531_p28_H


title: Mammary tumor initiation treated with SFN, biological rep4

description: Primary Tumor


title: BT-4_K27M-Tag_RNA-seq

value: Nestin-creERT2; H3f3aLSL-K27M-Tag/+; LSL-PDGFRαV544ins; Trp53flox/flox


title: 1530_p28_P

value: Proliferative zone


title: Mammary tumor initiation treated with SFN, biological rep2

description: Primary Tumor


title: BT-3_K27M-Tag_RNA-seq


title: 1529_p28_R


title: NSH-A_K27M-Tag_RNA-seq


title: Mammary tumor initiation treated with SFN, biological rep1

description: Primary Tumor


title: Mammary tumor growth treated with Saline, biological rep10

description: Primary Tumor

value: Mammary Primary Tumor Growth. Tissue removed 35 days post cell injectiom


title: NSH-C_K27M-Tag_input_DNA

data_processing:
We used BWA (version 0.7.12, default parameter) to align the reads to the mouse mm9 genome
marked duplicated reads with Picard with only nonduplicated reads kept by samtools
To control the quality of the data and estimate the fragment size, the nonduplicated version of SPP (version 1.11) was used to draw cross-correlation with support of R (version 2.14.0)
peaks were called using MACS2 or Sicer V1.1
bam was converted to BigWig using bedtools (v2.25.0) and UCSC tools (20150811). Read coverage was scaled  according to spike-in normalization factor (Orlando et al., 2014)
Genome_build: mm9
Supplementary_files_format_and_content: bed files containing locations of defined peaks
Supplementary_files_format_and_content: bigWig files containing normalized read coverage

extract_protocol:
Tumors were snap frozen and ground to a powder before fixation.  Single cell suspensions were generated from cultured cells using Accutase before fixation. Samples were fixed for 5 minutes with 1% paraformaldehyde in PBS (from a frozen stock) at room temperature. Bare nuclei were suspended in shearing buffer + protease inhibitors (10 Tris HCL pH 8.0, 1 mM EDTA pH 8.0, 0.1% SDS) and sheared on a Covaris M220 ultrasonicator (Microtube, 75W, 5% duty cycle, 200 cycles per burst, 5 minutes or Millitube, 75W, 10% duty cycle, 200 cycles per burst, 15 minutes). Sonication size was verified on an Agilent Bioanalyzer using a High Sensitivity DNA Assay.  For ChIP-seq, sheared chromatin from drosophila melanogaster S2 cells was added to the mammalian chromatin prior to ChIP at a set ratio for each histone mark to allow for sample normalization.  400 ng of chromatin was used per ChIP reaction and for ChIP-seq, multiple ChIPs were performed and pooled as needed to generate enough chromatin for library construction. 10-20 ng of pre-IP chromatin containing spike in was kept as an input control.   ChIP reactions were performed using a modified Upstate Biotechnology protocol.  Briefly, sheared chromatin was diluted 1:10 with dilution buffer + protease inhibitors (21 Tris HCL pH 8.0, 1 mM EDTA pH 8.0, 167 mM NaCl, 1.1% Triton X-100, 0.1% SDS), precleared with 30 ul Fast Flow Protein A sepharose beads (GE Healthcare) and 50 μg bovine serum albumin (BSA) by rotating in a siliconized eppendorf tube at 4 C for 1-2 hours.  The precleared chromatin was transferred to a tube containing the antibody of interest (see below), 30 ul Protein A sepharose beads and 50 ug BSA and rotated overnight at 4 C.  The bead bound chromatin was washed once each with low salt buffer (20 mM Tris HCl pH 8.0, 2 mM EDTA pH 8.0, 150 mM NaCl, 1% Triton X-100, 0.1% SDS), high salt buffer (20 mM Tris HCl pH 8.0, 2 mM EDTA pH 8.0, 500 mM NaCl, 1% Triton X-100, 0.1% SDS), LiCl buffer (10 mM Tris HCl pH 8.0, 1 mM EDTA pH 8.0, 250 mM LiCl, 1% Nonidet P-40, 1% Deoxycholate) and twice with TE (10 mM Tris HCl pH 8.0, 1 mM EDTA pH 8.0).  The chromatin was eluted off the beads with 0.1 M NaHCO3 /1% SDS by rotating at room temperature for 30 minutes, then the supernatant was transferred to a tube with 200nM NaCl and cross links were reversed by incubating overnight at 65 C (input controls were processed along with the ChIP samples from this point on).  10ug Proteinase K was added and the tube was incubated for 2 hours at 37 C, then the DNA was cleaned up using a QiaQuick PCR Purification Kit (Qiagen) and eluted in 50 μl 10 mM Tris HCl pH 8.5.  Antibodies used were (μl antibody per IP shown): H3K27me3 (Cell Signaling 9733, lot 8; 4 μl), H3K27ac (Cell Signaling 8173, lot 1; 4 μl) and H3K4me3 (Cell Signaling 9751, lot 8; 5 μl).
Libraries were prepared from 5-10 ng of DNA using the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina with NEBNext Q5 Hot Start HiFi PCR Master Mix according to the manufacturer’s instructions (New England Biolabs) with the following modifications: a second 1:1 Ampure cleanup was added after adaptor ligation. The Ampure size selection step prior to PCR was eliminated. Completed libraries were analyzed for insert size distribution on a 2100 BioAnalyzer High Sensitivity kit (Agilent) or Caliper LabChip GX DNA High Sensitivity Reagent Kit (Perkin Elmer).  Libraries were quantified using the Quant-iT PicoGreen dsDNA assay (Life Technologies), Kapa Library Quantification kit (Kapa Biosystems) or low pass sequencing on a MiSeq Nano v2 run (Illumina).

value: Nestin-cre; H3f3aLSL-K27M-Tag/+

tag: chip antibody


title: 1528_p2_H


title: 1527_p2_P


title: 1526_p2_R


title: NSF-D_WT-Tag_RNA-seq

value: Grown under neural precursor cell conditions


title: NSH-F_WT-Tag_H3K27me3_ChIP-seq

value: H3K27m3 (Cell Signoneling, 9733, lot 8)


title: NSH-C_K27M-Tag_H3K27me3_ChIP-seq


title: 1525_p2_H

value: Ethanol


title: NSH-F_WT-Tag_input_DNA

value: Nestin-cre; H3f3aLSL-WT-Tag/+

value: male


title: Mammary tumor growth treated with Saline, biological rep7

description: Primary Tumor


title: 1523_p2_R

value: Growth plate cartilage


title: 1522_p2_H


title: Mammary tumor growth treated with Saline, biological rep9

description: Primary Tumor


title: 1524_p2_P


title: NSF-C_K27M-Tag_input_DNA

value: female


title: Mammary tumor growth treated with Saline, biological rep6

description: Primary Tumor

value: mouse


title: Mammary tumor growth treated with Saline, biological rep8

description: Primary Tumor


title: Mammary tumor growth treated with Saline, biological rep3

description: Primary Tumor


title: NSF-F_WT-Tag_input_DNA


title: NSH-B_K27M-Tag_input_DNA


title: Mammary tumor growth treated with Saline, biological rep4

description: Primary Tumor


title: NSF-C_K27M-Tag_H3K27me3_ChIP-seq


title: Mammary tumor growth treated with Saline, biological rep5

description: Primary Tumor


title: NSH-B_K27M-Tag_H3K27me3_ChIP-seq


title: NSH-E_WT-Tag_input_DNA


title: 1519_p2_H


title: Mammary tumor growth treated with SFN, biological rep10

description: Primary Tumor


title: Mammary tumor growth treated with Saline, biological rep2

description: Primary Tumor


title: 1517_p2_R

value: Resting zone


title: Mammary tumor growth treated with Saline, biological rep1

description: Primary Tumor

value: Daily i.p. injection of 0.9% Saline


title: NSF-B_K27M-Tag_input_DNA


title: NSH-E_WT-Tag_H3K27me3_ChIP-seq


title: 1518_p2_P


title: 1516_p2_H


title: NSF-B_K27M-Tag_H3K27me3_ChIP-seq


title: Mammary tumor growth treated with SFN, biological rep9

description: Primary Tumor

value: Daily i.p. injection of 50mg SFN/kg


title: 1521_p2_P


title: 1514_p2_R


title: NSF-E_WT-Tag_input_DNA


title: Mammary tumor growth treated with SFN, biological rep8

description: Primary Tumor


title: 1515_p2_P


title: NSH-A_K27M-Tag_H3K27me3_ChIP-seq


title: Mammary tumor growth treated with SFN, biological rep7

description: Primary Tumor


title: 1520_p2_R


title: Mammary tumor growth treated with SFN, biological rep5

description: Primary Tumor


title: NSH-D_WT-Tag_input_DNA


title: NSH-D_WT-Tag_H3K27me3_ChIP-seq


title: 1511_p2_R


title: 1512_p2_P


title: 1513_p2_H

value: Hypertrophic zone


title: Mammary tumor growth treated with SFN, biological rep6

description: Primary Tumor


title: Mammary tumor growth treated with SFN, biological rep4

description: Primary Tumor


title: NSF-A_K27M-Tag_input_DNA


title: NSH-A_K27M-Tag_input_DNA


title: NSF-A_K27M-Tag_H3K27me3_ChIP-seq


title: Mammary tumor growth treated with SFN, biological rep2

description: Primary Tumor


title: NSF-D_WT-Tag_input_DNA


title: Mammary tumor growth treated with SFN, biological rep1

description: Primary Tumor


title: Patient 35 day 43

city: Pittsburgh

first: Lazar

last: Vujanovic

state: PA

address: L1.33 Hillman Cancer Center, 5117 Centre Ave

department: Medicine

institute: University of Pittsburgh

hyb_protocol: Unique pairs of a “capture” and a “reporter” probe are provided for each gene of interest, allowing up to 800 genes to be multiplexed, and their mRNA transcript levels measured, in a single experiment, for each sample. The “reporter” probe carries the signal, and the “capture” probe allows the complex to be immobilized for data collection.

scan_protocol: Single molecule imaging was performed on the nCounter SPRINT Profiler (NanoString Technologies)

data_processing:
Gene expression data were analyzed using the R statistical software.  Gene expression data from nCounter platform were log2 transformed and normalized using stable expression of housekeeping genes. Genes and the weights involved in calculations of metagenes were developed a priori by NanoString
Following calculation of the metagene values for each sample, scores were used to evaluate association of each score to patient outcome. The outcome here was defined either as a binary value based on “better” [partial responder (PR), stable disease (SD) and patients with resected tumors and no evidence of disease (NED)] and “worse” (progressive disease) prognosis. Each outcome was regressed against the scores calculated. In the case of the binary outcome, a univariate linear model regressing each score on the binary outcome generated expected log2 ratios of scores for the patients with better prognosis relative to those with worse prognosis.

label: Biotin capture probe, fluorescent barcoded reporter probe

source_name: Melanoma

label_protocol: PanCancer Immune Profiling Panel (NanoString Technologies, Inc.; Seattle, WA)

extract_protocol: RNeasy Mini Kit - QIAGEN

tag: individual

value: Patient 35

value: F

tag: age

tag: time

value: day 43

tag: disease state

value: Melanoma

tag: disease site

value: Left iliac

tag: clinical outcome

value: Stable Disease

tag: overall survival (mo)

tag: progression-free survival (mo)


title: Patient 35 day 89+

value: day 89+


title: Cell line MDA-MD-231 D3H1 Luci treated with 7.5uM of SFN for 48hs 2

description: Monolayer Cell Line

source_name: Monolayer Cell Line

value: Cell Line

value: Monolayer Cell Line

value: 7.5uM of SFN for 48hs


title: Cell line MDA-MD-231 D3H1 Luci treated with 7.5uM of SFN for 48hs 1

description: Monolayer Cell Line


title: BT-6_K27M-Tag_H3K4me3_ChIP-seq

tag: experiment id

value: Nestin-creERT2; H3f3aLSL-K27M-Tag/+; LSL-PDGFRαV544ins; Trp53flox/flox

value: Cell Signoneling H3K4me3 #9751 (lot 8)


title: Patient 35 day 0

value: day 0


title: BT-6_K27M-Tag_input_DNA

value: female


title: BT-6_K27M-Tag_H3K27ac_ChIP-seq

value: Cell Signoneling H3K27ac #8173 (lot 1)


title: Patient 34 day 43

value: Patient 34

value: M

value: Right lung


title: Mammary tumor growth treated with SFN, biological rep3

description: Primary Tumor

value: mouse

value: Mammary Primary Tumor Growth. Tissue removed 35 days post cell injectiom

value: Daily i.p. injection of 50mg SFN/kg


title: BT-6_K27M-Tag_H3K27me3_ChIP-seq

value: H3K27m3 (Cell Signoneling, 9733, lot 8)


title: Cell line MDA-MD-231 D3H1 Luci treated with 0.9% Saline for 48hs 2

description: Monolayer Cell Line

value: 0.9% saline for 48hs


title: Cell line MDA-MD-231 D3H1 Luci treated with 0.9% Saline for 48hs 1

description: Monolayer Cell Line


title: Patient 33 day 0

value: Patient 33

value: F

value: Melanoma

value: Right medial thigh

value: Progressive Disease


title: BT-11_WT-Tag_H3K27ac_ChIP-seq

value: Nestin-creERT2; H3f3aLSL-WT-Tag/+; LSL-PDGFRαV544ins; Trp53flox/flox


title: Mammary tumor initiation treated with Saline, biological rep6

description: Primary Tumor

value: Mammary Primary Tumor Initiation. Tissue removed less then 20 days post cell injectiom

value: Daily i.p. injection of 0.9% Saline


title: Patient 28 day 43

value: Patient 28

value: day 43

value: Right neck soft tissue


title: Patient 28 day 0

value: M

value: day 0

value: Right neck


title: Patient 34 day 0

value: Patient 34

value: Left lung

value: Stable Disease


title: Mammary tumor initiation treated with Saline, biological rep3

description: Primary Tumor

value: mouse


title: BT-11_WT-Tag_H3K27me3_ChIP-seq

value: female

value: H3K27m3 (Cell Signoneling, 9733, lot 8)


title: Mammary tumor initiation treated with Saline, biological rep4

description: Primary Tumor


title: BT-11_WT-Tag_input_DNA


title: Mammary tumor initiation treated with Saline, biological rep5

description: Primary Tumor


title: BT-10_WT-Tag_H3K4me3_ChIP-seq

value: Cell Signoneling H3K4me3 #9751 (lot 8)


title: BT-10_WT-Tag_H3K27ac_ChIP-seq

value: Cell Signoneling H3K27ac #8173 (lot 1)


title: Patient 22 day 43

value: Patient 22

value: F

value: Melanoma

value: Left axilla

value: Progressive Disease


title: Mammary tumor initiation treated with SFN, biological rep6

description: Primary Tumor

value: Mammary Primary Tumor Initiation. Tissue removed less then 20 days post cell injectiom

value: Daily i.p. injection of 50mg SFN/kg


title: Patient 18 day 0

value: Patient 18

value: M

value: day 0

value: Scalp

value: No Evidence of Disease


title: Mammary tumor initiation treated with Saline, biological rep1

description: Primary Tumor

value: mouse

value: Daily i.p. injection of 0.9% Saline


title: Patient 13 day 0

value: Patient 13


title: BT-10_WT-Tag_H3K27me3_ChIP-seq

value: Nestin-creERT2; H3f3aLSL-WT-Tag/+; LSL-PDGFRαV544ins; Trp53flox/flox

value: female

value: H3K27m3 (Cell Signoneling, 9733, lot 8)


title: Patient 22 day 0

value: Patient 22

value: F


title: Mammary tumor initiation treated with SFN, biological rep5

description: Primary Tumor


title: Patient 11 day 43

value: Patient 11

value: day 43

value: Melanoma

value: Neck


title: Mammary tumor initiation treated with SFN, biological rep4

description: Primary Tumor

value: Mammary Primary Tumor Initiation. Tissue removed less then 20 days post cell injectiom

value: Daily i.p. injection of 50mg SFN/kg


title: Patient 24 day 0

value: Patient 24

value: day 0

value: Right intramuscular mass

value: Progressive Disease


title: BT-9_WT-Tag_H3K4me3_ChIP-seq

value: male

value: Cell Signoneling H3K4me3 #9751 (lot 8)


title: BT-9_WT-Tag_H3K27ac_ChIP-seq

value: Nestin-creERT2; H3f3aLSL-WT-Tag/+; LSL-PDGFRαV544ins; Trp53flox/flox

value: Cell Signoneling H3K27ac #8173 (lot 1)


title: Patient 11 day 0

value: M

value: Right paracervical bx


title: BT-9_WT-Tag_input_DNA


title: Mammary tumor initiation treated with SFN, biological rep2

description: Primary Tumor

value: mouse


title: BT-9_WT-Tag_H3K27me3_ChIP-seq

value: H3K27m3 (Cell Signoneling, 9733, lot 8)


title: Mammary tumor initiation treated with SFN, biological rep3

description: Primary Tumor


title: Patient 10 day 89+

value: Patient 10

value: day 89+

value: Right retroperitoneal mass

value: Partial Responder


title: Patient 10 day 43

value: day 43

value: Melanoma


title: BT-8_WT-Tag_H3K27ac_ChIP-seq

value: female


title: BT-10_WT-Tag_input_DNA


title: Mammary tumor initiation treated with Saline, biological rep2

description: Primary Tumor

value: Mammary Primary Tumor Initiation. Tissue removed less then 20 days post cell injectiom

value: Daily i.p. injection of 0.9% Saline


title: Patient 10 day 0

value: day 0

value: Retroperitoneal soft tissue mass


title: Mammary tumor initiation treated with SFN, biological rep1

description: Primary Tumor

value: Daily i.p. injection of 50mg SFN/kg


title: Mammary tumor growth treated with Saline, biological rep12

description: Primary Tumor

value: Mammary Primary Tumor Growth. Tissue removed 35 days post cell injectiom


title: Mammary tumor growth treated with Saline, biological rep11

description: Primary Tumor


title: Patient 9 day 43

value: Patient 9

value: M

value: Deep left axillary lymph node

value: Stable Disease


title: Mammary tumor growth treated with Saline, biological rep10

description: Primary Tumor

value: mouse


title: Patient 9 day 0

value: Right chest


title: Patient 8 day 89+ E

value: Patient 8

value: F

value: day 89+

value: Left hand


title: BT-7_WT-Tag_H3K4me3_ChIP-seq

value: Nestin-creERT2; H3f3aLSL-WT-Tag/+; LSL-PDGFRαV544ins; Trp53flox/flox

value: female

value: Cell Signoneling H3K4me3 #9751 (lot 8)


title: Patient 8 day 89+ D

value: Melanoma

value: Right cheek


title: Mammary tumor growth treated with Saline, biological rep9

description: Primary Tumor

value: Daily i.p. injection of 0.9% Saline


title: Mammary tumor growth treated with Saline, biological rep8

description: Primary Tumor

value: Mammary Primary Tumor Growth. Tissue removed 35 days post cell injectiom


title: BT-7_WT-Tag_input_DNA


title: BT-7_WT-Tag_H3K27ac_ChIP-seq

value: Cell Signoneling H3K27ac #8173 (lot 1)


title: Patient 8 day 89+ C

value: Right forehead


title: BT-8_WT-Tag_H3K27me3_ChIP-seq

value: H3K27m3 (Cell Signoneling, 9733, lot 8)


title: BT-5_K27M-Tag_input_DNA

value: Nestin-creERT2; H3f3aLSL-K27M-Tag/+; LSL-PDGFRαV544ins; Trp53flox/flox


title: Patient 8 day 89+ B

value: Stable Disease


title: BT-7_WT-Tag_H3K27me3_ChIP-seq


title: BT-5_K27M-Tag_H3K27ac_ChIP-seq


title: BT-8_WT-Tag_input_DNA


title: Patient 8 day 43

value: day 43

value: Right inner arm


title: Patient 8 day 89+ A

value: Patient 8

value: F

value: Right temple


title: BT-5_K27M-Tag_H3K27me3_ChIP-seq


title: Mammary tumor growth treated with Saline, biological rep5

description: Primary Tumor

value: mouse


title: Mammary tumor growth treated with Saline, biological rep4

description: Primary Tumor


title: Mammary tumor growth treated with Saline, biological rep6

description: Primary Tumor


title: Mammary tumor growth treated with Saline, biological rep7

description: Primary Tumor


title: Patient 8 day 0

value: day 0


title: Mammary tumor growth treated with Saline, biological rep2

description: Primary Tumor


title: Patient 7 day 89+

value: Patient 7

value: M

value: day 89+

value: Cervical lymph node


title: Patient 7 day 43

value: Melanoma

value: Right cervical lymph node


title: Mammary tumor growth treated with Saline, biological rep1

description: Primary Tumor

value: Mammary Primary Tumor Growth. Tissue removed 35 days post cell injectiom

value: Daily i.p. injection of 0.9% Saline


title: BT-4_K27M-Tag_input_DNA

value: Nestin-creERT2; H3f3aLSL-K27M-Tag/+; LSL-PDGFRαV544ins; Trp53flox/flox

value: male


title: BT-4_K27M-Tag_H3K27ac_ChIP-seq

value: Cell Signoneling H3K27ac #8173 (lot 1)


title: Patient 7 day 0

value: Right neck node

value: Stable Disease


title: BT-4_K27M-Tag_H3K27me3_ChIP-seq

value: H3K27m3 (Cell Signoneling, 9733, lot 8)


title: BT-3_K27M-Tag_H3K27ac_ChIP-seq


title: Mammary tumor growth treated with SFN, biological rep12

description: Primary Tumor

value: Daily i.p. injection of 50mg SFN/kg


title: BT-3_K27M-Tag_input_DNA


title: Mammary tumor growth treated with Saline, biological rep3

description: Primary Tumor

value: mouse


title: Patient 6 day 89+

value: Patient 6

value: Nasal lesion


title: Patient 6 day 43

value: M

value: day 43


title: Patient 6 day 0

value: day 0

value: Sinonasal


title: Mammary tumor growth treated with SFN, biological rep11

description: Primary Tumor


title: Mammary tumor growth treated with SFN, biological rep10

description: Primary Tumor


title: Mammary tumor growth treated with SFN, biological rep9

description: Primary Tumor


title: Patient 5 day 0

value: Patient 5

value: Melanoma

value: Left flank

value: Progressive Disease


title: Mammary tumor growth treated with SFN, biological rep7

description: Primary Tumor

value: Mammary Primary Tumor Growth. Tissue removed 35 days post cell injectiom


title: Patient 4 day 0

value: Patient 4

value: Left shoulder


title: BT-2_K27M-Tag_H3K27ac_ChIP-seq

value: Nestin-creERT2; H3f3aLSL-K27M-Tag/+; LSL-PDGFRαV544ins; Trp53flox/flox

value: male

value: Cell Signoneling H3K27ac #8173 (lot 1)


title: BT-2_K27M-Tag_input_DNA


title: Patient 3 day 43

value: Patient 3

value: F

value: Left upper arm


title: BT-2_K27M-Tag_H3K4me3_ChIP-seq

value: Cell Signoneling H3K4me3 #9751 (lot 8)


title: Patient 3 day 0


title: BT-2_K27M-Tag_H3K27me3_ChIP-seq

value: H3K27m3 (Cell Signoneling, 9733, lot 8)


title: Patient 2 day 43

value: Patient 2

value: M

value: day 43

value: Left chest wall


title: BT-1_K27M-Tag_H3K27ac_ChIP-seq


title: Mammary tumor growth treated with SFN, biological rep4

description: Primary Tumor

value: mouse

value: Daily i.p. injection of 50mg SFN/kg


title: Mammary tumor growth treated with SFN, biological rep6

description: Primary Tumor

value: Mammary Primary Tumor Growth. Tissue removed 35 days post cell injectiom


title: Mammary tumor growth treated with SFN, biological rep5

description: Primary Tumor


title: BT-1_K27M-Tag_H3K27me3_ChIP-seq

value: H3K27m3 (Cell Signaling, 9733, lot 8)


title: Patient 2 day 0

value: day 0

value: Melanoma

value: Progressive Disease


title: BT-3_K27M-Tag_H3K27me3_ChIP-seq

value: Nestin-creERT2; H3f3aLSL-K27M-Tag/+; LSL-PDGFRαV544ins; Trp53flox/flox

value: male


title: Patient 1 day 43

value: Patient 1

value: F

value: Left scalp


title: Huh7 AdPCK1 rep2

status: Public on Jan 02 2019

city: chongqing

first: tang

last: ni

address: yixueyuan Road NO.1

institute: Chongqing Medical University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
MapSplice mapping to reference genome
count counting
Genome_build: GRCh37
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: Huh 7 cells

growth_protocol: Huh7 cells were cultured in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum, 100 IU penicillin, and 100 mg/ml streptomycin at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Invitrogen)
cDNA Library Construction:  The cDNA libraries were constructed for each pooled RNA sample using the VAHTSTM Total RNA-seq (H/M/R) according to the manufacturer’s instructions. Generally, the protocol consists of the following steps: depletion of rRNA and fragmented into 150-200 bp using divalent cations at 94 ℃ for 8 min. The cleaved RNA fragments were reverse-transcribed into first-strand cDNA, second-strand cDNA synthesis, fragments were end repaired, A-tailed and ligated with indexed adapters. Target bands were harvested through VAHTSTM DNA Clean Beads .The products were purified and enriched by PCR to create the final cDNA libraries and quantified by Agilent2200. The tagged cDNA libraries were pooled in equal ratio and used for 150 bp paired-end sequencing in a single lane of the Illumina Xten with 51 plus 7 cycles by NovelBio Corp. Laboratory, Shanghai.

treatment_protocol: Adenoviral recombinant AdGSTZ1 or AdPCK1 were generated using the AdEasy system, and green fluorescent protein-expressing analogous adenovirus (AdGFP) was used as a control.

tag: cell type

value: hepatoma cells

value: liver

tag: adenovirus

value: adenovirus overexpression PCK1


title: Huh7 AdPCK1 rep1


title: Mammary tumor growth treated with SFN, biological rep8

description: Primary Tumor

tag: sample identification

tag: host


title: Patient 1 day 0

tag: gender


title: Huh7 AdGSTZ1 rep4

tag: tissue

value: adenovirus overexpression GSTZ1


title: Mammary tumor growth treated with SFN, biological rep1

description: Primary Tumor

tag: treatment


title: Mammary tumor growth treated with SFN, biological rep2

description: Primary Tumor


title: Huh7 AdGSTZ1 rep3


title: Huh7 AdGFP rep3

value: adenovirus with GFP control


title: Huh7 AdGFP rep2


title: Huh7 AdGFP rep1


title: SEM-CX4945-Input

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: Cells with CX4945 treatment

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Illumina HiSeq and NextSeq output,respectively.
Both ChIP-seq and RNA-seq reads were trimmed from the 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19  using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

source_name: SEM

growth_protocol: Cell medium was composed as follow: DMEM 1X (Thermo Fisher), 10%  serum (Corning), 1X glutamine (Life Technologies), 1X penicillin/streptomycin (Life  Technologies), cells were grown in a CO2 incubator (5% CO2) at 37˚C

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit

value: MLL rearranged leukemia cells

tag: passages

value: Low passages (6-10)

tag: cell line

value: SEM

tag: agent


title: SEM-CX4945-AFF1CT

description: Cells with CX4945 treatment

tag: chip antibody

value: AFF1CT (homemade)


title: SEM-CX4945-ELL2

description: Cells with CX4945 treatment

value: ELL2 (homemade)


title: BT-1_K27M-Tag_input_DNA

tag: full genotype


title: SEM-CX4945-AFF4

description: Cells with CX4945 treatment

value: AFF4 (homemade)


title: SEM-DMSO-AFF4

description: Cells with DMSO vehicle treatment

value: embyronic kidney cells

value: DMSO vehicle


title: SEM-DMSO-ELL2

description: Cells with DMSO vehicle treatment


title: Mammary tumor growth treated with SFN, biological rep3

description: Primary Tumor

value: mouse

value: Mammary Primary Tumor Growth. Tissue removed 35 days post cell injectiom

value: Daily i.p. injection of 50mg SFN/kg


title: 293T-TTP22-Input

description: Cells with TTP22 treatment


title: Huh7 AdPCK1 rep3


title: 293T-DMSO-Input

description: Cells with DMSO vehicle treatment


title: 293T-CX4945-MLL1C

description: Cells with CX4945 treatment

value: MLL1 C-terminus (CST)


title: 293T-CX4945-Input

description: Cells with CX4945 treatment


title: 293T-DMSO-MLL1C

description: Cells with DMSO vehicle treatment


title: 293T-TTP22-MLL1C

description: Cells with TTP22 treatment


title: 293T-TASP1KO-MLLAF4-ELL2

description: Cells knocked out of TASP1 gene by CRISPR/Cas9, and overexpressed with MLLAF4

tag: genotype/variation


title: Huh7 AdGSTZ1 rep2

value: hepatoma cells


title: SEM-DMSO-AFF1CT

description: Cells with DMSO vehicle treatment


title: MCF7-TASP1KO-MLL1C

description: Cells knocked out of TASP1 gene by CRISPR/Cas9

value: breast cancer cell


title: 293T-WT-MLLAF4-Input

description: Cells overexpressed with MLLAF4

value: overexpressed with MLLAF4


title: 293T-WT-MLLAF4-ELL2

description: Cells overexpressed with MLLAF4


title: MCF7-TASP1KO-MLL1N

value: MLL1 N-terminus (CST)

value: knocked out of TASP1 gene by CRISPR/Cas9


title: MCF7-WT-MLL1C

description: Cells with DMSO vehicle treatment


title: SEM-DMSO-Input

description: Cells with DMSO vehicle treatment

value: MLL rearranged leukemia cells


title: MCF7-WT-MLL1N

description: Cells with CX4945 treatment

value: Low passages (6-10)


title: 293TKOTASP1-shMLL1-MLL1N

description: Cells knocked out of TASP1 gene by CRISPR/Cas9, and treated with human MLL1 dsRNA


title: MCF7-WT-Input


title: 293TKOTASP1-shCtrl-Input

description: Cells knocked out of TASP1 gene by CRISPR/Cas9, and treated with non-targeting dsRNA


title: 293TKOTASP1-shCtrl-MLL1N

value: knocked out of TASP1 gene by CRISPR/Cas9, and treated with non-targeting dsRNA


title: 293TKOTASP1-shCtrl-MLL1C


title: 293TWT-shMLL1-MLL1C

description: Cells treated with human MLL1 dsRNA

value: human MLL1 dsRNA


title: 293TWT-shMLL1-Input

description: Cells treated with human MLL1 dsRNA


title: 293TWT-shCtrl-Input

description: Cells treated with non-targeting dsRNA

value: non-targeting dsRNA


title: 293T-TASP1KO-MLLAF4-Input

value: knocked out of TASP1 gene by CRISPR/Cas9, and overexpressed with MLLAF4


title: 293TWT-shCtrl-MLL1C

description: Cells treated with non-targeting dsRNA

value: embyronic kidney cells


title: 293T-C104-MLL2C

value: MLL2 C-terminus (homemade)


title: 293T-C104-MLL1C


title: MCF7-TASP1KO-Input


title: 293TKOTASP1-shMLL1-Input

value: knocked out of TASP1 gene by CRISPR/Cas9, and treated with human MLL1 dsRNA


title: 293TKOTASP1-shMLL1-MLL1C


title: 293T-WT-MLL2C


title: 293T-C49-MLL2C


title: 293T-C49-MLL1C


title: 293T-WT-Input


title: 293T-C49-MLL1N


title: 293T-C49-Input-20160502


title: 293T-C49-H3K4me3-20160502

value: H3K4me3 (homemade)


title: 293T-WT-MLL1N


title: 293T-C49-H3K4me1-20160502

value: H3K4me1 (homemade)


title: 293TWT-shMLL1-MLL1N

description: Cells treated with human MLL1 dsRNA


title: 293T-WT-Input-20160502


title: 293T-WT-H3K4me3-20160502


title: 293T-WT-H3K4me1-20160502


title: 293TWT-shCtrl-MLL1N

description: Cells treated with non-targeting dsRNA


title: 293T-WT-H3K4me2-20160502

value: H3K4me2 (homemade)


title: 293T-C104-MLL1N


title: 293T-C104-Input


title: 293T-C49-Input


title: 293T-TASP1KO-shMLL1-R2


title: SEM-DMSO-R2

description: Cells with DMSO vehicle treatment

value: SEM

value: DMSO vehicle


title: SEM-DMSO-R1

description: Cells with DMSO vehicle treatment


title: 293T-TASP1KO-shMLL1-R1


title: 293T-TASP1KO-sc-R1


title: 293T-TASP1KO-sc-R2


title: 293T-WT-MLL1C

value: MLL1 C-terminus (CST)


title: 293T-WT-shMLL1-R2

description: Cells treated with human MLL1 dsRNA


title: 293T-WT-shMLL1-R1

description: Cells treated with human MLL1 dsRNA


title: ND412-MAIT-CD8pos

first: Marcus

last: Buggert

address: C2:94; Karolinska Universitetssjukhuset Huddinge

department: Microbiology

institute: Karolinska Institutet

data_processing:
Sequencing reads were aligned to the hg38 reference genome using STAR 2.5.2a
Data was normalized using DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file include log2 normalized read counts for each sample

source_name: peripheral blood

growth_protocol: Cells were thawed and rested overnight at 37C in RPMI + 10% FBS + 1% L-glut + 1% Pen/Strep media

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

treatment_protocol: Cells were not treated with any compound

value: Mucosa-associated invariant T (MAIT) cells

tag: cell markers


title: 293T-WT-sc-R2

description: Cells treated with non-targeting dsRNA


title: 293T-C49-H3K4me2-20160502

value: knocked out of TASP1 gene by CRISPR/Cas9


title: ND434-MAIT-CD8pos


title: ND434-MAIT-CD8neg


title: 293T-WT-sc-R1

description: Cells treated with non-targeting dsRNA


title: ND365-MAIT-CD8pos


title: ND410-MAIT-CD8neg


title: ND365-MAIT-CD8neg


title: ND412-MAIT-CD8neg


title: ND410-MAIT-CD8pos


title: SEM-CX4945-R2

description: Cells with CX4945 treatment

value: MLL rearranged leukemia cells


title: SEM-CX4945-R1

description: Cells with CX4945 treatment

value: Low passages (6-10)


title: EAS [Beaumont]

city: Dublin

first: Catherine

last: Mooney

address: Belfield

department: School of Computer Science

country: Ireland

institute: University College Dublin

data_processing:
Total RNA was extracted from 200 µl of plasma using the miRCURY RNA isolation kit for biofluids (Exiqon).
Purified RNA was eluted in 50 µl RNAase free water. Total RNA was extracted using miRCURY RNA isolation kit and small RNA libraries were generated using NEBNEXT library generation kit (New England Biolabs Inc.).
Samples were sequenced on the Illumina system by Exiqon Services, Denmark.
Intensity correction, base calling and assigning of Q-scores were then performed as part of measures to assess the quality of the data obtained.
Differential expression analysis was performed using the EdgeR statistical software package.

source_name: plasma

extract_protocol:
Total RNA was extracted from 200 μl of plasma using the miRCURY RNA isolation kit-biofluid (Exiqon) according to the manufacturer’s protocol
Next Generation Sequencing process for biofluids microRNA and small RNA sequencing at Exiqon.

tag: sample type

value: 16 pooled samples

tag: disease state

value: Epilepsy, post seizure

tag: centre

value: Beaumont


title: EBS [Beaumont]

value: Epilepsy, pre seizure


title: control [Beaumont]

value: Control


title: EAS [Marburg]

value: Marburg


title: EBS [Marburg]


title: control [Marburg]


title: H3K27ac_Sox9_2 [E13.5]

first: Christopher

last: Futtner

state: Il

address: 303 E. Superior St, Lurie 7-220

department: Endocrinology

institute: Northwestern University

data_processing:
Files were trimmed for quality using trim_galore with a stringency setting of 5
Reads were aligned to the mm9 genome with bowtie using the parameters -m 1 and --best
Unmapped reads were eliminated with samtools view using -F 4 settings
Peaks were called using Homer. For ATAC-seq: the --nomodel and --broad settings were used. For ChIP-seq: the --broad setting was used, H3K27ac was used as treament (-t) and H3 as control (-c)
bigwig files were created from .bdg files using BedGraphToBigWig for visualization on the UCSC genome browser. For optimal visualization, ChIP-seq replicates were concatenated to increase number of reads.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files contain tracks for visualization on the UCSC genome browser

source_name: FACS-sorted Sertoli cells

extract_protocol:
Embryonic gonads were micro-dissected at according stage, removed from the mesonephros and incubated in 0.05% trypsin for 5 minutes at 37C. Gonads were then mechanically dissasociated in PBS/3% BSA and passed through a filter cap to obtain a single cell suspension. Fluorescently-labeled cells were collected by Fluorescence Activated Cell Sorting (FACS). For ATAC-seq, 60K cells were collected per replicate. For ChIP-seq, 50-100K cells were collected per replicate.
ATAC-seq libraries were prepared according to Buenrostro et al.2013. ChIP-seq libraries were prepared according to Van Galen et al., 2016. For ChIP-seq, corresponding H3 ChIP was used as Input.

tag: embryonic stage

tag: Sex

value: male

tag: transgenic line

tag: chip-antibody

value: H3K27ac Active Motif 39133

tag: protocol

value: Van Galen et al, 2016


title: H3_Sox9_2 [E13.5]

value: H3 Active Motif 39763


title: H3K27ac_Sox9_1 [E13.5]


title: H3_Sox9_1 [E13.5]


title: H3_TESm_1 [E13.5]

source_name: FACS-sorted granulosa cells

value: female

value: TESm-CFP


title: H3_TESm_2 [E13.5]


title: H3K27ac_SF1_M_2 [E10.5]

source_name: FACS-sorted XY gonadal progenitor cells


title: H3K27ac_TESm_2 [E13.5]


title: H3K27ac_TESm_1 [E13.5]


title: H3K27ac_SF1_M_1 [E10.5]


title: H3_SF1_M_2 [E10.5]


title: H3_SF1_F_2 [E10.5]

source_name: FACS-sorted XX gonadal progenitor cells


title: ATAC_BipotentialFemaleDM_24 [E10.5]

value: Buenrostro et al., 2013


title: H3K27ac_SF1_F_1 [E10.5]


title: ATAC_BipotentialFemaleDM_19 [E10.5]


title: H3_SF1_F_1 [E10.5]


title: ATAC_Sertoli_DM16 [E13.5]


title: ATAC_Sertoli_DM15 [E13.5]


title: H3_SF1_M_1 [E10.5]


title: H3K27ac_SF1_F_2 [E10.5]


title: ATAC_BipotentialMale_DM22 [E10.5]


title: ATAC_Granulosa_DM12 [E13.5]


title: ATAC_BipotentialMale_DM21 [E10.5]


title: F480Hi_NCD_rep1

city: La Jolla

first: Jason

middle: Samuel

last: Seidman

state: CA

address: 9500 Gilman Drive, Mail code 0651

department: Cellular and Molecular Medicine

institute: University of California San Diego

data_processing:
Fastq files from sequencing experiments were mapped to the mouse mm10 genome using default parameters for STAR .Mapped data were analyzed with HOMER's "analyzeRepeats" function with "-raw - count exons -condenseGenes". Short transcripts (<200bp) were removed prior to TPM calculation and identification of differentially expressed genes with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text files of the folllowing: Table of unnormalized read counts RNA-seq,  table of TPM values for RNA-Seq, table of rlog normalized expression values and differential expression results from DESeq2

source_name: F480 High Islet Macrophages

extract_protocol:
NCD and HFD mice were euthanized, and freshly-prepared collagenase P (Roche, Indianapolis, IN) solution (0.5 mg/ml) was injected into the pancreas via the common bile duct. The perfused pancreas was digested at 37°C for 20 min, and the islets were handpicked under a stereoscopic microscope, and then dispersed into single cell suspensions. Macrophages were labeled with mAbs against CD11b, CD11c, F4/80 and sorted using FACSAria II (BD, San Jose, CA).
Sequencing libraries were prepared according to the Smart-seq2 method (Picelli, et al. 2013) with some modifications. 3000-5000 FACS isolated cells in Trizol (Thermo Fisher) were used as starting material. RNA was extracted with the Direct-zol MicroPrep kit (Zymo Research) with on-column DNAseI treatment. 10 µL of purified RNA was mixed with 5.5 µL of SMARTScribe 5X First-Strand Buffer (Clontech), 1 µL polyT-RT primer (2.5 µM, 5’-AAGCAGTGGTATCAACGCAGAGTAC(T30)VN-3’), 0.5 µL SUPERase-IN (Ambion), 4 µL dNTP mix (10 mM, Invitrogen), 0.5 µL DTT (20 mM, Clontech) and 2 µL Betaine solution (5 M, Sigma), incubated 50C 3 min. 3.9 µL of first strand mix, containing 0.2 µL 1% Tween-20, 0.32 µL MgCl2 (500 mM), 0.88 µL Betaine solution (5 M, Sigma), 0.5 µL SUPERase-IN (Ambion) and 2 µL SMARTScribe Reverse Transcriptase (100 U/µL, Clontech) was added and incubated one cycle 25C 3 min., 42C 60 min. 1.62 µL template switch (TS) reaction mix containing 0.8 µL biotin-TS oligo (10 µM, Biotin-5’-AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3’), 0.5 µL SMARTScribe Reverse Transcriptase (100 U/µL Clontech) and 0.32 µL SMARTScribe 5X First-Strand Buffer (Clontech) was added, then incubated at 50C 2 min., 42C 80 min., 70C 10 min. 14.8 µL second strand synthesis, pre-amplification mix containing 1 µL pre-amp oligo (10 µM, 5’AAGCAGTGGTATCAACGCAGAGT-3’), 8.8 µL KAPA HiFi Fidelity Buffer (5X, KAPA Biosystems), 3.5 µL dNTP mix (10 mM, Invitrogen) and 1.5 µL KAPA HiFi HotStart DNA Polymerase (1U/µL, KAPA Biosystems), was added,  then amplified by PCR: 95C 3 min., 8 cycles 98C 20 seconds, 67C 15 sec and 72C 6 min, final extension 72C 5 min.  The synthesized dsDNA was purified using Sera-Mag Speedbeads (Thermo Fisher Scientific) with final 8.4% PEG8000, 1.1M NaCl, then eluted with 13 µL UltraPure water (Invitrogen). The product was quantified by Qubit dsDNA High Sensitivity Assay Kit (Invitrogen) and libraries were prepared using the Nextera DNA Sample Preparation kit (Illumina). Tagmentation mix containing 11 µL 2X Tagment DNA Buffer and 1 µL Tagment DNA Enzyme was added to 10 µL purified DNA, then incubated at 55C 15 min. 6 µL Nextera Resuspension Buffer (Illumina) was added and incubated at room temperature for 5 min. Tagmented DNA was purified using Sera-Mag Speedbeads (Thermo Fisher Scientific) with final 7.8% PEG8000, 0.98M NaCl, then eluted with 25 µL UltraPure water (Invitrogen). Final enrichment amplification was performed with Nextera primers, adding 1 µL Index 1 primers (100 µM, N7xx), 1 µL Index 2 primers (100 µM, N5xx) and 27 µL NEBNext High-Fidelity 2X PCR Master Mix (New England BioLabs), then amplified by PCR: 72C 5 min., 98C 30 sec., 8-13 cycles 98C 10 seconds, 63C 30 sec., and 72C 1 min. Libraries were size selected, quantified Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific), pooled and sequenced on a NextSeq 500 (Illumina) for 76 cycles at a depth of 25 to 40 million single end reads per sample.

tag: cell type

value: sorted ex vivo pancreatic islet macrophages

value: F480 High Islet Macrophages

value: Normal chow diet

tag: strain


title: F480Hi_NCD_rep2

tag: treatment


title: CD11cHi_NCD_rep1

source_name: CD11c High Islet Macrophages

value: CD11c High Islet Macrophages


title: CD11cHi_NCD_rep2


title: CD11cHi_HFD_rep3

value: High fat diet


title: CD11cHi_HFD_rep2


title: F480Hi_HFD_rep2


title: CD11cHi_HFD_rep1


title: CAP31-C92

city: Lausanne

first: Federico

last: Santoni

address: rue du Bugnon, 7

country: Switzerland

institute: CHUV

description:
Single cell lymphoblastoid
ASE_gene_cell_ind.csv

data_processing:
Genome sequencing: For each individual,we used the Burrows- Wheeler Aligner (BWA mem v.0.7.10) to align the sequencing reads (fastq) to the human reference genome (GRCh37/hg19). We used SAMtools v.1.4 to remove paired-end duplicates and pile up the remaining reads. BCFtools v.1.4 was used to call the SNVs and Annovar (2016Feb01) for the annotation. SNVs with quality score <100 where excluded from the analysis.
Single cell RNA-seq: RNA sequences were mapped with GEM. Uniquely mapping reads were extracted by filtering for mapping quality (MQ>=150). An in-house algorithm was used to quantify RPKM expression using GENCODE v26. Cells with less than 1 million uniquely mapped reads were excluded from further analysis
Allele specific expression: For each gene on the X chromosome, the aggregate monoallelic ratio (AR) per cell was calculated by averaging the allelic ratio of the reads covering the respective heterozygous sites (AR = sum of number of reads from the active X allele / total SNV reads; 0≤AR≤1). Since we do not have the availability of parental genotype for all the individuals, we designed an algorithm to estimate the active X allele per site based on the assumption that the active X allele is, on average, more transcribed than the inactive X. We validated this assumption comparing the prediction of our algorithm with the phasing of twins’ X alleles based on parental information (more details in Methods S1). According to this metric, inactivated genes cluster around AR=1 while known escapees appear as been uniformly distributed between 0.5≤AR≤0.95 (linear phase of the cumulative distribution, Figure S12). As support of this observation, AR distribution of autosomal genes clearly indicates AR=0.95 as the threshold separating biallelically expressed genes from monoallelic expressed genes (Figure S13). Therefore, we consider a gene as escapee in the relaxed set when the aggregate AR is ≤ 0.95 in at least 1 individual and as escapee in the robust set when the aggregate AR is ≤ 0.95 in at least 2 individuals. To reduce the effect of allele dropout, we only consider for the analysis SNV sites covered by at least 5 reads in at least three cells. To reduce sampling bias effects a gene is included in the analysis if detectable in more than 5 different cells and/or SNVs per sample.
Genome_build: GRCh37/hg19

source_name: Gencord collection (Borel et al 2015)

growth_protocol: Cells were cultured in DMEM GlutaMAX™ (Life Technologies) supplemented with 10% fetal bovine serum (Life Technologies) and 1% penicillin/streptomycin/fungizone mix (Amimed, BioConcept) at 37°C in a 5% CO2 atmosphere as described

extract_protocol:
Single-cell capture was performed using the C1 single-cell auto prep system (Fluidigm) following the manufacturer’s procedure. The integrated fluidic circuit used for the study is the C1™ Single-Cell mRNA Seq IFC, 17–25 μm with a capacity of 96 chambers. During the capture, all 96 chambers were inspected under an inverted phase contrast microscope; only chambers containing a non-damaged single cell were considered for downstream analysis. SMARTer Ultra Low RNA kit for Illumina sequencing (version 2, Clontech) was used for the cell lysis and cDNA synthesis.
Libraries were prepared with 0.3 ng of pre-amplified cDNA using Nextera XT DNA kit (Illumina)
Libraries were sequenced on an Illumina HiSeq2000 sequencer as 100 bp single ended reads. RNA sequences were mapped with GEM. Uniquely mapping reads were extracted by filtering for mapping quality (MQ>=150). An in-house algorithm was used to quantify RPKM expression using GENCODE v26. Cells with less than 1 million uniquely mapped reads were excluded from further analysis.

tag: cell culture

value: LCL

tag: individual id

value: Individual 5


title: CAP31-C93


title: CAP31-C86


title: CAP31-C91


title: ATAC_Granulosa_DM13 [E13.5]


title: CAP31-C80


title: CAP31-C87


title: CAP31-C74


title: CAP31-C85


title: CAP31-C63


title: CAP31-C68


title: CAP31-C69


title: CAP31-C67


title: CAP31-C62


title: CAP31-C56


title: CAP31-C73


title: CAP31-C57


title: F480Hi_HFD_rep1


title: CAP31-C50


title: CAP31-C49


title: CAP31-C51


title: CAP31-C43


title: CAP31-C44


title: CAP31-C41


title: CAP31-C38


title: CAP31-C39


title: CAP31-C40


title: CAP31-C37


title: CAP31-C32


title: CAP31-C27


title: CAP31-C33


title: CAP31-C34


title: CAP31-C55


title: CAP31-C25


title: CAP31-C21


title: CAP31-C20


title: CAP31-C24


title: CAP31-C35


title: CAP31-C18


title: CAP31-C07


title: CAP31-C11


title: CAP31-C12


title: CAP31-C06


title: CAP31-C09


title: TN2A-C96

description:
Single cell fibroblast
ASE_gene_cell_ind.csv

source_name: Dahoun et al 2008

value: primary skin fibroblast

value: Individual 4


title: TN2A-C94


title: CAP31-C26


title: TN2A-C92


title: TN2A-C93


title: TN2A-C91


title: CAP31-C13


title: CAP31-C15


title: CAP31-C03


title: CAP31-C19


title: TN2A-C82


title: TN2A-C88


title: TN2A-C81


title: TN2A-C86


title: TN2A-C84


title: TN2A-C90


title: TN2A-C87


title: TN2A-C73


title: TN2A-C70


title: TN2A-C69


title: TN2A-C60


title: TN2A-C79


title: TN2A-C44


title: TN2A-C64


title: TN2A-C45


title: TN2A-C68