title: Ndt80 untagged control YPA 2

data_processing:
Quality analysis performed with FastQC
ChIP-seq reads were aligned to the S. cerevisiae genome assembly using bowtie2 and default parameters
Files were converted to sorted .bam files using Samtools
Peak separation distance was determined using the binding.characteristics function in the SPP package in R
Peaks and fold enrichment were calculated using MACS2, using peak separation distances calculated from SPP and --nomodel parameter
Genome_build: S. cerevisiae genome was downloaded from the Candida Gene order Browser in May 2015
Supplementary_files_format_and_content: bedGraph.wig files were generated from indexed, sorted .bam file using genomeCoverageBed tool in BedTools, followed by a .bed to .wig conversion script in Python.  FE.bdg.wig files were generated by MACS2 using the -SPMR parameter, and converted to .wig using the same Python script.  Peaks.xls files were generated for experiments with tagged proteins using untagged strains as a control in MACS2.

organism: Saccharomyces cerevisiae

source_name: SK1 a/alpha cell

growth_protocol: Cells were grown overnight in YPD, diluted back to OD = 0.1 in YPA (1% Peptone, 2% Potassium Acetate, 1% Yeast Extract) and grown for 16 hours.

value: YPA media (2% Peptone, 2% Potassium Acetate, 1% Yeast Extract)


title: pTef1-Ndt80A-myc_2

status: Public on May 01 2017

type: SRA

city: San Francisco

first: Isabel

last: Nocedal

state: CA

country: USA

institute: UCSF

library_source: genomic

data_processing:
Quality analysis performed with FastQC
ChIP-seq reads were aligned to the S. stipitis genome assembly using bowtie2 and default parameters
Files were converted to sorted .bam files using Samtools
Peak separation distance was determined using the binding.characteristics function in the SPP package in R
Peaks and fold enrichment were calculated using MACS2, using peak separation distances calculated from SPP and --nomodel parameter
Genome_build: S. stipitis genome was downloaded from the Candida Gene Order Browser in December 2015.
Supplementary_files_format_and_content: bedGraph.wig files were generated from indexed, sorted .bam file using genomeCoverageBed tool in BedTools, followed by a .bed to .wig conversion script in Python.  FE.bdg.wig files were generated by MACS2 using the -SPMR parameter, and converted to .wig using the same Python script.  Peaks.xls files were generated for experiments with tagged proteins using untagged strains as a control in MACS2.

molecule: genomic DNA

organism: Scheffersomyces stipitis

source_name: prototrophic cell

growth_protocol: Cells were grown overnight in YPD diluted back to OD = 0.02 in YPD and grown for 4-6 hours until log-phase.

extract_protocol:
Cells were lysed with glass bead vortexing, sonicated for 3 15-minute cycles, and immunoprecipitated at 4˚C overnight
Libraries were prepared using the NEBNext ChIP-Seq library prep kit for Illumina (New England Biolabs)

tag: media condition

value: YPD

tag: chip antibody

value: human c-myc

tag: strain number


title: Ndt80 untagged control YPA 1


title: pTef1-Ndt80A-myc_1


title: WT_SPO_1

library_source: transcriptomic

data_processing:
Quality analysis performed with FastQC
Reads were aligned to the P. pastoris genome assembly using TopHat
Transcripts assembled using Cufflinks
Transcripts merged using Cuffmerge
Differential expression calculated using CuffDiff
Genome_build: P. pastoris genome was downloaded from NCBI in December 2015, genome annotated using Yeast Gene Annotation Pipeline in December 2015.
Supplementary_files_format_and_content: .gtf files were generated by Cufflinks from reads aligned to the genome using TopHat

molecule: total RNA

organism: Komagataella pastoris

source_name: diploid cell

growth_protocol: Cells were grown overnight in YPD diluted back to OD = 0.1 in YPD or sporulation media and grown for 4-6 hours (for YPD) or 30  hours (for spo media).

extract_protocol:
mRNA isolated using Qiagen Oligotex mRNA mini kit
Libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs)

treatment_protocol: Total RNA isolated using Ambion RiboPure kit

value: 0.5% sodium acetate, 1% potassium chloride, 1% glucose, 2% agar plates

tag: genotype

value: wildtype

tag: cell cycle

value: meiotic


title: Ndt80-myc_YPA_1


title: pTef1-Ndt80B-myc_1


title: KO_SPO_1

value: Ndt80 del


title: Ndt80-myc_YPA_2


title: DlaT-3

city: Gainesville

first: Minghao

last: Gong

state: Florida

address: 1395 Center Drive, D6-18c

department: Pathology

institute: University of Florida

description: DdlaT

data_processing:
Standard Illumina demultiplex procedure were done in Basespace (Illumina) after the sequencing
The demultiplexed sequence reads first underwent data preprocessing and quality evaluation including trimming off the low quality ends of reads.
Rockhopper was used to map sequence reads to annotated P. UF1 genome, normalize the counts values by upper quartile normalization and perform differential expression analysis using NB statistical model
Genome_build: P. UF1
Supplementary_files_format_and_content: comma seperated text files include raw counts for all the samples

organism: Propionibacterium freudenreichii

source_name: Bacteria culture

growth_protocol: The P. UF1 and its genetically modified strains (mutants) were grown at 30°C in MRS medium supplemented with 1% sodium lactate in an anaerobic chamber.

extract_protocol:
The PowerMicrobiome™ RNA Isolation Kit was used for RNA extraction.
ScriptSeq Complete Gold Kit(Epidemiology) was used for rRNA depletion and cDNA library generation

tag: strain

value: P. UF1

value: deltadlaT


title: WT_YPD_1

value: mitotic


title: Ndt80 untagged control SRaff 2

source_name: W303 a-cell

growth_protocol: Cells were grown overnight in Sraffinose, diluted back to OD = 0.02 in Sraffinose and grown for 15 hours, then galactose (1.7% total) was added and cells were grown for 5 hours.

value: Sraffinose + 1.7% galactose


title: Ndt80 untagged control SRaff 1


title: DlaT-2

description: DdlaT


title: PpNdt80-myc_2


title: DlaT-1

description: DdlaT


title: P.UF1-3

description: wild-type

value: wild-type


title: Ndt80 untagged control 1

data_processing:
Quality analysis performed with FastQC
ChIP-seq reads were aligned to the P. pastoris genome assembly using bowtie2 and default parameters
Files were converted to sorted .bam files using Samtools
Peak separation distance was determined using the binding.characteristics function in the SPP package in R
Peaks and fold enrichment were calculated using MACS2, using peak separation distances calculated from SPP and --nomodel parameter
Genome_build: P. pastoris genome was downloaded from NCBI in December 2015, genome annotated using Yeast Gene Annotation Pipeline in December 2015.
Supplementary_files_format_and_content: bedGraph.wig files were generated from indexed, sorted .bam file using genomeCoverageBed tool in BedTools, followed by a .bed to .wig conversion script in Python.  FE.bdg.wig files were generated by MACS2 using the -SPMR parameter, and converted to .wig using the same Python script.  Peaks.xls files were generated for experiments with tagged proteins using untagged strains as a control in MACS2.


title: PpNdt80-myc_1


title: P.UF1-2

description: wild-type


title: pTef1-Ndt80-myc_1


title: pGal1-Ndt80-myc_1


title: P.UF1-1

description: wild-type


title: Wild-type mouse #8 : CB-17_L001_2

status: Public on Apr 30 2017

city: Boston

first: Lisa

last: Goldberg

state: Massachusetts

address: 72 E Concord St, R604

institute: Boston University School of Medicine

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-17_L001_2

data_processing:
Samples were run across four lanes (L001, L002, L001_2, L002_2) and reads for each sample were generated via the Illumina HiSeq 2500 (~10,000,000 reads per replicate, totalling ~40,000,000 per sample)
Fastq files are quality checked via FastQC (v0.10.1) and possessed Phred quality scores > 30 (i.e. less than 0.1% sequencing error)
Fastq files were utilized in TopHat (v2.0.0)  to align reads to the reference genome (mm10; UCSC Genome Browser).
We computed the read counts per gene using the HTSeq (v0.6.1p1) Python package and edgeR (v2.14), a Bioconductor package for differential gene expression analysis that models read counts using a negative binomial distribution to account for variability in the number of reads via generalized linear models
Genome_build: mm10 (UCSC)
Supplementary_files_format_and_content: HTseq output for each sample is in the form of a TXT (.txt) file that consists of a list of genes along side respective read counts.

organism: Mus musculus

source_name: Brain

extract_protocol:
Csnk1e KO and WT mice at about 50 days of age were live-decaptitated for brain dissections. As mentioned before, 2.5mm strialtal punches (left and right hemispheres) were pooled per mouse, and collected tissue was immediately places into RNAlater (QIAGEN) for 48 hours. After incubation, RNA was extracted via miRNeasy Mini Kit and quality was assessed by Bioanalyzer analysis.
RNA that was deemed high quality was send to the University of Chicago Genomics Core Facility for cDNA library preparation. Libraries were prepared according to Illumina's detailed instructions accompanying the TruSeq® Stranded mRNA LT Kit  (oligo-dT; 50bp single-end reads; Part# RS-122-2101).  The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2500 following the manufacturer's protocols

value: wild type

tag: brain area

value: Striatum


title: i4g1-1

city: Wuhan

first: Qiang

last: Li

state: Saskatchewan

address: #1 Shizishan Street

country: China

institute: Huazhong Agricultural University

data_processing:
Trimming using Trimmomatics-0.32
Read mapping using STAR-2.4.0j
Alignment using StringTie-1.0.3
Raw counts using htseq-count-0.6.0
Differentially expression analysis using DESeq2 1.12.4
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited .csv files include normalized counts for each Sample

organism: Arabidopsis thaliana

source_name: developing seeds

growth_protocol: All plants were grown in a growth chamber with 22/17°C (day/night temperature) under long day (16 hours light (~120 μmol m-2 s-1) /8 hour dark).

extract_protocol:
Total RNA from developing seeds at 12-13 days after flowering were extracted using a Plant RNA Isolation Mini Kit (Agilent Technologies, Mississauga, ON).
Six cDNA libraries were constructed using the TruSeq RNA Sample Preparation Kit v2 (Illumina) with two replicates for ar21, i4g1 and wild type, respectively.

treatment_protocol: For harvesting developing seeds, only primary shoots were used and secondary shoots were removed. To harvest seeds at defined developmental stage, individual flowers were tagged on the same day of flowering using colored tape. Siliques from 13 days after flowering were harvested and the seeds were dissected out on dry ice. Pools of seeds were stored at -80°C for further analysis.

tag: Stage

value: 13 DAF

tag: tissue type

value: seeds


title: ar21-2


title: WT1


title: Wild-type mouse #7 : CB-16_L002_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-16_L002_2


title: Wild-type mouse #8 : CB-17_L002

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-17_L002


title: Wild-type mouse #7 : CB-16_L002

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-16_L002


title: Ndt80 untagged control 2


title: Wild-type mouse #7 : CB-16_L001

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-16_L001


title: Wild-type mouse #6 : CB-15_L002_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-15_L002_2


title: Wild-type mouse #6 : CB-15_L001_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-15_L001_2


title: Wild-type mouse #6 : CB-15_L002

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-15_L002


title: pTef1-Ndt80-myc_2


title: Wild-type mouse #6 : CB-15_L001

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-15_L001


title: pGal1-Ndt80-myc_2


title: Csnk1e knockout mouse #8 : CB-13_L001_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-13_L001_2

value: Csnk1e knockout


title: Csnk1e knockout mouse #8 : CB-13_L002_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-13_L002_2


title: Csnk1e knockout mouse #8 : CB-13_L002

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-13_L002


title: Csnk1e knockout mouse #8 : CB-13_L001

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-13_L001


title: Wild-type mouse #5 : CB-12_L002_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-12_L002_2


title: i4g1-2


title: ar21-1


title: Wild-type mouse #5 : CB-12_L002

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-12_L002


title: Wild-type mouse #5 : CB-12_L001_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-12_L001_2


title: WT2


title: Wild-type mouse #5 : CB-12_L001

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-12_L001


title: Wild-type mouse #8 : CB-17_L002_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-17_L002_2


title: Csnk1e knockout mouse #7 : CB-11_L002_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-11_L002_2


title: Wild-type mouse #8 : CB-17_L001

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-17_L001


title: Wild-type mouse #7 : CB-16_L001_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-16_L001_2


title: Csnk1e knockout mouse #7 : CB-11_L002

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-11_L002


title: Wild type control [L13_B]

city: Singapore

first: Bruno

last: Reversade

state: Singapore

address: #05-40 Immunos Building, 8A Biomedical Grove,, Institute of Medical Biology/ Bruno Reversade laboratory, 138648, Singapore

country: Singapore

institute: Institute of Medical Biology/A*STAR, Singapore

description:
Melanocytes isolated from fresh skin biopsy taken from the back
processed data file:
L10_L13_COUNTS_TABLE_FILT_NORM
L13_L11_COUNTS_TABLE_FILT_NORM
L13_L12_COUNTS_TABLE_FILT_NORM

data_processing:
Data quality check using FASTQC (version 0.11.2)
Random subsampling of the data to create pseudo-replicates using seqtk program
Alignment of the data to reference (UCSC hg19) using bwa version 0.7.10 (Burrows Wheeler Aligner)
Sorting and indexing of the alignment file (BAM file) using samtools (version 0.1.19)
Counting of the number of aligned reads per gene using htseq-count program (version 0.6.0)
Filtering to remove those genes with low level counts (<10 reads)
Normalisation of sequenced data for coverage by TMM in EdgeR (version 3.2.4)
Genome_build: UCSC hg19
Supplementary_files_format_and_content: In txt format and with normalized counts generated by TMM in EdgeR

organism: Homo sapiens

source_name: Wild type control

extract_protocol:
The samples were  depleted of ribosomal RNA using the Low Input Ribo Minus Eukaryote v2 kit from Thermo Fischer Scientific and then processed using the NEBNext Ultra RNA Directional Library Preparation kit from NEB.
The  library size was assessed on the Agilent® BioAnalyzer High Sensitivity Chip and the concentration of each library was determined using the KAPA quantification kit. The libraries were then pooled together in equimolar amounts and sequenced on the Hiseq 2500 High output 100PE.

tag: age

value: 28 years

tag: Sex

value: Female

tag: tissue

value: skin biopsy

tag: cell type

value: melanocytes


title: Wild-type mouse #4 : CB-10_L002_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-10_L002_2


title: Wild-type mouse #4 : CB-10_L001_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-10_L001_2


title: Csnk1e knockout mouse #7 : CB-11_L001

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-11_L001


title: Wild type control [L13_C]


title: Csnk1e knockout mouse #7 : CB-11_L001_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-11_L001_2


title: Wild type control [L13_A]


title: Wild-type mouse #4 : CB-10_L002

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-10_L002


title: Patient Hyper-pigmented melanocytes [L12_C]

description:
Melanocytes isolated from fresh skin biopsy taken from the posterior upper thigh
processed data file:
L10_L12_COUNTS_TABLE_FILT_NORM
L11_L12_COUNTS_TABLE_FILT_NORM
L13_L12_COUNTS_TABLE_FILT_NORM

source_name: Patient Hyper-pigmented melanocytes

value: 7 years

value: Male


title: Patient Hyper-pigmented melanocytes [L11_C]

description:
Melanocytes isolated from fresh skin biopsy taken from the posterior upper thigh
processed data file:
L10_L11_COUNTS_TABLE_FILT_NORM
L11_L12_COUNTS_TABLE_FILT_NORM
L13_L11_COUNTS_TABLE_FILT_NORM


title: Csnk1e knockout mouse #6 : CB-9_L002_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-9_L002_2


title: Patient Hyper-pigmented melanocytes [L12_B]


title: Patient Hyper-pigmented melanocytes [L12_A]


title: Wild-type mouse #4 : CB-10_L001

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-10_L001


title: Patient Hyper-pigmented melanocytes [L11_B]


title: Csnk1e knockout mouse #6 : CB-9_L002

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-9_L002


title: Csnk1e knockout mouse #6 : CB-9_L001_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-9_L001_2


title: Wild-type mouse #3 : CB-8_L002_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-8_L002_2


title: Heterozygous control [L10_B]

description:
Melanocytes isolated from fresh skin biopsy taken from the posterior upper thigh
processed data file:
L10_L11_COUNTS_TABLE_FILT_NORM
L10_L12_COUNTS_TABLE_FILT_NORM
L10_L13_COUNTS_TABLE_FILT_NORM

source_name: Heterozygous control

value: 6 years


title: Heterozygous control [L10_C]


title: Csnk1e knockout mouse #6 : CB-9_L001

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-9_L001


title: Wild-type mouse #3 : CB-8_L001_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-8_L001_2


title: Heterozygous control [L10_A]


title: Wild-type mouse #3 : CB-8_L002

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-8_L002


title: Wild-type mouse #3 : CB-8_L001

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-8_L001


title: Csnk1e knockout mouse #5 : CB-7_L001_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-7_L001_2


title: Csnk1e knockout mouse #5 : CB-7_L002_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-7_L002_2


title: Csnk1e knockout mouse #5 : CB-7_L001

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-7_L001


title: Csnk1e knockout mouse #4 : CB-6_L002_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-6_L002_2


title: Csnk1e knockout mouse #5 : CB-7_L002

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-7_L002


title: Csnk1e knockout mouse #4 : CB-6_L001_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-6_L001_2


title: Csnk1e knockout mouse #3 : CB-4_L002_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-4_L002_2


title: Csnk1e knockout mouse #4 : CB-6_L002

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-6_L002


title: Csnk1e knockout mouse #4 : CB-6_L001

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-6_L001


title: Patient Hyper-pigmented melanocytes [L11_A]

description:
Melanocytes isolated from fresh skin biopsy taken from the posterior upper thigh
processed data file:
L10_L11_COUNTS_TABLE_FILT_NORM
L11_L12_COUNTS_TABLE_FILT_NORM
L13_L11_COUNTS_TABLE_FILT_NORM


title: Wild-type mouse #2 : CB-5_L002_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-5_L002_2


title: Wild-type mouse #2 : CB-5_L001

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-5_L001


title: Wild-type mouse #2 : CB-5_L002

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-5_L002


title: Csnk1e knockout mouse #3 : CB-4_L002

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-4_L002


title: Csnk1e knockout mouse #3 : CB-4_L001_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-4_L001_2


title: Csnk1e knockout mouse #3 : CB-4_L001

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-4_L001


title: Wild-type mouse #1 : CB-3_L001_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-3_L001_2


title: Csnk1e knockout mouse #2 : CB-2_L002_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-2_L002_2


title: Wild-type mouse #1 : CB-3_L002_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-3_L002_2


title: Wild-type mouse #1 : CB-3_L001

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-3_L001


title: Csnk1e knockout mouse #2 : CB-2_L001_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-2_L001_2


title: Csnk1e knockout mouse #1 : CB-1_L001_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-1_L001_2


title: Csnk1e knockout mouse #2 : CB-2_L001

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-2_L001


title: Csnk1e knockout mouse #1 : CB-1_L002

description:
sample run across L001 & L002 on flow cell1 and flow cell2
CB-1_L002


title: Atf4-/- ASNase rep3

city: New Brunswick

first: William

middle: J.

last: Belden

state: NJ

address: 59 Dudley Rd

department: Animal Sciences

institute: Rutgers, The State University of New Jersey

data_processing:
RNA-seq data from the fastq files was mapped to the mouse mm10 genome using Tophat
Differences in expression were determined using Cuffdiff
All the statistical analyses were done using cummeRbund
Genome_build: mm10

molecule: polyA RNA

growth_protocol: Mice were young adults, 8-12 weeks of age.

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

treatment_protocol: Mice were once daily intraperitoneally injected with either L-asparaginase (Elspar) at 3 international units per gram body weight or equivolume phosphate buffered saline for 8 days.  Mice were injected in the morning each day (~8:00 AM) and were killed by decapitation 7.5 hours later.

tag: strain background

tag: genotype/variation

value: Atf4 deletion

value: 8-16 wk old

tag: gender

value: female

tag: treated with

value: asparaginase

value: liver


title: Csnk1e knockout mouse #1 : CB-1_L002_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-1_L002_2


title: Csnk1e knockout mouse #1 : CB-1_L001

description:
sample run across L001 & L002 on flow cell1 and flow cell2
CB-1_L001


title: Atf4-/- ASNase rep2

value: male


title: Wild-type mouse #2 : CB-5_L001_2

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-5_L001_2

value: wild type

value: Striatum


title: Atf4-/- PBS rep1

value: phosphate buffered saline


title: Atf4-/- PBS rep3


title: Atf4-/- ASNase rep1


title: Gcn2-/- ASNase rep1

value: Gcn2 deletion


title: Gcn2-/- ASNase rep2


title: Wild-type mouse #1 : CB-3_L002

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-3_L002


title: Gcn2-/- ASNase rep3


title: Gcn2-/- PBS rep3


title: WT ASNase rep2


title: WT ASNase rep3


title: Gcn2-/- PBS rep1


title: Gcn2-/- PBS rep2


title: WT PBS rep1


title: WT PBS rep3


title: WT PBS rep2


title: Csnk1e knockout mouse #2 : CB-2_L002

description:
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-2_L002

value: Csnk1e knockout


title: 083012_Bcl11bKO_DL1_d12_FLDN2_2

city: Irvine

first: Weihua

last: Zeng

address: 2300E Bio Sci III

department: Dev & Cell Biology

institute: UCIrvine

data_processing:
RNA-seq read alignment and gene expression quantification were done using Rsem (v1.2.12)
The Rsem transcriptome reference file was generated with mm9 reference genome and mouse GENCODE M1 gene annotation file.
Gene level FPKM values were merged into data matrix for further processing.  Small RNAs such as rRNA, tRNA, snRNA, snoRNA as well as miRNA were removed from the matrix and genes with < 1 FPKM in all the samples were also filtered out.
The data matrix was further batch corrected with ComBat and 0.1 pseudocount was added.
Genome_build: mm9 and GENCODE mouse M1 gene annotation
Supplementary_files_format_and_content: tab-delimited text file including FPKM values from each Sample with batch effect adjustment and 0.1 pseudocount

source_name: T cell precursors

growth_protocol: Bcl11b conditional knockout samples were obtained from two different sources: from Bcl11bL2/L2 homozygously floxed stock repeatedly crossed to a C57BL6/J (B6) background, and from PLBD homozygously floxed Bcl11bfl/fl mice with a Cre-ERT2 transgene ubiquitously expressed from the ROSA26 locus.  Some Bcl11b floxed mouse strains were crossed with ROSA26R-EYFP mice to introduce a reporter for successful Cre excision.  Hematopoietic precursor cells were purified from fetal liver and induced to differentiate on OP-DL1 or OP9-DL4 stromal layers with 5 ng/ml each Flt3L and IL-7, except as indicated.  In some early samples, the IL-7 concentration was reduced at the first feeding of the cultures to promote faster differentiation, but this was abandoned in later cultures because of effects on viable cell recovery and RNA quality.  In some samples as indicated, bone marrow cells were used as the source of precursors instead of fetal liver cells, but these were cultured similarly on OP9-DL stroma to promote T-cell differentiation.  Other samples were derived freshly from thymus tissue of mice of the indicated genotypes.  For some samples, 13145, 13219 and 13221, cells from mice with a tamoxifen-inducible Cre transgene were taken freshly from the thymus, then treated with 100 nM 4-OH tamoxifen in culture and incubated for further differentiation on OP9-DL4 stroma for 3 or 4 more days before harvest and sorting.

extract_protocol:
Total RNA was extracted from 2.5∼20 million cells using Trizol (Invitrogen).
The total RNA is subjected to two rounds of selection using Oligo-dT coupled magnetic beads (Dynabeads) according to the manufacturer's protocol.  cDNA library building was performed as described (Mortazavi et al., 2008). Briefly, mRNA was fragmented to an average length of 200 bp by Mg2+-catalyzed hydrolysis and then converted into cDNA by random priming. cDNA was then subjected to end repairing, adaptor ligation (using Illumina ChIP-seq sample preparation kit #IP-102-1001), size selection and one round of PCR amplification.

treatment_protocol: For Fetal liver derived precursor cultures, E13.5 fetal liver (FL) cell samples from Bcl11bfl/fl-ROSA26R-YFP, Bcl11bfl/fl, and control C57BL/6-ROSA26R-YFP or C57BL/6 mouse embryos were retrovirally transduced with a Cre retrovirus and then incubated in culture with OP9-DL1 or OP9-DL4 stromal cells in the presence of 5 ng/mL each of Flt3L, IL-7 and SCF for 24 hours. Successfully transduced cells were re-sorted for YFP expression (or for a fluorescent protein in the retroviral vector if ROSA26R-eYFP was not present in the background genotype) as well as progenitor-enriched phenotype (Kit+CD27+), and returned to the OP9-DL1 or OP9-DL4 stromal co-culture. After  8.5-14 days of culture as indicated, the cells were harvested and sorted for YFP+ DN2a phenotype (YFP+ Kit++CD45+CD25+Lin-) from Bcl11bfl/fl samples, and YFP+ DN2b phenotype (YFP+c-Kitint CD45+CD25+Lin-) from Bcl11b-intact controls.  If ROSA26R-EYFP was not present in the background genotype, cells were sorted on DN2a/2b/3 phenotype alone, as Bcl11b deletion has a very obvious effect on cell surface markers.  In some samples derived from mice with a Cre-ERT2 transgene, the effect of Bcl11b deletion after its normal time of expression was tested. Bcl11b floxed cells as well as controls were obtained from the thymus, sorted as DN3a cells (after Bcl11b is normally expressed), and then treated with 4-OH tamoxifen to induce deletion; these cells were then cultured for 3-4 days on OP9-DL4 with cytokines before harvest as described above.  In other experiments, to test the possibility that Bcl11b deletion mimicked Notch inhibition, we incubated normal B6 fetal liver derived precursors to generate DN2a or DN2b cells with addition of 1 microM gamma-secretase inhibitor (GSI) for the last 12 hr before harvest.

value: T cell precursors

tag: developmental stage

tag: bcl11b knockout

tag: cell source and growth

value: Fetal liver derived precursors differentiated by culture on OP9-DL1 and sorted

tag: retroviral transduction

value: Cre transduced before differentiation

tag: gsi treatment

value: control


title: 091012_PLBD_ThyDN3

value: Sorted thymocytes with CreERT2 transgene and floxed Bcl11b gene, no deletion


title: 083012_B6Cre_DL1_d12_FLDN2b_2


title: 091412_PLBD_ThyDN3Cre_DL4_d4

value: Sorted thymocytes with CreERT2 transgene and floxed Bcl11b, tamoxifen-induced,  cultured for 4 d on OP9-DL4 and re-sorted


title: 091412_ERTII_ThyDN3Cre_DL4_d4

value: Sorted thymocytes with CreERT2 transgene, tamoxifen-induced, cultured for 4 d on OP9-DL4 and re-sorted


title: Atf4-/- PBS rep2

value: Atf4 deletion

value: 8-16 wk old


title: 082012_Bcl11bKO_DL1_d9_FLDN2_1


title: 091012_ERTII_ThyDN3

value: Sorted thymocytes with CreERT2 transgene, no deletion


title: 012111_ERTII_ThyDN3_Cre_DL4_d3

value: Sorted thymocytes with CreERT2 transgene, tamoxifen-induced, cultured for 3 d on OP9-DL4 and re-sorted


title: 082312_B6Cre_DL1_d12_FLDN2b_1


title: 082312_Bcl11bKO_DL1_d12_FLDN2b_1


title: 082312_B6Cre_DL1_d12_FLDN2b_MSCV-EV_36hr

value: Cre transduced before differentiation; then empty vector transduced 36 hr before harvest


title: 082312_Bcl11bKO_DL1_d12_FLDN2b_Bcl11b124_36hr

value: Cre transduced before differentiation; then transduced with Bcl11b (exon 1-2-4 isoform) 36 hr before harvest


title: 082312_Bcl11bKO_DL1_d12_FLDN2b_MSCV-EV_36hr


title: 072712_Bcl11bKO_DL1_d12_FLDN2


title: 072712_B6Cre_DL1_d12_FLDN2


title: WT ASNase rep1

value: wild type

value: female

value: asparaginase

value: liver


title: 072412_B6Cre_DL1_d9_FLDN2

value: T cell precursors


title: 072512_Bcl11bKO_DL1_d10_FLDN2

value: Fetal liver derived precursors differentiated by culture on OP9-DL1 and sorted


title: 072512_B6Cre_DL1_d10_FLDN2

value: Cre transduced before differentiation


title: 072412_Bcl11bKO_DL1_d9_FLDN2

value: control


title: 021012_B6Cre_DL1_FLDN2b_(d9.5)


title: 03/21n27/12_LckCre_B6_ThyDN3

value: sorted thymocytes expression LckCre in vivo


title: 092811_ERT2_BM_Cre_DL4_DN2

value: Bone marrow derived precursors from CreERT2; Bcl11b wildtype mice, tamoxifen-induced, differentiated by culture on OP-DL4


title: 092811_PLBD_BM_Cre_DL4_DN2

value: Bone marrow derived precursors from CreERT2; Bcl11b floxed mice, tamoxifen-induced, differentiated by culture on OP-DL4


title: 100711_B6_Cre_DL4_FLDN2b_(d8.5)

value: Fetal liver derived precursors differentiated by culture on OP9-DL4 and sorted


title: 100711_Bcl11bKO_DL4_FLDN2a_(d8.5)


title: 090811_B6_Cre_DL4_FLDN2b_IL7_High


title: 090811_Bcl11bKO_DL4_FLDN2a_IL7_Low

value: Fetal liver derived precursors differentiated by culture on OP9-DL4 and sorted; IL7 level reduced to enhance differentiation


title: 080411_Bcl11bKO_DL4_d9_FLDN2a


title: 0725n080511_FLDN2a(d8.5)_DL1_mRNA


title: 081911_FLDN2a(d4.5)_DL1_mRNA


title: 090811_Bcl11bKO_DL4_FLDN2a_IL7_High


title: 121010FLDN2bd8.5DL1


title: 091310and121010FLDN2aDL1


title: 091310and121010FLDN2aDL1+1uMGSI12hr


title: 121010FLDN2bd8.5DL1+1uMGSI12hr


title: 09/03/10_Bcl11b_KO_FLDN2a_DL4


title: 09/03/10_B6_FLDN2b_DL4


title: 09/03/10_B6_FLDN2b_DL1

value: Fetal liver derived precursors differentiated by culture on OP9-DL1 and sorted; IL7 level reduced to enhance differentiation


title: 03/27/12_Bcl11bKO_FLDN2a_DL1_d9_w/IL7


title: 07and0810FLDN2aDL1+1uMGSI12hr


title: 07and0810FLDN2aDL1


title: 073010_Bcl11bKO_DL1_DN2a


title: 071610FLDN3d8.5


title: 073010_Bcl11bKO_DL4_DN2a

value: Fetal liver derived precursors differentiated by culture on OP9-DL4; IL7 level reduced to enhance differentiation


title: Mock control

city: Paris

first: Antonin

last: Thiébaut

address: 7-9 quai Saint Bernard, building C, floor 3, room C321B

country: France

institute: Sorbonne Université

data_processing:
Quality of FASTQ files was controlled, using FASTQC program.
Nucleotides with a QC < 20 in 5' and 3' were trimmed using a home made Python program.
Reads were mapped on the reference genome (downloaded from Genolevures – http://genolevures.org/download.html#, C. glabrata CBS138) with default parameters, except for -m 1
BAM files were converted into BED files for peak calling with bPeaks program, using the genomeCov tool available in Bedtools.
Genome_build: C. glabrata CBS138; ASM254v2 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000002545.3)
Supplementary_files_format_and_content: text files used to perform peak calling with bPeaks; [1] chromosome ID [2] position on the chromosome and [3] the number of reads at this exact position columns

organism: Nakaseomyces glabratus

source_name: Candida glabrata

growth_protocol: All cultures were conducted in a rotative shaker at 30°C in YPD (Glucose 2%, yeast extract 1%, Bactopeptone 1%).

extract_protocol:
Cells were lysed and DNA was sheared by sonication into ~500 bp fragments. DNA-protein complexes were selected using the antibody specifically targeting the protein of interest.
Libraries were prepared according to Illumina's instructions

treatment_protocol: For ChIP, myc-tagged CgHap5 strains were grown in YPD until exponential phase (OD=0.8). Cross-linking of the cells and ChIP were performed as described previously (Lelandais et al., Methods Mol Biol, 2016). Meanwhile, the parental DHTL (untagged strain) was grown and processed the same way to provide the mock-IP sample.

value: parental DHTL (untagged strain)

tag: chip antibody

value: anti-myc

tag: chip antibody producer/distributor

value: Roche/Sigma-Aldrich

tag: chip antibody cat. #

tag: chip antibody lot #


title: 071610FLDN3d8.5+12hrGSI


title: Input DNA control

value: myc-tagged CgHap5 strain


title: NT-PolII

status: Public on Apr 29 2017

city: Pyeongchang

first: Pil Joong

last: Chung

state: Gangwondo

address: Pyeongchang daero 1447

department: Crop Biotechnology Institute

country: South Korea

institute: Seoul National University

data_processing:
Illumina Hiseq 2000 with 101 bp single end read
checked the read quality through the average quality score from FASTQ files and nucleotide distribution at each position using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) to identify potential sequencing errors and biases.
Reads was mapped using the alignment software BOWTIE (http://bowite-bio.sourceforge.net/index.shtml)
and analyzed using HOMER (Hypergeometric Optimization of Motif EnRichment, http://liulab.dfci.harvard.edu/MACS/)
Genome_build: IRGSP-1.0

organism: Oryza sativa

source_name: α-PolII ChIPseq

growth_protocol: Rice was germinated on MS (Murashige and Skoog) media at 28C for 4 days, and transplanted into soil pots (4x4x6 cm; 3 plants per pot) and grown in a greenhouse.

extract_protocol:
roots of NT and RCc3::6xmyc-OsNAC6 plants were cross-linked with a buffer (0.4 M sucrose, 10 mM Tris-HCl [pH 8], 5 mM β –mercaptoethanol, and 1 % formaldehyde) by vacuum infiltration for 15 min. The chromatin was isolated using sucrose cushion and sonicated to shear DNA to size range of 100-300 bp.
The ChIP-Seq library was constructed according to Illumina’s instructions with some modifications. The library was purified using an Agencourt AMPure XP system. Purified DNA were used to prepare libraries with Illumina TruSeq ChIP sample preparation protocol

value: roots

tag: age

value: 2 weeks

tag: ecotype

value: Ilmi

value: α-PolII

value: NT (nontransgenic rice plant)


title: 443-myc

source_name: α-myc ChIPseq

tag: tissue

value: α-myc (sc-789, Santa Cruz)

value: OsNAC6-myc (overexpression transgenic plant)


title: 073010_B6_DL1_DN2b

tag: cell type

value: T cell precursors

value: control

value: Cre transduced before differentiation


title: Hap5 IP standard growth media


title: NT-myc

source_name: α-myc ChIPseq (negative control)


title: Liver differentiation day 13

status: Public on Apr 28 2017

city: Shenzhen

first: Andrew

middle: P

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

institute: Southern University of Science and Technology

description: Presumed early hepatocyte-like

data_processing:
rsem v1.2.17/bowtie2 v2.2.0 was used to align to the ensembl transcriptome (mm10, v76)
transcripts with more than 25 sequence tags in 2 or more timepoints were kept for further analysis
mapping tag counts were GC normalised using EDASeq v2.0.0
Genome_build: hg19
Supplementary_files_format_and_content: tab delimeted text file containing ensembl transcript accession, gene name and normalised abundance estimates for each transcript

source_name: Differentiated hESCs

growth_protocol: Undifferentiated human H1 ES cells were maintained in monolayer culture on Matrigel (BD Biosciences, 354277) in mTeSR1 medium (Stemcell Technologies, 05850) at 37°C with 5% CO2. Cells were manually passaged at 1:4 to 1:6 split ratios every 3 to 5 days.

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

treatment_protocol: For hepatic differentiation, we established a serum-free protocol based on previously described protocols with minor modifications (Si-Tayeb et al., 2010; Song et al., 2009). Briefly, cells were cultured for 3 days in RPMI/B27 medium (Insulin minus, Gibco, A18956-01) supplemented with 100 ng/ml Activin A (Peprotech, A120-14E), followed by 4 days with 20 ng/ml BMP2 (Peprotech, 120-02)and 30 ng/ml FGF-4 (Peprotech, 100-31) in RPMI/B27(complete with Insulin, Gibco,17504-044) medium, then 6 days with 20 ng/ml HGF (Peprotech, 100-39) and KGF (Peprotech, 100-19) in RPMI/B27 (complete with Insulin), then 8 days with 20 ng/ml Oncostatin-M (R&D Systems, 295-OM/CF) in Hepatocyte Culture Media (Lonza, cc-3198) supplemented with SingleQuots (without EGF).

tag: day

tag: treatment

value: OSM

tag: presumed cell type

value: Hepatocyte-like

tag: cell line


title: Liver differentiation day 11

description: Presumed hepatoblast

value: HGF+KGF

value: Hepatoblast


title: NT-total

source_name: total input DNA

tag: genotype/variation


title: 030311Bcl11bKOThyDN2a

tag: developmental stage

tag: bcl11b knockout

value: Sorted thymocytes; deletion in vivo with LckCre


title: Liver differentiation day 9

description: Presumed hepatoblast


title: Liver differentiation day 5

description: Presumed hepatoblast

value: Early hepatoblast


title: Liver differentiation day 7

description: Presumed hepatoblast


title: Liver differentiation day 2

description: Presumed definitive endoderm

value: Activin A

value: Definitive endoderm


title: Liver differentiation day 1

description: Presumed definitive endoderm

value: Early definitive endoderm


title: Liver differentiation day 0 (hESC cells)

description: Human embryonic stem cells

source_name: hESCs

value: hESCs


title: 443-PolII

value: roots

value: 2 weeks

value: Ilmi

value: α-PolII


title: Female_Achl_RNAi_3

city: St. Louis

first: Jiajia

state: Missouri

address: 435 Research Building, One University Boulevard

department: Biology

institute: University of Missouri-St. Louis

data_processing:
RUM (Grant et al. 2011) was used to align raw reads to the reference Drosophila genome and transcriptome using the following parameters:  “--strand-specific --variable-length-reads --bowtie-nu-limit 10 --nu-limit 10”.
Genome_build: dm3

organism: Drosophila melanogaster

source_name: heads

growth_protocol: 3-5 day old adult flies were maintained on standard food at 25 degrees under a 12hr:12hr light:dark condition and samples were collected at ZT2.

extract_protocol:
fly heads were manually dissected in PBS and homogenized in Ttizol (Life Technologies), total RNAs were collected using Phase lock gels (5Prime) and RNeasy mini kit (Qiagen)
libraries were prepared with 200ng total RNA per sample using TruSeq Stranded mRNA LT prep kit (Illumina)

value: heads

value: 3-5 day old

tag: develpomental stage

value: adult


title: Female_Achl_RNAi_2


title: Female_Control_1


title: Female_Control_3


title: Female_Control_2


title: Male_Control_4


title: Female_Achl_RNAi_1


title: Male_Achl_RNAi_2


title: Male_Control_2


title: Male_Control_1


title: Male_Control_3


title: Male_Achl_RNAi_3


title: Male_Achl_RNAi_1


title: Male_Achl_RNAi_4


title: R273H-mutant-Replicate2

city: Kolkata

first: Raghunath

last: Chatterjee

state: WB

address: 203 BT Road, HGU, Indian Statistical Institute

department: Human Genetics Unit

country: India

institute: Indian Statistical institute

description: mutant p53R273H expressing cell line

data_processing:
Raw sequence reads were pre-processed using FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) to generate high quality reads.
Reads were trimmed at 3’ end and checked for base quality value calculated using Phred score (Q≥ 20). We only considered the sequencing reads between 17 bp to 35 bp read length.
Processed reads were then mapped to rRNAs, tRNAs, 3’ adapter sequence and mature miRNA sequences (miRBase 20) using the SHRiMP aligner (http://compbio.cs.toronto.edu/shrimp).
After the alignment, an in-house Perl script was used for counting the reads mapping to each of miRNA, tRNA, rRNA and adapter sequence.
miRNAs having 3 or more reads were used for differential expression analysis using R package DESeq.
Genome_build: hg19
Supplementary_files_format_and_content: DESeq generated csv files contain normalized read counts and differential expression of miRNAs between different pairs.
Supplementary_files_format_and_content: normalized_EVUT_vs_EVT.csv: Normalized read counts of two replicates of both EVU and EVT
Supplementary_files_format_and_content: differential_EVUT_vs_EVT.csv: Differential expression betwqeen EVU and EVT
Supplementary_files_format_and_content: normalized_EV_vs_R273H.csv: Normalized read counts of two replicates of both EVU and R273H-mutant
Supplementary_files_format_and_content: differential_EV_vs_R273H.csv: Differential expression between EVU and R273H-mutant
Supplementary_files_format_and_content: normalized_R273HUT_vs_R273HT.csv: Normalized read counts of two replicates of both R273H-mutant and R273HT-mutant
Supplementary_files_format_and_content: differential_R273HUT_vs_R273HT.csv: Differential expression between R273H-mutant and R273HT-mutant

source_name: Human non-small cell lung carcinoma cell line derived from the lymph node

growth_protocol: To generate mutant p53R273H expressing stable H1299 cell line, cells were first transfected with pCMV expression vector containing R273H mutant p53 cDNA (pCMV-Neo-Bam-p53 R273H, kindly provided by Dr. Bert Vogelstein, Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21205, USA) using Lipofectamine2000 Reagent (Invitrogen, Thermo Fisher Scientific Inc., MA USA). Forty-eight hours post transfection, cells were sub-cultured at 1:6 and allowed to grow in media supplemented with G418 ( Life Technologies, Thermo Fisher Scientific Inc., MA USA) at a final concentration of 800 µg/ml. After 15-20 days, G418 resistant colonies were picked up and propagated in G418 containing (400 µg/ml) media to generate stable cell lines expressing mutant p53R273H . The H1299 cell line infected with an empty vector was kindly provided by Prof. Varda Rotter (Weizmann Institute of Science, Rehovot, Israel). All cell lines were cultured in RPMI 1640 medium (Life Technologies, Thermo Fisher Scientific Inc., MA USA) supplemented with 10% fetal calf serum, 1% Pen Strep and 0.006% Gentamicin (Life Technologies, Thermo Fisher Scientific Inc., MA USA). The cells were treated with 10 mM Etoposide (Sigma Aldrich, St. Louis, USA) for 24 hours before harvesting.

extract_protocol:
Small RNA fractions from cells were isolated using PureLink miRNA Isolation kit (Ambion, USA) according to the manufacturer’s protocol. Briefly, in a two-column based purification method, cells were first resuspended in binding buffer containing guanidine isothiocyanate and mixed with ethanol (final concentration of 35%). The mix was then passed through a spin column and flow through containing small RNAs was collected. Ethanol (final concentration 70%) was added to the flow through fraction and the mix was processed through a silica based column to bind the small RNAs to the silica membrane. The impurities were subsequently removed by washing the column with wash buffer and small RNAs were eluted in RNase free water.
Total RNA-Seq kit V2.0 (Life Technologies, Thermo Fisher Scientific Inc., MA USA) was used to prepare small RNA cDNA libraries. Briefly, small RNAs (~150-250 ng) were first mixed with Hybridization Solution and Ion Adaptor Mix v2 and hybridization reaction was performed in thermal cycler. Ligation enzyme mix was then added to the hybridization reactions and incubated in a thermal cycler at 16°C for 16 hours. Adapter ligated small RNA samples were subsequently reverse transcribed with Ion RT Primer v2 and SuperScript® III Enzyme Mix to make cDNAs. The cDNA products were then purified and size-selected using the magnetic bead cleanup module and PCR amplified with Ion 5’ and 3’ PCR Primers. The amplified DNAs were quantified and assessed for size distribution using Agilent® DNA 1000 Kit in Agilent® 2100 Bioanalyzer.   Each cDNA library was then clonally amplified on Ion Sphere™ Particles (ISPs) by emulsion PCR in Ion OneTouch™ System using Ion OneTouch™ 200 Template Kit v2 DL (Life Technologies, Thermo Fisher Scientific Inc., MA USA). Enrichment of the template positive ion spheres was carried out in Ion OneTouch™ Enrichment System. Template enriched ion sphere particles were subsequently sequenced on the Ion PGM™ sequencer using the Ion PGM™ 200 Sequencing Kit ((Life Technologies, Thermo Fisher Scientific Inc., MA USA) and Ion 316™ Chip.

treatment_protocol: Human non-small cell lung carcinoma cell line H1299 either harboring an empty vector (EV) or stably expressing R273H mutant p53 (p53R273H ) were used in this study. The cells were left untreated or treated with 10 µM Etoposide (Sigma Aldrich, St. Louis, USA) for 24 hours before harvesting.

value: non-small cell lung carcinoma

tag: passages

value: mutant p53R273H expressing


title: EVT-damage-induced-Replicate2

description: p53 null cell line with etoposide treatment

value: p53 null


title: EVT-damage-induced-Replicate1


title: s136M2

city: Minato-ku

first: Kei

last: Sato

state: Tokyo

address: 4-6-1 Shiroganedai

department: Department of Microbiology and Immunology

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

data_processing:
Illumina Casava 1.8 software used for basecalling.
Removal of adapter sequences for each sample was manually confirmed from FastQC output. Sequenced reads were mapped to hg19 whole genome using bowtie2 v2.2.5 with the default parameters, and Tophat2 2.1.0 to detect splicing junctions.
Raw read counts were extracted using a bioconductor package Rsubread with the default parameters. Raw read counts were then normalized by a bioconductor package TCC which iteratively applys an edgeR or DESeq2 normalization method.
Genome_build: hg19
Supplementary_files_format_and_content: a single tab-delimited text file includes normalized counts for all samples

source_name: Humanized mouse

extract_protocol:
RNA was extracted from splenic human mononuclear cells using QIAamp RNA Blood Mini kit (Qiagen)
RNA libraries were prepared for sequencing in Medical & Biological Laboratories, co (Nagoya, Japan).

treatment_protocol: HIV-1 was intraperitoneally inoculated into the 4 humanized mice

value: Splenic mononuclar cells

tag: agent

value: HIV-1 infected

tag: time point

value: 6 weeks post-infection


title: EVU-Replicate2

description: p53 null cell line


title: s224M5


title: Liver differentiation day 3

description: Presumed definitive endoderm

value: Activin A


title: EVU-Replicate1

description: p53 null cell line


title: R273HT-mutant-damage-induced-Replicate1

description: mutant p53R273H expressing cell line with etoposide treatment


title: s135F4


title: R273HT-mutant-damage-induced-Replicate2


title: R273H-mutant-Replicate1

description: mutant p53R273H expressing cell line


title: s225F4

value: Mock infected


title: s135F3


title: s136M3


title: s136M4


title: GES1_Mock_hMeDIPseq

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

description: 5-hmC antibody (#39769, Active Motif lot#10310001)

data_processing:
Reads were aligned with BWA (version 0.5.9) for hMeDIP-seq and MeDIP-Seq.
Number of reads were counted for 10 slidings of 300 bp window size and size of each slidings was 100 bp, and the read count within a 300 bp window was divided by total read count with coustom script for hMeDIP-seq.
Aligned reads were converted to BedGraph format with bedtools v2.20.1 for MeDIP-Seq.
Read were aligned with TopHat v1.3.2 and Bowtie (version 0.12.9). Command line options for Tophat were '-r 100' for RNA-Seq.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.0.2. Command line options for cufflinks were '--max-bundle-flags 4000000' for RNA-seq
Genome_build: hg19
Supplementary_files_format_and_content: csv files containing number of reads for each regions of genes divided by total read count were generated from coustom script and converted to xls files. Bedgraph files are generated from bedtools and converted to bigwig file. gtf files include FPKM values were generated using Cufflinks v2.0.2.

source_name: Fetal gastric mucosal cell line

growth_protocol: These cells were cultured in RPMI 1640 (Wako, Tokyo, Japan) with 10% fetal bovine serum (FBS) (HyClone SH30910.03, GE Healthcare, Chicago, IL) and Penicillin-Streptomycin (Sigma-Aldrich, St. Louis, MO) at 37 °C in 5% CO2 incubator.

extract_protocol:
DNA was extracted using QIAamp DNA Mini Kit (QIAGEN, Hilden, Germany) and RNA was extracted using RNeasy Mini Kit (QIAGEN) following included protocol and treated with DNaseI (QIAGEN).
Libraries were prepared using NEBNext ChIP-Seq Library Preparation Set for Illumina (New England Biolabs) for hMeDIP-seq and MeDIP-seq and TruSeq Stranded mRNA Sample Prep Kit (Illumina) for RNA-seq following the manufacturer’s protocol.

treatment_protocol: To transfect TET2 overexpressiong vector and Mock vector, cells were cultured from 16 hours before transfection in RPMI 1640 medium with 10% FBS without Penicillin-Streptomycin, and 2 ug of each vector were transfected with lipofectamine 2000 (Invitrogen, Carlsbad, CA). The transfectants were selected with 2 ug/mL  puromycin (Sigma-Aldrich) and cultured for 30 days.

value: Mock vector

value: stomach


title: GES1_TET2OE_hMeDIPseq

value: TET2 overexpressed


title: MKN7_EB#1_RNAseq

source_name: Gastric cancer cell line

value: EBV infected


title: GES1_EBV_MeDIPseq

description: 5-mC antibody (#33D3, Diagenode lot#GF-003)

tag: antibody

value: 5-mC (#33D3, Diagenode lot#GF-003)


title: MKN7_WT_RNAseq

value: wild type


title: Control 2 (Cyrano KD)

city: Chapel Hill

first: Joshua

last: Starmer

state: NORTH CAROLINA

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina at Chapel Hill

data_processing:
Initial processing and basecalling was done using the Illumina Pipeline (v.1.8.2)
Alignment to the mm9 genome was performed using Tophat
Reads per gene were counted using HTseq-count
bedGraph files were created using samtools to count the number of reads (for normalization) and bedtools made the bedGraph
Genome_build: mm9
Supplementary_files_format_and_content: all processed data files are tab delimited

source_name: ES cells

growth_protocol: ES cells were maintained in Dulbecco's Modified Eagle Medium supplemented with 10% FBS, 10% Knockout Serum Replacement, 2mM L-glutamate, 1mM sodium pyruvate, 0.1mM b-mercaptoethanol, and 100U/ml penicillin-streptomycin and LIF on gelatin-coated dishes

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen) or the Quick-RNA MiniPrep Kit (Zymo)
Libraries for RNA-Seq were prepared using total RNA with a modified dUTP Strand Specific method (Zhong et al., 2011) including Poly A+ selection, RNA fragmentation, purification, first and second strand synthesis, end repair and A-tailing, followed by standard Illumina Library preparation.

treatment_protocol: shRNA constructs targeting Cyrano or NTC in pSicoR-Ef1a-mCh-Puro (Salomonis et al., 2010) were transfected into embryonic stem cells using Lipofectamine LTX reagent (ThermoFisher), followed by selection/enrichment upon passaging at d1 post-transfection using puromycin selection or flow cytometry at the UNC Flow Cytometry Core Facility

tag: strain

value: embryonic stem cells

tag: genotype

value: Non-targeting control


title: shRNA Cyrano knockdown 1

value: shRNA Cyrano knockdown


title: 64821-blood_Ly6Chi

city: Philadelphia

first: Robert

middle: L

last: Bowman

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were mapped to the mouse genome mm10 using the STAR aligner v2.5.0e with default parameters.
Reads were mapped to genes using the default parameters provided b STAR (based on HT-Seq counts).
Gene counts were normalized and analyzed for differential exprssion with DESeq2 in R.
Genome_build: mm10
Supplementary_files_format_and_content: txt file of raw counts from STAR

source_name: Ly6C high blood monocyte

growth_protocol: For the glioma generation intracranial injections were performed on 5-6 week old mice as previously described (Pyonteck et al., 2013).  Briefly, mice were fully anesthetized with ketamine/xylazine and bupivacaine was applied as a local anesthetic.  Using a stereotactic apparatus, cells were injected into the right frontal cortex (1 mm caudal, 1.5 mm lateral from bregma, 2-3 mm deep).   3x10^5 DF1 cells (1:1 mixture of DF1: RCAS-PDGFB-HA, and DF1:RCAS:shP53)  were injected at week 6 of age into Flt3:Cre Rosa26:mTmG mice.

extract_protocol:
RNA was isolated from TriZOL with a chloroform extraction, following by isopropanol precipitation with glycogen carrier.
Libraries were generated using the Smart-Seq kit (Clonetech).

treatment_protocol: Tumor bearing mice were anesthetized with 1.25% Avertin, and transcardially perfused with PBS. Tumors were macrodissected and dissociated using the Mouse Tumor Dissociation Kit (mTDK, Miltenyi) using the OctoMACS disocciator.  Tumors were filtered through a 40 μM mesh filter and underwent RBC lysis (PharmLyse BD).  Tissue underwent myelin removal using the Myelin Removal Beads (Miltenyi).  Single cell suspensions were FC blocked (BD cat #553141) for 15 minutes at 4 degrees Celsius.  Cells were then incubated with directly conjugated antibody panels for 15 minutes at 4 degrees Celsius.  Cell suspensions were washed (PBS +2% fetal bovine serum) and resuspended in a DAPI solution.  All flow cytometry analysis was completed on a BD Fortessa device at the Flow Cytometry Core Facility (FCCF) at MSKCC.  All cell sorting was completed on an Aria III device at the FCCF at MSKCC. Tumor assocaited microglia (MG) were isoalted as Cd45+Cd11b+Ly6c-Ly6g-GFP-TdTomato+ cells while tumor associated bone marrow derived macrophages (BMDM) were isolated  as  Cd45+Cd11b+Ly6c-Ly6g-GFP+TdTomato- cells.  Samples were sorted directly into TriZOL LS.

tag: strain background

value: Blood

value: Blood Monocytes


title: 64819-blood_Ly6Chi

tag: tissue


title: shRNA Cyrano knockdown 2


title: Control 1 (Cyrano KD)


title: s136M5

tag: cell type


title: 64817-blood_Ly6Chi


title: 80767-MG_GL261

source_name: tumor associated microglia

value: TAM Microglia


title: 80766-MG_GL261


title: 67574-Brain_MG

source_name: normal brain microglia

value: Normal brain

value: Normal Microglia


title: 67573-Brain_MG


title: 80769-BMDM_GL261

source_name: tumor associated macrophage

value: TAM Bone marrow derived macrophage


title: 80766-BMDM_GL261


title: Mouse: 6RC87; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D90

city: Lausanne

first: Mark

last: Ibberson

address: Genopode building

department: Vital-IT

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

data_processing:
42nt single reads from 341 mouse islet samples (mean ~40Mio reads/sample) were mapped to mm9 reference genome using Tophat software version 1.3.3 (Trapnell, Roberts et al. 2012) with option --segment-length=20.
File format conversions and statistics for aligned reads were performed using Samtools (Version 0.1.16).
Read counts for genes were generated using htseq-count (Version 0.5.3p3) with UCSC mm9 refFlat genes in GTF format as a reference.
Percent mapped reads were calculated and 3 samples were removed with low percentage (<45%) of mapped reads. The remaining 338 samples were used for subsequent analysis.
The raw count data were first filtered for an average of 5 reads in all the samples, normalized to library size using the trimmed mean (TMM) method in edgeR (Robinson, McCarthy et al. 2010)
Genome_build: mm9
Supplementary_files_format_and_content: The raw counts file contains the counts per gene for each sample. The normalized counts file are TMM normalized and are log2 transformed

source_name: pancreatic islets

extract_protocol:
At least 150 islets were selected and transferred to a 1.5mL DNA/RNA free tube. After centrifugation (1000 rpm, 10s) and disposal of the supernatant, islets were lysed in 350µL RLT Buffer (Qiagen, France). Samples were kept at -80°C before RNA extraction and RNA seq.
The Sequencing library preparation was performed using 200 ng of total RNA input with the TrueSeq RNA Sample Prep Kit v2-Set B (RS-122-2002, Illumina Inc, San Diego, CA) producing a 275bp Fragment including adapters in average size.

tag: mouse id

tag: diet

value: Regular Chow (RC)

tag: time

value: pancreatic islets


title: 67572-Brain_MG


title: Mouse: 6RC89; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D90

description:
[[delete]]
[[delete]]


title: 80769-MG_GL261


title: Mouse: 6RC82; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D90


title: Mouse: 6RC75; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D02


title: 80767-BMDM_GL261


title: Mouse: 6RC81; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D90


title: Mouse: 6RC78; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D02


title: Mouse: 6RC5; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D02


title: Mouse: 6RC48; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D90


title: Mouse: 6RC6; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D02


title: 64818-blood_Ly6Chi


title: Mouse: 6RC47; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D90


title: Mouse: 6RC46; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D90


title: Mouse: 6RC42; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D90


title: 64820-blood_Ly6Chi


title: Mouse: 6RC41; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D90


title: Mouse: 6RC31; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 6RC32; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 6RC30; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 6RC25; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 6RC3; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D02


title: Mouse: 6RC2; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D02


title: Mouse: 6RC26; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 6RC14; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D10


title: Mouse: 6RC4; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D02


title: Mouse: 6RC27; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 6RC28; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 6RC29; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 6RC13; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D10


title: Mouse: 6RC15; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D10


title: Mouse: 6HF99; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D90

value: High Fat, High Sugar (HFHS)


title: Mouse: 6RC1; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D02


title: Mouse: 6RC44; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D90


title: Mouse: 6RC17; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D10


title: Mouse: 6HF85; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: Mouse: 6HF90; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: Mouse: 6HF96; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 6HF6; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: Mouse: 6HF84; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: Mouse: 6HF5; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: Mouse: 6RC43; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D90


title: Mouse: 6HF47; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 6HF46; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 6HF86; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: Mouse: 6HF48; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 6RC16; Strain: 129S2/SvPas; Diet: Regular Chow (RC); Time-point: D10


title: Mouse: 6HF44; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 6HF30; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Mouse: 6HF3; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: Mouse: 6HF41; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 6HF31; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Mouse: 6HF42; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 6HF27; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Mouse: 6HF26; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Mouse: 6HF25; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Mouse: 6HF45; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 6HF2; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: Mouse: 6HF18; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: Mouse: 6HF17; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: Mouse: 6HF13; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: Mouse: 6HF14; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: Mouse: 6HF16; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: Mouse: 5RC5; Strain: AKR/J; Diet: Regular Chow (RC); Time-point: D02

value: AKR/J


title: Mouse: 6HF1; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: Mouse: 5RC48; Strain: AKR/J; Diet: Regular Chow (RC); Time-point: D90


title: Mouse: 5RC47; Strain: AKR/J; Diet: Regular Chow (RC); Time-point: D90


title: Mouse: 5RC46; Strain: AKR/J; Diet: Regular Chow (RC); Time-point: D90


title: Mouse: 5RC43; Strain: AKR/J; Diet: Regular Chow (RC); Time-point: D90


title: Mouse: 5RC44; Strain: AKR/J; Diet: Regular Chow (RC); Time-point: D90


title: Mouse: 5RC45; Strain: AKR/J; Diet: Regular Chow (RC); Time-point: D90


title: Mouse: 6HF43; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 6HF4; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: Mouse: 5RC42; Strain: AKR/J; Diet: Regular Chow (RC); Time-point: D90


title: Mouse: 5RC29; Strain: AKR/J; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 6HF32; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Mouse: 5RC32; Strain: AKR/J; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 5RC26; Strain: AKR/J; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 5RC30; Strain: AKR/J; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 5RC27; Strain: AKR/J; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 5RC41; Strain: AKR/J; Diet: Regular Chow (RC); Time-point: D90


title: Mouse: 5RC3; Strain: AKR/J; Diet: Regular Chow (RC); Time-point: D02


title: Mouse: 5RC4; Strain: AKR/J; Diet: Regular Chow (RC); Time-point: D02


title: Mouse: 6HF29; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Mouse: 5RC28; Strain: AKR/J; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 5RC2; Strain: AKR/J; Diet: Regular Chow (RC); Time-point: D02


title: Mouse: 5RC18; Strain: AKR/J; Diet: Regular Chow (RC); Time-point: D10


title: Mouse: 5RC25; Strain: AKR/J; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 5RC31; Strain: AKR/J; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 5RC15; Strain: AKR/J; Diet: Regular Chow (RC); Time-point: D10


title: Mouse: 5RC17; Strain: AKR/J; Diet: Regular Chow (RC); Time-point: D10


title: Mouse: 6HF15; Strain: 129S2/SvPas; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: Mouse: 5HF6; Strain: AKR/J; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: Mouse: 5HF5; Strain: AKR/J; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: Mouse: 5HF48; Strain: AKR/J; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 5HF45; Strain: AKR/J; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 5RC16; Strain: AKR/J; Diet: Regular Chow (RC); Time-point: D10


title: Mouse: 5RC13; Strain: AKR/J; Diet: Regular Chow (RC); Time-point: D10


title: Mouse: 5RC14; Strain: AKR/J; Diet: Regular Chow (RC); Time-point: D10


title: Mouse: 5RC1; Strain: AKR/J; Diet: Regular Chow (RC); Time-point: D02


title: Mouse: 5HF47; Strain: AKR/J; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 5HF46; Strain: AKR/J; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 5HF44; Strain: AKR/J; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 5HF31; Strain: AKR/J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Mouse: 5HF32; Strain: AKR/J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Mouse: 5HF42; Strain: AKR/J; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 5HF4; Strain: AKR/J; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: Mouse: 5HF43; Strain: AKR/J; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 5HF41; Strain: AKR/J; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 5HF28; Strain: AKR/J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Mouse: 5HF17; Strain: AKR/J; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: Mouse: 5HF2; Strain: AKR/J; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: Mouse: 5HF26; Strain: AKR/J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Mouse: 5HF25; Strain: AKR/J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Mouse: 5HF27; Strain: AKR/J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Mouse: 5HF13; Strain: AKR/J; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: Mouse: 4RC6; Strain: A/J; Diet: Regular Chow (RC); Time-point: D02

value: A/J


title: Mouse: 5HF14; Strain: AKR/J; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: Mouse: 4RC43; Strain: A/J; Diet: Regular Chow (RC); Time-point: D90


title: Mouse: 4RC47; Strain: A/J; Diet: Regular Chow (RC); Time-point: D90


title: Mouse: 4RC48; Strain: A/J; Diet: Regular Chow (RC); Time-point: D90


title: Mouse: 4RC45; Strain: A/J; Diet: Regular Chow (RC); Time-point: D90


title: Mouse: 4RC42; Strain: A/J; Diet: Regular Chow (RC); Time-point: D90


title: Mouse: 5HF1; Strain: AKR/J; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: Mouse: 5HF30; Strain: AKR/J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Mouse: 5HF3; Strain: AKR/J; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: Mouse: 5HF29; Strain: AKR/J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Mouse: 5HF18; Strain: AKR/J; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: Mouse: 4RC41; Strain: A/J; Diet: Regular Chow (RC); Time-point: D90


title: Mouse: 4RC32; Strain: A/J; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 4RC4; Strain: A/J; Diet: Regular Chow (RC); Time-point: D02


title: Mouse: 4RC31; Strain: A/J; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 5HF15; Strain: AKR/J; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: Mouse: 5HF16; Strain: AKR/J; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: Mouse: 4RC30; Strain: A/J; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 4RC29; Strain: A/J; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 4RC27; Strain: A/J; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 4RC2; Strain: A/J; Diet: Regular Chow (RC); Time-point: D02


title: Mouse: 4RC18; Strain: A/J; Diet: Regular Chow (RC); Time-point: D10


title: Mouse: 4RC3; Strain: A/J; Diet: Regular Chow (RC); Time-point: D02


title: Mouse: 4RC46; Strain: A/J; Diet: Regular Chow (RC); Time-point: D90


title: Mouse: 4RC16; Strain: A/J; Diet: Regular Chow (RC); Time-point: D10


title: Mouse: 4RC26; Strain: A/J; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 4RC25; Strain: A/J; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 4RC13; Strain: A/J; Diet: Regular Chow (RC); Time-point: D10


title: Mouse: 4RC44; Strain: A/J; Diet: Regular Chow (RC); Time-point: D90


title: Mouse: 4RC14; Strain: A/J; Diet: Regular Chow (RC); Time-point: D10


title: Mouse: 4RC1; Strain: A/J; Diet: Regular Chow (RC); Time-point: D02


title: Mouse: 4HF48; Strain: A/J; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 4HF6; Strain: A/J; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: Mouse: 4HF5; Strain: A/J; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: Mouse: 4HF46; Strain: A/J; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 4HF45; Strain: A/J; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 4HF44; Strain: A/J; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 4HF43; Strain: A/J; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 4HF41; Strain: A/J; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 4HF42; Strain: A/J; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 4HF4; Strain: A/J; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: Mouse: 4RC28; Strain: A/J; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 4HF31; Strain: A/J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Mouse: 4HF3; Strain: A/J; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: Mouse: 4HF29; Strain: A/J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Mouse: 4HF28; Strain: A/J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Mouse: 4HF30; Strain: A/J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Mouse: 4HF27; Strain: A/J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Mouse: 4HF26; Strain: A/J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Mouse: 4HF47; Strain: A/J; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 4HF25; Strain: A/J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Mouse: 4HF15; Strain: A/J; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: Mouse: 4HF16; Strain: A/J; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: Mouse: 4HF13; Strain: A/J; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: Mouse: 3RC47; Strain: BALB/cJ; Diet: Regular Chow (RC); Time-point: D90

value: BALB/cJ


title: Mouse: 3RC6; Strain: BALB/cJ; Diet: Regular Chow (RC); Time-point: D02


title: Mouse: 4HF18; Strain: A/J; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: Mouse: 4HF32; Strain: A/J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: ATOH1-HA_ChIP-seq_rep2 Spinal metastatic tumor

city: Sioux Falls

first: Haotian

last: Zhao

state: SD

address: 2301 E. 60th St. North

department: Children's Health Research Center

institute: Sanford Research

data_processing:
The raw reads were mapped to reference mouse genome (mm10) using Bowtie2.
Peak calling for uniquely mapped reads of ATOH1 and histone binding sites was performed using MACS2, with IgG as background control, at q <0.05 (FDR <5%) (15).
Peaks (for ATOH1 and histone-bound regions) were annotated with Genomic Regions Enrichment Annotations Tool (GREAT) using mm10 reference mouse genome
The BedGraph files of peaks produced by MACS2 were converted into bigWig format for downstream data analysis and visualization
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: SHH medulloblastoma

growth_protocol: Primary tumors and matched spinal metastatic tumors from Math1-cre;A1G;Ptch1+/- mice were collected.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone- or ATOH1-bound DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: tissue type

value: Spinal metastatic tumor

value: mixed

tag: chip antibody

value: anti-HA antibody (ab9110, abcam)


title: H3K27Ac_ChIP-seq_rep2 Spinal metastatic tumor

value: H3k27Ac antibody (ab4729; Abcam)


title: Control IgG_ChIP-seq_rep3 Primary tumor

value: Primary tumor

value: Control IgG


title: Mouse: 4HF14; Strain: A/J; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: Mouse: 4HF2; Strain: A/J; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: Mouse: 3RC5; Strain: BALB/cJ; Diet: Regular Chow (RC); Time-point: D02


title: Mouse: 4HF17; Strain: A/J; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: Mouse: 3RC46; Strain: BALB/cJ; Diet: Regular Chow (RC); Time-point: D90


title: Mouse: 3RC45; Strain: BALB/cJ; Diet: Regular Chow (RC); Time-point: D90


title: ATOH1-HA__ChIP-seq_rep3 Primary tumor


title: Mouse: 3RC43; Strain: BALB/cJ; Diet: Regular Chow (RC); Time-point: D90


title: Mouse: 3RC44; Strain: BALB/cJ; Diet: Regular Chow (RC); Time-point: D90


title: H3K27Ac_ChIP-seq_rep3 Primary tumor


title: Mouse: 4HF1; Strain: A/J; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: Mouse: 3RC48; Strain: BALB/cJ; Diet: Regular Chow (RC); Time-point: D90


title: ATOH1-HA_ChIP-seq_rep1 Spinal metastatic tumor


title: Control IgG_ChIP-seq_rep2 Primary tumor


title: ATOH1-HA_ChIP-seq_rep2 Primary tumor


title: Mouse: 3RC41; Strain: BALB/cJ; Diet: Regular Chow (RC); Time-point: D90


title: H3K27Ac_ChIP-seq_rep2 Primary tumor


title: Mouse: 3RC31; Strain: BALB/cJ; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 3RC30; Strain: BALB/cJ; Diet: Regular Chow (RC); Time-point: D30


title: ATOH1-HA_ChIP-seq_rep1 Primary tumor


title: Mouse: 3RC32; Strain: BALB/cJ; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 3RC4; Strain: BALB/cJ; Diet: Regular Chow (RC); Time-point: D02


title: H3K27Ac_ChIP-seq_rep1 Primary tumor


title: Mouse: 3RC29; Strain: BALB/cJ; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 3RC3; Strain: BALB/cJ; Diet: Regular Chow (RC); Time-point: D02


title: Mouse: 3RC27; Strain: BALB/cJ; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 3RC28; Strain: BALB/cJ; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 3RC26; Strain: BALB/cJ; Diet: Regular Chow (RC); Time-point: D30


title: Cerebellum_rep1

data_processing:
Base calls generated with v1.3.0 of the Torrent Suite software.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: Cerebellum

extract_protocol:
Primary tumors from Math1-cre;A1G;Ptch1+/- and Ptch1+/-  mice, and cerebellum from wild type adult mice wereremoved, homogenized in Trizol reagent, and flash frozen on dry ice. RNA was harvested using Life Technologies PureLink RNA Mini Kit (Cat#12183018A).
Total RNA extracted from these samples were ribo-depleted using the Ribominus Eukaryote System (Life Technologies), and used to generate libraries of barcoded fragment using the Ion Total RNA-Seq Kit V2 (Life Technologies). Libraries were sequenced on the Ion Proton sequencer, three libraries per Ion Proton PI Chip, using 200 bp sequencing reagents.

value: Wild type adult cerebellum

value: Wild type


title: Ptch tumor_rep2


title: Ptch tumor_rep3


title: Mouse: 3RC42; Strain: BALB/cJ; Diet: Regular Chow (RC); Time-point: D90


title: Mouse: 3RC25; Strain: BALB/cJ; Diet: Regular Chow (RC); Time-point: D30


title: Ptch tumor_rep1


title: Primary tumor_rep3


title: Control IgG_ChIP-seq_rep1 Primary tumor


title: Primary tumor_rep2


title: Mouse: 3RC17; Strain: BALB/cJ; Diet: Regular Chow (RC); Time-point: D10


title: Cerebellum_rep2


title: Mouse: 3RC18; Strain: BALB/cJ; Diet: Regular Chow (RC); Time-point: D10


title: Primary tumor_rep1


title: Cerebellum_rep3


title: Mouse: 3RC16; Strain: BALB/cJ; Diet: Regular Chow (RC); Time-point: D10


title: Mouse: 3RC15; Strain: BALB/cJ; Diet: Regular Chow (RC); Time-point: D10


title: pkl_sRNA_rep3

city: Shanghai

first: Heng

last: Zhang

address: 3888 Chenhua Rd, Gate 3

department: Shanghai Center for Plant Stress Biology

institute: Chinese Academy of Sciences

data_processing:
Basecalling performed using CASAVA v1.8
Adapter sequences and low quality bases (q<30) removed using trim_galore v0.4.0 and catadapt v1.8.3
Reads aligned to the Arabidopsis TAIR10 genome using BWA 0.7.15
Read counts in every 100 bp window of the genome were generated using the bedtools package
Differential expression analyses performed using the edgeR package in R using the following cutoffs: BH adjusted p-value < 0.01, fold chagne > 2
Genome_build: TAIR10
Supplementary_files_format_and_content: tdf files at single bp resolution; scores represent library size normalized coverage for 24-nt siRNAs (counts per 10 million); tab-delimited text files include RPTM values in 100-bp window for each Sample

source_name: 2-week-old seedlings

growth_protocol: On 1/2 MS plates at 22ºC with 12h:12h day-night cycle in the growth chamber

extract_protocol:
Total RNA extracted from 2-week-old seedlings using trizol reagent and small RNA purified using 15% TBE-urea gels
Constructed using Illumina TruSeq small RNA library prep kit


title: nrpd1_sRNA_rep3


title: Mouse: 3RC13; Strain: BALB/cJ; Diet: Regular Chow (RC); Time-point: D10


title: Mouse: 3RC14; Strain: BALB/cJ; Diet: Regular Chow (RC); Time-point: D10


title: Mouse: 3RC1; Strain: BALB/cJ; Diet: Regular Chow (RC); Time-point: D02


title: nrpe1_sRNA_rep3


title: WT_sRNA_rep3

value: WT


title: nrpe1_sRNA_rep2


title: Mouse: 3HF6; Strain: BALB/cJ; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: Mouse: 3HF5; Strain: BALB/cJ; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: nrpd1_sRNA_rep2


title: Mouse: 3RC2; Strain: BALB/cJ; Diet: Regular Chow (RC); Time-point: D02


title: Mouse: 3HF46; Strain: BALB/cJ; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: WT_sRNA_rep2


title: Mouse: 3HF45; Strain: BALB/cJ; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 3HF47; Strain: BALB/cJ; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: pkl_sRNA_rep1


title: Mouse: 3HF44; Strain: BALB/cJ; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: nrpe1_sRNA_rep1


title: Mouse: 3HF42; Strain: BALB/cJ; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: WT_sRNA_rep1


title: Mouse: 3HF43; Strain: BALB/cJ; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 3HF41; Strain: BALB/cJ; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: nrpd1_sRNA_rep1


title: pkl_mRNA_rep3

data_processing:
Basecalling performed using CASAVA v1.8
Adapter sequences and low quality bases (q<30) removed using trim_galore v0.4.0 and catadapt v1.8.3
Reads aligned to the Arabidopsis TAIR10 genome and read counts generated using subread v1.5.1
Differential expression analyses performed using the edgeR package in R using the following cutoffs: BH adjusted p-value < 0.01, fold chagne > 2
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Total RNA extracted from 2-week-old seedlings using the trizol reagent and messenger RNA purified using poly-T maganetic beads
Constructed using Illumina TruSeq Stranded mRNA Library Prep Kit


title: nrpd1_mRNA_rep3


title: nrpe1_mRNA_rep3


title: Mouse: 3HF4; Strain: BALB/cJ; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: WT_mRNA_rep3


title: Mouse: 3HF31; Strain: BALB/cJ; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Mouse: 3HF32; Strain: BALB/cJ; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: pkl_mRNA_rep2


title: Mouse: 3HF30; Strain: BALB/cJ; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Mouse: 3HF3; Strain: BALB/cJ; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: nrpd1_mRNA_rep2


title: pkl_sRNA_rep2


title: Mouse: 3HF28; Strain: BALB/cJ; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: pkl_mRNA_rep1


title: Mouse: 3HF29; Strain: BALB/cJ; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: nrpe1_mRNA_rep1


title: nrpd1_mRNA_rep1


title: Mouse: 3HF27; Strain: BALB/cJ; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Mouse: 3HF26; Strain: BALB/cJ; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: WT_mRNA_rep1


title: Mouse: 3HF25; Strain: BALB/cJ; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Mouse: 3HF2; Strain: BALB/cJ; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: Mouse: 3HF18; Strain: BALB/cJ; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: nrpe1_wgbs

data_processing:
Basecalling performed using CASAVA v1.8
Adapter sequences and low quality bases (q<30) removed using trim_galore v0.4.0 and catadapt v1.8.3
Reads aligned to the Arabidopsis TAIR10 genome using bsmap 2.74
Genome_build: TAIR10
Supplementary_files_format_and_content: tdf files of cytosine methylation ratio at single basepair resolution, only cytosines with a coverage > 4 are included

extract_protocol:
Genomic DNA extracted from 2-week-old seedlings using the Qiagen Plant DNeasy Maxi kit
Constructed using Illumina TruSeq DNA Library Prep Kit


title: nrpd1_wgbs


title: pkl_wgbs


title: Mouse: 3HF16; Strain: BALB/cJ; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: Mouse: 3HF15; Strain: BALB/cJ; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: nrpe1_mRNA_rep2


title: WT_wgbs


title: Mouse: 3HF14; Strain: BALB/cJ; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: Mouse: 3HF13; Strain: BALB/cJ; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: Highly differentiated P40T

city: Fuzhou

first: Yi

last: Huang

state: Fujian Province

address: 134 Dong Street

department: Department of Pathology

institute: Fujian Provincial Hospital

description: polyA RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw sequencing reads were firstly filtered for adapters and ribosomal RNA. Reads containing five or more low quality (quality score < 20) bases were also removed. The remaining high-quality reads were then aligned to human genome (hg19) by using Tophat (v2.0.9) with default parameters.
Gene expression level measured by FPKM (fragments per kilobase per million) was calculated by Cufflinks (v2.1.1), the GTF file was provided by Illumina iGenomes UCSC hg19 (ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz),
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *N.txt, *T.txt: Tab-delimited text files include: #(unique id) and FPKM values for each sample.
Supplementary_files_format_and_content: genelist.txt provides the gene information, includes 5 columns: #, Entrez_ID, GeneSymbol, des and locus (#:unique id, matched with the first column in expression files; Entrez_ID: Entrez gene id; GeneSymbol: gene symbol; des: gene description by Ref Seq database; locus: the gene location in hg19, output by Cufflinks).

source_name: liver, tumor

extract_protocol:
Sequencing libraries were prepared by using TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA, USA) according to standard protocols.
Briefly, total RNA was firstly randomly fragmented and poly-A-selected. Secondly, the RNA fragments were reverse transcribed to cDNA, end-repaired and ligated with adapters. The libraries then underwent size selection, PCR and purification. The quality of libraries was assessed by using Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA). Sequencing was then performed on an Illumina HiSeq 2500 sequencer with 125 bp pair-end reads.

tag: disease state

value: hepatocellular carcinoma (HCC)

value: liver tumor

tag: differentiation

value: Highly

tag: tumor stage

tag: patient id


title: Mouse: 2RC99; Strain: DBA/2J; Diet: Regular Chow (RC); Time-point: D02

value: Regular Chow (RC)

value: pancreatic islets


title: Mouse: 3HF1; Strain: BALB/cJ; Diet: High Fat, High Sugar (HFHS); Time-point: D02

value: High Fat, High Sugar (HFHS)


title: Mouse: 2RC98; Strain: DBA/2J; Diet: Regular Chow (RC); Time-point: D02


title: LFYGRINPUT1

city: Dublin

first: Pat

last: Ryan

address: College Green

country: Ireland

institute: TCD

description: Input sample

data_processing:
Quality Control: Fastqc was used to assess read quality
Mapping: Burrows Wheeler aligner used to align reads to Arabidopsis genome
Peak Calling: Performed using MACS v1.4, Input sample used as control for peak calling on test.
Peak Annotation: performed using HOMER annotatepeaks.pl
Visualisation: Integrated Genome Viewer
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab delimited .csv file. This is a list of peaks, along with associated annotations where available.

source_name: Inflorescence

growth_protocol: Arabidopsis plants grown for 4 weeks at 20C in 2:1:1 soil:perlite:vermiculite

extract_protocol:
Tissue harvested 4hours after treatment. 500 μL of inflorescence tissue was vacuum infiltrated four times for 15 min in Cross Linking solution (1% formaldehyde, 10 mM NaPi pH 7.0, 50 mM NaCl, 100 mM sucrose) at room temperature. The cross-linking reaction was stopped by adding glycine to a final concentration of 0.1 M and vacuum infiltrating for five minutes. The tissue was washed three times with water before being ground to a fine powder in liquid nitrogen. Chromatin was isolated using Extraction Buffers 1, 2 and 3 (Plant ChIP-Seq kit, Diagenode) and resuspended in Nuclei Lysis Buffer (50 mM Tris-HCl pH 8.1, 10 mM EDTA, 1% SDS) and then sonicated to achieve an average fragment size of approximately 200 – 500 bp. Cellular debris were removed by centrifugation. The chromatin solution was then diluted to 1 mL with 1x ChIP Dilution Buffer (Plant ChIP-Seq Kit, Diagenode) and precleared by incubating 60 uL of protein-A agarose beads (50% suspension in 1x ChIP dilution buffer; Santa Cruz Biotech) for 90 min at 4°C. Fifty microliters of the pre-cleared chromatin solution was then removed and stored at -80°C to be used as Input control. Immunoprecipitation was carried out using rabbit polyclonal antibodies raised against a LFY overnight at 4°C and 60 uL of protein-A agarose beads (50% suspension in 1x ChIP dilution buffer; Santa Cruz Biotech) was added to the chromatin-antibody solution and incubated for 2 hours at 4°C. The beads were then washed 5 times using 1x ChIP Dilution Buffer (Plant ChIP-Seq Kit, Diagenode) before the immunocomplexes were eluted by adding 400 uL Elution Buffer 1 (Plant ChIP-Seq Kit, Diagenode) and incubating at 65°C for 30 min with shaking at 1300 r.p.m. Samples were spun to remove remaining agarose beads and 16 uL of Elution buffer 2 (Plant ChIP-Seq Kit, Diagenode) was added with samples being incubated overnight at 65°C with shaking at 1300 r.p.m. The Input control samples were treated similarly, with the addition of 400 uL of Elution Buffer 1 and 16 uL of Elution buffer 2 (Plant ChIP-Seq Kit, Diagenode), followed by overnight incubation at 65°C with shaking at 1300 r.p.m. DNA was purified and precipitated from these samples using buffers from the Plant ChIP-Seq Kit (Diagenode) according to the manufacturer’s instructions.
MicroPlex Library preparation kit v2

treatment_protocol: treatment with a solution containing 10 μM dexamethasone (Sigma-Aldrich), 0.01% (v/v) ethanol, and 0.015% (v/v) Silwet L-77 (De Sangosse).

value: ap1 cal1

value: Inflorescence

tag: construct

tag: chip-antibody

value: NA – Input sample


title: Highly differentiated P24N

description: polyA RNA

source_name: liver, non-tumor

value: adjacent non-tumorous liver

value: B(BCLC)


title: Highly differentiated P40N

description: polyA RNA


title: Highly differentiated P24T

description: polyA RNA


title: Mouse: 2RC97; Strain: DBA/2J; Diet: Regular Chow (RC); Time-point: D02


title: Mouse: 2RC123; Strain: DBA/2J; Diet: Regular Chow (RC); Time-point: D90


title: Mouse: 2RC124; Strain: DBA/2J; Diet: Regular Chow (RC); Time-point: D90


title: MKN7_EB#3_RNAseq

tag: cell line

tag: genotype/variation

value: EBV infected

value: stomach


title: Highly differentiated P21N

description: polyA RNA


title: Mouse: 2RC122; Strain: DBA/2J; Diet: Regular Chow (RC); Time-point: D90

tag: strain


title: Moderately differentiated P36T

description: polyA RNA

value: Moderately


title: WT_mRNA_rep2

tag: genotype


title: MKN7_EB#2_RNAseq

tag: tissue


title: Mouse: 3HF17; Strain: BALB/cJ; Diet: High Fat, High Sugar (HFHS); Time-point: D10

value: BALB/cJ


title: Mouse: 2RC120; Strain: DBA/2J; Diet: Regular Chow (RC); Time-point: D90


title: Moderately differentiated P36N

description: polyA RNA


title: Mouse: 2RC119; Strain: DBA/2J; Diet: Regular Chow (RC); Time-point: D90


title: LFYGR

description: ChIP-seq data set identifying LFY binding sites

value: Rabbit polyclonal whole serum raised against LFY


title: Highly differentiated P21T

description: polyA RNA


title: Moderately differentiated P29T

description: polyA RNA


title: Mouse: 2RC117; Strain: DBA/2J; Diet: Regular Chow (RC); Time-point: D90


title: Mouse: 2RC118; Strain: DBA/2J; Diet: Regular Chow (RC); Time-point: D90


title: Ad_Sk4

city: San Francisco

first: Niwa

last: Ali

state: California

address: 513 Parnassus Avenue HSW1201b

department: Dermatology

institute: UCSF

data_processing:
The primary sequencing output ( FASTQ) is produced by a combination of Illumina software (CASAVA v. 1.8.2) and EA developed tools. Low quality reads, bases, homopolymers and adapter sequences were removed with fastq-mcf (Expression Analysis)
Reads were then mapped to mm10 using the UCSC refFlat gene model
Reads were mapped using  Tophat (v2.0.12) with Bowtie2 (2.1.0.0) and sorted with Samtools (0.1.19.0).
Reads were counted with HTSeq (0.6.1) using the settings union and stranded=no
Genome_build: mm10
Supplementary_files_format_and_content: comma separated value file contains raw counts for each sample

source_name: Telogen skin Tregs

extract_protocol:
Sorted cells were pelleted flash frozen in liquid nitrogen. RNA was sent overnight on dry ice to Expression analysis, Quintiles to perform all subsequent processing and sequencing. RNA was isolated using by column purification.
RNA samples were converted into cDNA libraries using the Illumina SMARTer Ultra Low Input sample preparation kit.

value: Skin

tag: age

value: 6 weeks


title: Moderately differentiated P29N

description: polyA RNA

value: hepatocellular carcinoma (HCC)


title: Mouse: 2RC115; Strain: DBA/2J; Diet: Regular Chow (RC); Time-point: D30

tag: mouse id


title: Ad_Sk3


title: Mouse: 2RC114; Strain: DBA/2J; Diet: Regular Chow (RC); Time-point: D30

tag: diet


title: Moderately differentiated P26T

description: polyA RNA

value: liver tumor


title: Mouse: 2RC121; Strain: DBA/2J; Diet: Regular Chow (RC); Time-point: D90

value: Regular Chow (RC)

tag: time


title: Mouse: 2RC113; Strain: DBA/2J; Diet: Regular Chow (RC); Time-point: D30

value: pancreatic islets


title: Mouse: 2RC112; Strain: DBA/2J; Diet: Regular Chow (RC); Time-point: D30


title: Moderately differentiated P26N

description: polyA RNA


title: Mouse: 2RC110; Strain: DBA/2J; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 2RC111; Strain: DBA/2J; Diet: Regular Chow (RC); Time-point: D30


title: Poorly differentiated P17T

description: polyA RNA

value: Poorly


title: Ad_Sk1

value: skin draining lymph node


title: Ad_Sk2


title: Mouse: 2RC108; Strain: DBA/2J; Diet: Regular Chow (RC); Time-point: D10


title: Mouse: 2RC107; Strain: DBA/2J; Diet: Regular Chow (RC); Time-point: D10


title: Ad_LN3

source_name: skin draining lymph node Tregs


title: Poorly differentiated P17N

description: polyA RNA


title: GES1_WT_MeDIPseq

value: wild type

tag: antibody

value: 5-mC (#33D3, Diagenode lot#GF-003)


title: Mouse: 2RC105; Strain: DBA/2J; Diet: Regular Chow (RC); Time-point: D10


title: Mouse: 2RC104; Strain: DBA/2J; Diet: Regular Chow (RC); Time-point: D10


title: Poorly differentiated P14T

description: polyA RNA


title: Ad_LN2


title: Mouse: 2RC116; Strain: DBA/2J; Diet: Regular Chow (RC); Time-point: D30


title: Ad_LN1


title: Poorly differentiated P14N

description: polyA RNA

value: adjacent non-tumorous liver


title: Mouse: 2RC103; Strain: DBA/2J; Diet: Regular Chow (RC); Time-point: D10


title: Mouse: 2RC102; Strain: DBA/2J; Diet: Regular Chow (RC); Time-point: D02


title: DTR_DEP3D

data_processing:
The primary sequencing output ( FASTQ) is produced by a combination of Illumina software (CASAVA v. 1.8.2) and EA developed tools. Low quality reads, bases, homopolymers and adapter sequences were removed with fastq-mcf (Expression Analysis)
Reads were then mapped to mm10 using the UCSC refFlat gene model
Reads were mapped using  Tophat (v2.0.12) with Bowtie2 (2.1.0.0) and sorted with Samtools (0.1.19.0).
Reads were counted with HTSeq (0.6.1) using the settings union and reverse strandedness.
Genome_build: mm10
Supplementary_files_format_and_content: comma separated value file contains raw counts for each sample

source_name: Hair follicle stem cells

extract_protocol:
Sorted cells were pelleted flash frozen in liquid nitrogen. RNA was sent overnight on dry ice to Expression analysis, Quintiles to perform all subsequent processing and sequencing. RNA was isolated using Illumina TruSeq Stranded mRNA  Kit.
RNA samples were converted into cDNA libraries using the Illumina TruSeq Stranded mRNA sample preparation kit (Illumina # RS-122-2103).

value: Skin epidermis

tag: anagen stage

value: Day 4 post depilation

tag: treatment

value: 15ng/g DT intraperitoneally

tag: treg presence

value: Treg depleted


title: Poorly differentiated P10T

description: polyA RNA

tag: disease state

tag: differentiation

tag: tumor stage


title: Mouse: 2RC101; Strain: DBA/2J; Diet: Regular Chow (RC); Time-point: D02


title: Mouse: 2RC100; Strain: DBA/2J; Diet: Regular Chow (RC); Time-point: D02


title: Mouse: 2HF136; Strain: DBA/2J; Diet: High Fat, High Sugar (HFHS); Time-point: D90

value: High Fat, High Sugar (HFHS)


title: Poorly differentiated P10N

description: polyA RNA

tag: patient id


title: DTR_DEP3C


title: Mouse: 2HF135; Strain: DBA/2J; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 2RC109; Strain: DBA/2J; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 2HF134; Strain: DBA/2J; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 2HF133; Strain: DBA/2J; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: WT_DEP2C

value: WT

value: Treg present


title: WT_DEP2A


title: Mouse: 2HF132; Strain: DBA/2J; Diet: High Fat, High Sugar (HFHS); Time-point: D90