title: Nascent_ChORseq_RNApolIIS5phos_rep2

description: RNApolIIS5phos_totalChIP_replicated_peaks.bed

value: RNA polymerase II CTD repeat YSPTSPS (phospho S5) antibody - ChIP Grade (Abcam, ab5131)

value: Nascent

value: EdU-labelled genomic DNA


title: K562 ChIP-seq WDR5-D9E1l DMSO rep1

status: Public on Mar 12 2019

type: SRA

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

country: USA

institute: Vanderbilt University Medical Center

description:
Cells were cross-linked for 10 minutes in 1% formaldehyde and cross-linking quenched with 125 mM glycine. Cells were lysed and chromatin sheared to achieve a mean fragment length of 250 nucleotides. Samples were cleared by centrifugation and lysates incubated overnight with corresponding antibodies. Indexed libraries were made from precipitated DNA using the DNA Ultra II Kit (NEB) per the manufacturer's protocol and libraries assessed using the 2100 Bioanalyzer (Agilent). Libraries were quantified using the KAPA Library Quantification Kit (KAPA Biosystems) and libraries subjected to single-end sequencing according to manufacturer's protocol (Illumina).
N1_DM_peaks.narrowPeak

library_source: genomic

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using STAR after adapter trimming, and quantified by featureCounts.
Differential analysis were performed by DESeq2.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2.
Peaks were called by MACS2 with a q-value of 0.01.
Differential binding peaks were identified using DiffBind based on consensus peaks occurring at least two samples.
After adapter trimming and low quality sequence removal by cutadapt, PRO-seq reads longer than 15bp were reversed complemented using FastX tools.
Reverse complements of the trimmed reads were aligned to the human genome hg19 using Bowtie2.
Reads mapped to rRNA loci and reads with mapping quality less than 10 were removed.
Bam files were given to NRSA (http://bioinfo.vanderbilt.edu/NRSA/) to estimate RNA polymerase abundance in proximal-promoter and gene body regions of genes, to calculate pausing index and pausing index alterations, and to detect enhancers and quantify eRNA changes.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq: one peak file per Sample
Supplementary_files_format_and_content: RNA-seq: tab-delimited text file include raw counts for each Sample
Supplementary_files_format_and_content: PRO-seq: tab-delimited text file include raw counts for promoter-proximal and gene body region, and density for gene body

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: K562 and MV4:11 cells were cultured at 37ºC with 5% CO2 in Roswell Memorial Park Institute (RPMI) media supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 0.1 mg/ml penicillin/streptomycin (P/S).

extract_protocol:
For ChIP-Seq experiments, chromatin was clarified from sonicated cell lysates by centrifugation and incubated overnight with corresponding antibodies. For RNA-Seq, cells were washed in PBS then lysed in 500 uL Trizol and total RNA was isolated using the Zymo Research Direct-zol RNA MiniPrep kit (Zymo Research  #R2050) with on-column DNase digestion following the manufacturers instructions. For PRO-Seq experiments,  nuclei were extracted through hypotonic lysis with a low amount of non-ionic detergent.
For ChIP-Seq experiments, indexed libraries were made from precipitated DNA using the DNA Ultra II Kit (NEB) per the manufacturer's protocol. For RNA-Seq, library preperation was completed by Genewiz using their standard methods. For PRO-Seq experiments, libraries were made using RNA that was made through a biotin-run on reaction. Biotin-RNA was base hydrolyzed, and extracted. 3'-adaptors were ligated to ends and 5'caps were removed, repaired, and then 5'-adaptors were ligated as well. Purified and intact biotin-RNA containing adaptors was used in a reverase transcriptase reaction to generate cDNA and cDNA was used to amplify full library using NEB High Fidelity Phusion polymerase.

treatment_protocol: For ChIP-Seq experiments, cells were treated with either 0.1% DMSO, 2 µM C6, or 2 µM C6nc for 4 hours. For RNA-Seq experiments, cells were treated with either 0.1% DMSO, 2 µM C6, 2 µM C6nc ot 2 µM Nutlin for 72 hours. For PRO-Seq experiments, cells were treated with either DMSO for 1 hour, or C3 for 15 min, 30 min, or 60 min.

tag: cell line

tag: treatment

value: 0.1% DMSO for 4 hours

tag: chip antibody

value: Cell Signaling WDR5 (D9E1I)


title: D. mauritiana_stage2_replicate2

status: Public on Dec 04 2018

city: Davis

first: Susan

middle: E.

last: Lott

state: CA

address: 2320 Storer Hall

department: Evolution and Ecoloty

institute: University of California, Davis

library_source: transcriptomic

data_processing:
Genome_build:flybase genome used for alignment/processing: dana-all-chromosome-r1.3.fasta Dmau_MS17_all_chromosomes_r.1.0.fa
annotation file used: Dmau_annotation_5_sets_edited.gff4
a preprocessing step using cutadapt removed adapters, barcodes and low quality regions of reads
reads were aligned using Tophat2
transcriptome assembly was carried out using cufflinks
the assemblies were merged using cuffmerge
abundance estimates were calculated with cuffquant (using the merged assemblies) followed by cuffnorm
differential expression was determined using cuffdiff
Supplementary_files_format_and_content: Mean FPKM values for each species at each stage. One file (gene_exp_orthologs_any) provides FPKM values for all genes with any orthology in any species, the other (gene_exp_orthologs_all_14_species_present) provides FPKM values for all genes with one-to-one orthologs in all 14 species. The FPKM value for each gene is the sum of the FPKM values for all isoforms of that gene.

molecule: polyA RNA

organism: Drosophila mauritiana

source_name: single embryo

growth_protocol: All species were maintained on molasses food in uncrowded conditions

extract_protocol:
TRIzol reagent extraction of total RNA from single embryos.
Libraries were constructed using Illumina Tru-Seq kits and indices

treatment_protocol: Eggs were collected from vials, and imaged to determine stage

tag: embryonic stage

value: stage 2

tag: replicate number

value: replicate 2

tag: raw data mixed with d. melanogaster?

value: no


title: D. mauritiana_stage2_replicate1

data_processing:
Genome_build:flybase genome used for alignment/processing: dana-all-chromosome-r1.3.fasta Dmau_MS17_all_chromosomes_r.1.0.fa
annotation file used: Dmau_annotation_5_sets_edited.gff3
a preprocessing step using cutadapt removed adapters, barcodes and low quality regions of reads
reads were aligned using Tophat2
transcriptome assembly was carried out using cufflinks
the assemblies were merged using cuffmerge
abundance estimates were calculated with cuffquant (using the merged assemblies) followed by cuffnorm
differential expression was determined using cuffdiff
Supplementary_files_format_and_content: Mean FPKM values for each species at each stage. One file (gene_exp_orthologs_any) provides FPKM values for all genes with any orthology in any species, the other (gene_exp_orthologs_all_14_species_present) provides FPKM values for all genes with one-to-one orthologs in all 14 species. The FPKM value for each gene is the sum of the FPKM values for all isoforms of that gene.

value: replicate 1


title: D. mauritiana_stage5_replicate2

data_processing:
Genome_build:flybase genome used for alignment/processing: dana-all-chromosome-r1.3.fasta Dmau_MS17_all_chromosomes_r.1.0.fa
annotation file used: Dmau_annotation_5_sets_edited.gff7
a preprocessing step using cutadapt removed adapters, barcodes and low quality regions of reads
reads were aligned using Tophat2
transcriptome assembly was carried out using cufflinks
the assemblies were merged using cuffmerge
abundance estimates were calculated with cuffquant (using the merged assemblies) followed by cuffnorm
differential expression was determined using cuffdiff
Supplementary_files_format_and_content: Mean FPKM values for each species at each stage. One file (gene_exp_orthologs_any) provides FPKM values for all genes with any orthology in any species, the other (gene_exp_orthologs_all_14_species_present) provides FPKM values for all genes with one-to-one orthologs in all 14 species. The FPKM value for each gene is the sum of the FPKM values for all isoforms of that gene.

value: stage 5


title: D. mauritiana_stage2_replicate3

data_processing:
Genome_build:flybase genome used for alignment/processing: dana-all-chromosome-r1.3.fasta Dmau_MS17_all_chromosomes_r.1.0.fa
annotation file used: Dmau_annotation_5_sets_edited.gff5
a preprocessing step using cutadapt removed adapters, barcodes and low quality regions of reads
reads were aligned using Tophat2
transcriptome assembly was carried out using cufflinks
the assemblies were merged using cuffmerge
abundance estimates were calculated with cuffquant (using the merged assemblies) followed by cuffnorm
differential expression was determined using cuffdiff
Supplementary_files_format_and_content: Mean FPKM values for each species at each stage. One file (gene_exp_orthologs_any) provides FPKM values for all genes with any orthology in any species, the other (gene_exp_orthologs_all_14_species_present) provides FPKM values for all genes with one-to-one orthologs in all 14 species. The FPKM value for each gene is the sum of the FPKM values for all isoforms of that gene.

value: replicate 3


title: D. mauritiana_stage5_replicate3

data_processing:
Genome_build:flybase genome used for alignment/processing: dana-all-chromosome-r1.3.fasta Dmau_MS17_all_chromosomes_r.1.0.fa
annotation file used: Dmau_annotation_5_sets_edited.gff8
a preprocessing step using cutadapt removed adapters, barcodes and low quality regions of reads
reads were aligned using Tophat2
transcriptome assembly was carried out using cufflinks
the assemblies were merged using cuffmerge
abundance estimates were calculated with cuffquant (using the merged assemblies) followed by cuffnorm
differential expression was determined using cuffdiff
Supplementary_files_format_and_content: Mean FPKM values for each species at each stage. One file (gene_exp_orthologs_any) provides FPKM values for all genes with any orthology in any species, the other (gene_exp_orthologs_all_14_species_present) provides FPKM values for all genes with one-to-one orthologs in all 14 species. The FPKM value for each gene is the sum of the FPKM values for all isoforms of that gene.


title: D. simulans_stage5_replicate3

data_processing:
Genome_build:flybase genome used for alignment/processing: dana-all-chromosome-r1.3.fasta dsim-all-chromosome-r2.01.fa
annotation file used: dsim-all-r2.01.gff
a preprocessing step using cutadapt removed adapters, barcodes and low quality regions of reads
reads were aligned using Tophat2
transcriptome assembly was carried out using cufflinks
the assemblies were merged using cuffmerge
abundance estimates were calculated with cuffquant (using the merged assemblies) followed by cuffnorm
differential expression was determined using cuffdiff
Supplementary_files_format_and_content: Mean FPKM values for each species at each stage. One file (gene_exp_orthologs_any) provides FPKM values for all genes with any orthology in any species, the other (gene_exp_orthologs_all_14_species_present) provides FPKM values for all genes with one-to-one orthologs in all 14 species. The FPKM value for each gene is the sum of the FPKM values for all isoforms of that gene.

organism: Drosophila simulans

value: yes


title: D. simulans_stage5_replicate1


title: D. sechellia_stage5_replicate3

data_processing:
Genome_build:flybase genome used for alignment/processing: dana-all-chromosome-r1.3.fasta dsec-all-chromosome-r1.3.fa
annotation file used: dsec-all-r1.3.gff
a preprocessing step using cutadapt removed adapters, barcodes and low quality regions of reads
reads were aligned using Tophat2
transcriptome assembly was carried out using cufflinks
the assemblies were merged using cuffmerge
abundance estimates were calculated with cuffquant (using the merged assemblies) followed by cuffnorm
differential expression was determined using cuffdiff
Supplementary_files_format_and_content: Mean FPKM values for each species at each stage. One file (gene_exp_orthologs_any) provides FPKM values for all genes with any orthology in any species, the other (gene_exp_orthologs_all_14_species_present) provides FPKM values for all genes with one-to-one orthologs in all 14 species. The FPKM value for each gene is the sum of the FPKM values for all isoforms of that gene.

organism: Drosophila sechellia


title: D. simulans_stage5_replicate2


title: D. sechellia_stage2_replicate2


title: D. sechellia_stage5_replicate2


title: D. simulans_stage2_replicate3


title: K562 ChIP-seq C6 IgG rep2

description:
Cells were cross-linked for 10 minutes in 1% formaldehyde and cross-linking quenched with 125 mM glycine. Cells were lysed and chromatin sheared to achieve a mean fragment length of 250 nucleotides. Samples were cleared by centrifugation and lysates incubated overnight with corresponding antibodies. Indexed libraries were made from precipitated DNA using the DNA Ultra II Kit (NEB) per the manufacturer's protocol and libraries assessed using the 2100 Bioanalyzer (Agilent). Libraries were quantified using the KAPA Library Quantification Kit (KAPA Biosystems) and libraries subjected to single-end sequencing according to manufacturer's protocol (Illumina).
NA

value: 2 µM C6 for 4 hours

value: Cell Signaling IgG (2729S)


title: D. sechellia_stage2_replicate1


title: D. simulans_stage2_replicate2


title: K562 ChIP-seq C6nc IgG rep1

value: 2 µM C6nc for 4 hours


title: K562 ChIP-seq C6nc IgG rep2


title: KO3

status: Public on Nov 14 2018

city: Bethesda

first: Yves

last: Pommier

state: MD

address: 37 Convent Drive

department: NCI/CCR

institute: NIH

data_processing:
Base-calling: Software RTA 1.18.66.3; Software Parameters: Ilumina instrument run time analysis software
Demultiplexing: Software Bcl2fastq 2.17, Software Parameters: Barcode demultiplexed allowing 1 mismatch
Filtering (Adaptor and quality): Software: Trimmomatic 0.36, Software Parameters: PE-threads 16-phred33, ILLUMINACLIP: TruSeq_and_nextera_adapters.fa:2:36:10 LEADING:10 TRAILING:10 MAXINFO:50:0.97 MINLEN:20
Alignment: Software: STAR 2.5.1, Software Parameters: --genomeDir $star_genome --readFilesIn R1_trimmed.fastq R2_trimmed.fastq --outTmpDir /logs/star --outSAMunmapped Within --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --runThreadN 8 --genomeLoad NoSharedMemory --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM
counting reads to genomic features with subread package (Mus_musculus.GRCm38.74.gtf)
Genome_build: Mus_musculus.GRCm38.74
Supplementary_files_format_and_content: Generation of normalized abundance measurements: Software: Bioconductor package DESeq2

molecule: total RNA

organism: Mus musculus

source_name: Murine hepatocellular carcinoma

extract_protocol:
Murine heptaocellular carcinoma were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina Truseq Stranded RNA prep kit RS-122-2201 was used  for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Diethylnitrosamine was administered at postnatal day 14 and carbon tetrachloride was injected twice per week for a duration of 14 weeks (starting at 8 weeks of age). Liver tumor tissue was collected at the age of 22 weeks.

tag: strain

tag: tissue

value: liver tumor tissue

tag: genotype

value: Top1mt -/-


title: KO2


title: D. simulans_stage2_replicate1


title: WT3

value: WT


title: WT2


title: KO1


title: WT1


title: D. sechellia_stage5_replicate1


title: D. sechellia_stage2_replicate3


title: Peds NIBD Ileum 49

status: Public on Oct 01 2018

city: Chapel Hill

first: Terry

last: Furey

state: NC

address: 5022 Genetic Medicine Building

department: Department of Genetics

institute: The University of North Carolina at Chapel Hill

description:
PNIBD49 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt

data_processing:
miRquant 2.0 used for 3' adapter trimming (Cutadapt), two tier read alignment (Bowtie and SHRiMP), and miRNA annotation (miRBase, GtRNAdb, and GENCODE).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Data matrix of raw reads normalised to total microRNA reads; Reads Per Million Mapped to miRs Count Matrix.

source_name: Terminal ileum mucosal biopsy

growth_protocol: FFPE samples from the index colonoscopies from treatment naïve pediatric patients were collected as part of the University of North Carolina IRB protocol 15-0024.

extract_protocol:
miRNA was enriched from FFPE tissue samples using the Roche High Pure miRNA Isolation Kit (Penzberg, Germany). RNA purity and integrity were assessed with Thermo Scientific NanoDrop 2000 (Waltham, MA) and Agilent 2100 Bio- analyzer (Santa Clara, CA), respectively.
Small RNA libraries were generated using Illumina TruSeq Small RNA Sample Preparation Kit (San Diego, CA).
Single-end (50 bp) sequencing was performed on the Illumina HiSeq 2500 platform.

tag: age

value: Pediatric

value: Terminal ileum mucosa

tag: phenotypic status

value: Non-IBD

value: Naive


title: Peds NIBD Ileum 56

description:
PNIBD56 E
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 55

description:
PNIBD55 G
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 50

description:
PNIBD50 A
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 46

description:
PNIBD46 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 43

description:
PNIBD43 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 38

description:
PNIBD38 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 37

description:
PNIBD37 E
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 36

description:
PNIBD36 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 45

description:
PNIBD45 G
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 39

description:
PNIBD39 E
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 41

description:
PNIBD41 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 52

description:
PNIBD52 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 53

description:
PNIBD53 E
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 42

description:
PNIBD42 E
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 54

description:
PNIBD54 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 44

description:
PNIBD44 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 35

description:
PNIBD35 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 40

description:
PNIBD40 A
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 34

description:
PNIBD34 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 33

description:
PNIBD33 C
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 30

description:
PNIBD30 A
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 31

description:
PNIBD31 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 29

description:
PNIBD29 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 28

description:
PNIBD28 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 27

description:
PNIBD27 F
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 26

description:
PNIBD26 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 25

description:
PNIBD25 A
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 24

description:
PNIBD24 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 20

description:
PNIBD20 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 21

description:
PNIBD21 E
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: MV4:11 RNA-seq C6 rep1

description:
Cells were treated for 72 hours. Cells were washed in PBS then lysed in 500 uL Trizol. Total RNA was isolated using the Zymo Research Direct-zol RNA MiniPrep kit with on-column DNase digestion following the manufacturers instructions. Library preparation with rRNA depletion and paired-end 150 base pair sequencing on an Illumina HiSeq 30000 was performed by GENEWIZ. Prior to sequencing RNA integrity was assesed by 2100 Bioanlyser (Agilent) and concentration by Qubit assay.
K562-MV411_RNA-seq.count

value: 2 uM C6 for 72 hours


title: Peds NIBD Ileum 19

description:
PNIBD19 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 23

description:
PNIBD23 E
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 13

description:
PNIBD13 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 22

description:
PNIBD22 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 14

description:
PNIBD14 E
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 15

description:
PNIBD15 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 12

description:
PNIBD12 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 03

description:
PNIBD03 A
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 08

description:
PNIBD08 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 09

description:
PNIBD09 A
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 314

description:
PB314 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt

value: Crohn's disease


title: Peds CD Ileum 318

description:
PB318 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 312

description:
PB312 D1
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 07

description:
PNIBD07 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 16

description:
PNIBD16 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 05

description:
PNIBD05 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 319

description:
PB319 G
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 317

description:
PB317 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 10

description:
PNIBD10 G
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 11

description:
PNIBD11 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 02

description:
PNIBD02 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 311

description:
PB311 D1
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 306

description:
PB306 D1
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 18

description:
PNIBD18 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 17

description:
PNIBD17 E
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 227

description:
PB227 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 216

description:
PB216 D1
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Ileum 06

description:
PNIBD06 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 211

description:
PB211 F1
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 213

description:
PB213 D1
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 212

description:
PB212 D1
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 210

description:
PB210 C1
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 202

description:
PB202 D1
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 206

description:
PB206 D1
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 204

description:
PB204 D1
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 143

description:
PB143 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 148

description:
PB148 E
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 207

description:
PB207 C1
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 209

description:
PB209 D1
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 141

description:
PB141 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 150

description:
PB150 E
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 146

description:
PB146 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 147

description:
PB147 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 140

description:
PB140 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 144

description:
PB144 E
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 142

description:
PB142 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 201

description:
PB201 D1
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 145

description:
PB145 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 139

description:
PB139 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 303

description:
PB303 D1
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 137

description:
PB137 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 136

description:
PB136 E
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 135

description:
PB135 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 134

description:
PB134 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 208

description:
PB208 D1
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 132

description:
PB132 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 131

description:
PB131 F
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 129

description:
PB129 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 120

description:
PB120 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 123

description:
PB123 B
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 121

description:
PB121 G
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 128

description:
PB128 A
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 124

description:
PB124 E
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 112

description:
PB112 A1
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 113

description:
PB113 G1
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 109

description:
PB109 D1
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 105

description:
PB105 D1
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 104

description:
PB104 D1
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 108

description:
PB108 D1
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 102

description:
PB102 D1
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 107

description:
PB107 D1
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 114

description:
PB114 D1
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Colon 54

description:
PNIBD54 E
Small RNA
processed data file: pediatric_FFPE_Colon.txt

source_name: Ascending colon mucosal biopsy

value: Ascending colon mucosa


title: Peds NIBD Colon 55

description:
PNIBD55 D
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 56

description:
PNIBD56 F
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Ileum 101

description:
PB101 D1
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Colon 53

description:
PNIBD53 F
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 49

description:
PNIBD49 E
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Ileum 130

description:
PB130 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Colon 47

description:
PNIBD47 F
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Ileum 125

description:
PB125 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds CD Ileum 126

description:
PB126 E
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Colon 45

description:
PNIBD45 D
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Ileum 133

description:
PB133 D
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Colon 43

description:
PNIBD43 E
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Ileum 106

description:
PB106 D1
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Colon 44

description:
PNIBD44 E
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Ileum 111

description:
PB111 E1
Small RNA
processed data file: pediatric_FFPE_Ileum.txt


title: Peds NIBD Colon 41

description:
PNIBD41 E
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 40

description:
PNIBD40 B
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 34

description:
PNIBD34 E
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 35

description:
PNIBD35 E
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 36

description:
PNIBD36 E
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 39

description:
PNIBD39 F
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 37

description:
PNIBD37 F
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 31

description:
PNIBD31 E
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 38

description:
PNIBD38 E
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 30

description:
PNIBD30 B
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 29

description:
PNIBD29 E
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 42

description:
PNIBD42 F
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 27

description:
PNIBD27 D
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 28

description:
PNIBD28 F
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 25

description:
PNIBD25 B
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 23

description:
PNIBD23 F
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 22

description:
PNIBD22 E
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: D. mauritiana_stage5_replicate1

data_processing:
Genome_build:flybase genome used for alignment/processing: dana-all-chromosome-r1.3.fasta Dmau_MS17_all_chromosomes_r.1.0.fa
annotation file used: Dmau_annotation_5_sets_edited.gff6
a preprocessing step using cutadapt removed adapters, barcodes and low quality regions of reads
reads were aligned using Tophat2
transcriptome assembly was carried out using cufflinks
the assemblies were merged using cuffmerge
abundance estimates were calculated with cuffquant (using the merged assemblies) followed by cuffnorm
differential expression was determined using cuffdiff
Supplementary_files_format_and_content: Mean FPKM values for each species at each stage. One file (gene_exp_orthologs_any) provides FPKM values for all genes with any orthology in any species, the other (gene_exp_orthologs_all_14_species_present) provides FPKM values for all genes with one-to-one orthologs in all 14 species. The FPKM value for each gene is the sum of the FPKM values for all isoforms of that gene.

value: replicate 1

value: no


title: Peds NIBD Colon 20

description:
PNIBD20 E
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 18

description:
PNIBD18 E
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 19

description:
PNIBD19 E
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 16

description:
PNIBD16 E
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 21

description:
PNIBD21 F
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 17

description:
PNIBD17 F
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 15

description:
PNIBD15 E
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 13

description:
PNIBD13 E
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 33

description:
PNIBD33 D
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 12

description:
PNIBD12 E
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 24

description:
PNIBD24 E
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 26

description:
PNIBD26 E
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 11

description:
PNIBD11 E
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 14

description:
PNIBD14 F
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 216

description:
PB216 E1
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt

value: Low


title: Peds CD Colon 306

description:
PB306 E1
Small RNA
miR-31 High
processed data file: pediatric_FFPE_Colon.txt

value: High


title: Peds NIBD Colon 09

description:
PNIBD09 B
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 219

description:
PB219 D1
Small RNA
miR-31 High
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 214

description:
PB214 B9
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 217

description:
PB218 D1
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 223

description:
PB223 E1
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 05

description:
PNIBD05 E
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 318

description:
PB318 E
Small RNA
miR-31 High
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 312

description:
PB312 E1
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 311

description:
PB311 E1
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 03

description:
PNIBD03 B
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 317

description:
PB317 E
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 305

description:
PB305 B1
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 222

description:
PB222 D1
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 309

description:
PB309 A1
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 302

description:
PB302 E1
Small RNA
miR-31 High
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 10

description:
PNIBD10 D
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 314

description:
PB314 E
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 303

description:
PB303 E1
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 02

description:
PNIBD02 E
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 319

description:
PB319 D
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 06

description:
PNIBD06 E
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 07

description:
PNIBD07 E
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 227

description:
PB227 E
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 213

description:
PB213 E1
Small RNA
miR-31 High
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 211

description:
PB211 G1
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 308

description:
PB308 D1
Small RNA
miR-31 High
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 212

description:
PB212 F1
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds NIBD Colon 08

description:
PNIBD08 E
Small RNA
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 202

description:
PB202 E1
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 205

description:
PB205 E1
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 150

description:
PB150 G
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 207

description:
PB207 D1
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 206

description:
PB206 E1
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 142

description:
PB142 E
Small RNA
miR-31 High
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 148

description:
PB148 F
Small RNA
miR-31 High
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 147

description:
PB147 E
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 145

description:
PB145 E
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 210

description:
PB210 D1
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 144

description:
PB144 F
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 201

description:
PB201 E1
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 204

description:
PB204 E1
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 139

description:
PB139 E
Small RNA
miR-31 High
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 137

description:
PB137 E
Small RNA
miR-31 High
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 134

description:
PB134 E
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 209

description:
PB209 E1
Small RNA
miR-31 High
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 141

description:
PB141 E
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 132

description:
PB132 E
Small RNA
miR-31 High
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 133

description:
PB133 E
Small RNA
miR-31 High
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 149

description:
PB149 F
Small RNA
miR-31 High
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 208

description:
PB208 E1
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 140

description:
PB140 F
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 130

description:
PB130 F
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 146

description:
PB146 E
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 135

description:
PB135 E
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 136

description:
PB136 F
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 129

description:
PB129 F
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 116

description:
PB116 D1
Small RNA
miR-31 High
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 125

description:
PB125 E
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 123

description:
PB123 C
Small RNA
miR-31 High
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 131

description:
PB131 D
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 121

description:
PB121 D
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 128

description:
PB128 B
Small RNA
miR-31 High
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 115

description:
PB115 D1
Small RNA
miR-31 High
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 120

description:
PB120 E
Small RNA
miR-31 High
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 126

description:
PB126 F
Small RNA
miR-31 High
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 122

description:
PB122 F
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 143

description:
PB143 E
Small RNA
miR-31 High
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 105

description:
PB105 E1
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 109

description:
PB109 E1
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 110

description:
PB110 G1
Small RNA
miR-31 High
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 107

description:
PB107 E1
Small RNA
miR-31 High
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 108

description:
PB108 E1
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 111

description:
PB111 F1
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 103

description:
PB103 G1
Small RNA
miR-31 High
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 124

description:
PB124 F
Small RNA
miR-31 High
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 112

description:
PB112 B1
Small RNA
miR-31 High
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 104

description:
PB104 E1
Small RNA
miR-31 High
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 102

description:
PB102 F1
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 101

description:
PB101 E1
Small RNA
miR-31 High
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 114

description:
PB114 E1
Small RNA
miR-31 High
processed data file: pediatric_FFPE_Colon.txt


title: Peds CD Colon 106

description:
PB106 E1
Small RNA
miR-31 Low
processed data file: pediatric_FFPE_Colon.txt


title: ChIPseq_input_r1(GA4770)

status: Public on Sep 03 2018

first: Keji

last: Zhao

address: 9000 Rockville Pike

department: Systems Biology Center

institute: NHLBI,NIH

description:
Sample 28
HA-H3.3 ChIP in cell cycle arrested cells
PeakCoverageAnnotation.txt
NuRD_H3_ref_eachLevel.txt

data_processing:
ChIP-Seq reads of each library were mapped to the mouse genome (UCSC mm9) (Kent et al., 2002) from the Illumina iGenome database (http://support.illumina.com/sequencing/sequencing_software/igenome.html) using Bowtie (Langmead et al., 2009). Redundant mapped reads were removed. The Model Based Analysis of ChIP-Seq (MACS) (Zhang et al., 2008) version 1.4.2 was used to call peaks with default parameters of model fold between 10 and 30, and P-value cutoff of 1.00e-05. Overlapping peaks of NuRD subunits and H3.3 were merged using the merge function of the Bedtools package (Quinlan, 2014) to generate a reference peak set. Then each reference peak was annotated to be a certain genomic type if its center overlapped with a certain RefSeq genic region, i.e. exon, intron, promoter (3 kb upstream of TSS), 3’UTR, 5’UTR and downstream regions (5 kb downstream of TES). The Refseq genomic annotation of mm9 was downloaded from the UCSC genome browser. Gene Ontology and KEGG enrichment analysis was conducted for multiple peak libraries and combinations of peak existences by using the online tool of g:Profiler (Reimand et al., 2016) with False Discovery Rate(FDR) cutoff of 0.01 (NuRDH3vsH3only 0.05).  A NuRD peak was defined as: NuRD = (MTA1+ or Mbd2/3+) and Rbbp4+.
The reads from RNA-Seq libraries were mapped to the mouse genome (mm9) using TopHat (Trapnell et al., 2009). The gene expression level for each gene and gene isoform was then measured with expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) using Cufflinks (Trapnell et al., 2012). The expression levels of gene isoforms were linked with ChIP-Seq peaks located at TSS regions (-1k~1k) for conjoint analysis.
Differentially expressed genes of wild type/knockdown gene isoforms were identified with the following criteria: first, a comparison between the library of GA6536 and GA6537 vs GA6540 was executed by Cuffdiff, a program of the Cufflinks package; gene isoforms identified as significant differentially expressed were further checked if they met the criterion of: average_fpkm(GA6536&GA6537)<= fpkm(GA6538)<=fpkm(GA6539)<= fpkm(GA6540) or average_fpkm(GA6536&GA6537)>= fpkm(GA6538)>=fpkm(GA6539)>= fpkm(GA6540). Gene Ontology and KEGG enrichment analysis was conducted using the online tool of g:Profiler with FDR no more than 0.05 for up and down regulated genes respectively.
Genome_build: mm9
Supplementary_files_format_and_content: Two processed files for ChIP-seq data of samples #1-7(or 1-10) and 27-30: One is for the peak coverage annotation in tab-delimited text format; the score in matrix indicates the coverage for each reference peak (row) from each sample (column). The second is for the normalized read count in tab-delimited text format; the score in matrix indicates the RPKM for each reference peak (row) from eack sample (column); For other ChIP-seq samples (#8-10, #14-20), txt file contains coordinates and normalized read count for each peak called by MACS2. For Sequential ChIP-seq sample(#12; #13 is treated as control), xls file is the output of MACS2 that contains called peaks and annotations of parameters used. For each RNA-seq sample, txt file contains expression level (fpkm) for each gene.

source_name: NIH/3T3 Tet-On® 3G cells

growth_protocol: NIH/3T3 Tet-On® 3G MEFs (Clontech) were cultured in standard conditions with medium containing 10% FBS.

extract_protocol:
Cells were crosslinked with formaldehyde treatment and chromatin fragmented to 200-300 bp by sonication.
ChIP material was blunt-ended and phosphorylated with the End-it-Repair kit (EPICENTRE). Illumina genome sequencing adaptors were ligated with T4 DNA ligase (New England Biolabs) after addition of adenosine nucleotides, using exo-Klenow. Samples were PCR amplified with multiplexed Illumina genomic DNA sequencing primers. PCR products (250 to 450 bp in size) were gel-purified and submitted for Illumina deep sequencing.

treatment_protocol: FLAG/HA-H3.3 NIH 3T3 fibroblasts (Kraushaar et al., 2013) were cultured with aphidicolin and 2 mg/ml doxycycline

value: NIH/3T3 fibroblast cell line

tag: transduced with

value: HA/FLAG-H3.3 construct

value: wild type

value: HA (Roche)


title: ChIPseq_input_r2(GA4773)

description:
Sample 30
HA-H3.3 ChIP in cell cycle arrested cells
PeakCoverageAnnotation.txt
NuRD_H3_ref_eachLevel.txt


title: ChIPseq_H3.3_r2(GA4767)

description:
Sample 29
HA-H3.3 ChIP in cell cycle arrested cells
PeakCoverageAnnotation.txt
NuRD_H3_ref_eachLevel.txt


title: H3.3KD_Clone_2

description:
Sample 25
RNA-seq in H3.3KD MEFs

extract_protocol:
RNA extraction with Qiagen Rneasy kit
For RNA-Seq library construction, poly-adenylated RNA was isolated from 5 mg of total RNA isolated using the Dynabeads mRNA Direct kit (Invitrogen). Double-stranded cDNA was generated with the Double-stranded cDNA synthesis kit (Invitrogen), sonicated, and subsequently processed exactly like ChIP DNA.

treatment_protocol: FLAG/HA-H3.3 NIH 3T3 fibroblasts (Kraushaar et al., 2013) were cultured with 2 mg/ml doxycycline

value: H3.3 Knockdown


title: Peds CD Colon 113

description:
PB113 F1
Small RNA
miR-31 High
processed data file: pediatric_FFPE_Colon.txt


title: H3.3KD_Clone_1

description:
Sample 24
RNA-seq in H3.3KD MEFs


title: ChIPseq_input_KD

description:
Sample 21
Rbbp4 ChIP in H3.3KD MEFs


title: LUC/LUC_Clone_2

description:
Sample 23
RNA-seq in WT MEFs

value: GFP-Luciferase/OFP-Luciferase


title: H3.3KD_Clone_3

description:
Sample 26
RNA-seq in H3.3KD MEFs


title: ChIPseq_input_WT

description:
Sample 19
Rbbp4 ChIP in WT MEFs


title: ChIPseq_Rbbp4_KD

description:
Sample 20
Rbbp4 ChIP in H3.3KD MEFs

value: Rbbp4 (Abcam, ab79416)


title: ChIPseq_MTA1_WT

description:
Sample 14
MTA1 ChIP in WT MEFs

value: MTA1 (Santa Cruz, sc-9446)


title: ChIPseq_MTA1_KD

description:
Sample 16
MTA1 ChIP in H3.3KD MEFs


title: Sequential_ChIPseq_FLAG-IgG

description:
Sample 13
Sequential FLAG-H3.3/Rbbp4 ChIP

extract_protocol:
Cells were crosslinked with formaldehyde treatment and chromatin fragmented to 200-300 bp by sonication.
For sequential ChIP, 4x107 cells were lysed, and cross-linked DNA was subjected to immunoprecipitation with 50 ul of M2-Flag agarose (Sigma). Agarose beads were washed twice with RIPA buffer, re-suspended in 100 ul TE, followed by elution of the immunocomplexes with 3 ul of 5 g/ul FLAG peptide at 4°C for 2 hours. The supernatant was transferred and re-immunoprecipitated with Rbbp4 antibody (Abcam, ab79416) immobilized to Protein A beads (Dyna) before crosslinking was reversed and protein digested with Proteinase G. ChIP material was blunt-ended and phosphorylated with the End-it-Repair kit (EPICENTRE). Illumina genome sequencing adaptors were ligated with T4 DNA ligase (New England Biolabs) after addition of adenosine nucleotides, using exo-Klenow. Samples were PCR amplified with multiplexed Illumina genomic DNA sequencing primers. PCR products (250 to 450 bp in size) were gel-purified and submitted for Illumina deep sequencing.

value: M2-FLAG (Sigma)/IgG (Santa Cruz)


title: ChIPseq_H3K9ac

description:
Sample 10
Histone modification ChIP
NuRD_H3_ref_eachLevel.txt

value: H3K9ac (Abcam, ab4441)


title: ChIPseq_input_histoneMod

description:
Sample 11
Histone modification ChIP


title: Sequential_ChIPseq_FLAG-Rbbp4

description:
Sample 12
Sequential FLAG-H3.3/Rbbp4 ChIP

value: M2-FLAG (Sigma)/Rbbp4 (Abcam, ab79416)


title: ChIPseq_Rbbp4

description:
Sample 6
NuRD subunit ChIP
PeakCoverageAnnotation.txt
NuRD_H3_ref_eachLevel.txt


title: ChIPseq_MTA1

description:
Sample 5
NuRD subunit ChIP
PeakCoverageAnnotation.txt
NuRD_H3_ref_eachLevel.txt


title: ChIPseq_H3.3_r1(GA4764)

description:
Sample 27
HA-H3.3 ChIP in cell cycle arrested cells
PeakCoverageAnnotation.txt
NuRD_H3_ref_eachLevel.txt


title: ChIPseq_H3K4me3

description:
Sample 9
Histone modification ChIP
NuRD_H3_ref_eachLevel.txt

value: H3K4me3 (Millipore, 17-614)


title: ChIPseq_input

description:
Sample 7
NuRD subunit ChIP
PeakCoverageAnnotation.txt
NuRD_H3_ref_eachLevel.txt


title: ChIPseq_3T3_Mbd2/3

description:
Sample 4
NuRD subunit ChIP
PeakCoverageAnnotation.txt
NuRD_H3_ref_eachLevel.txt


title: ChIPseq_3T3_HDAC2

description:
Sample 3
NuRD subunit ChIP
PeakCoverageAnnotation.txt
NuRD_H3_ref_eachLevel.txt

value: HDAC2 (Abcam, ab7029)


title: ChIPseq_Rbbp4_WT

description:
Sample 18
Rbbp4 ChIP in WT MEFs


title: ChIPseq_3T3_HDAC1

description:
Sample 2
NuRD subunit ChIP
PeakCoverageAnnotation.txt
NuRD_H3_ref_eachLevel.txt

value: HDAC1 (Abcam, ab7028)


title: ChIPseq_H3K27ac

description:
Sample 8
Histone modification ChIP
NuRD_H3_ref_eachLevel.txt

value: H3K27ac (Abcam, ab4729)


title: PRO-seq Hdac3-KO rep2 [YZ-4]

status: Public on Jul 31 2018

description:
3178-YZ-4
processed data file:
PROseq-pp_gb_normalized_counts.txt
Enhancer.txt

data_processing:
Library strategy: PRO-Seq
After last N removal, adapter trimming and low quality sequence removal by cutadapt, PRO-seq reads longer than 15bp were reversed complemented using FastX tools.
Reverse complements of the trimmed reads were aligned to the human genome mm10 using Bowtie2.
Reads mapped to rRNA loci and reads with mapping quality less than 10 were removed.
Bam files were given to NRSA (http://bioinfo.vanderbilt.edu/NRSA/) to estimate RNA polymerase abundance in proximal-promoter and gene body regions of genes, to calculate pausing index and pausing index alterations, and to detect enhancers and quantify eRNA changes.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes normalized counts for proximal-promoter (ppc) and gene body region (gbc), and density for proximal-promoter (ppd) and gene body (gbd), and tab-delimited text file includes enhancer information

source_name: PRO-seq Hdac3-KO_liver

growth_protocol: Mice containing a conditional allele (fl) and a null allele (-) for Hdac3 were crossed with transgenic mice expressing albumin promoter-driven Cre (Alb-Cre). Offspring from these mice were bred to generate mice expressing WT (+/+) and conditional/null (F/F and F/-) alleles in conjugation with Alb-Cre.

extract_protocol:
Nuclei isolation by douncing in isotonic buffer. Nuclear run-on assays were performed with ATP, UTP, GTP, and biotin-11-CTP or with all 4 biotin-11-NTPs. Nuclei were lyzed with TRIzol, nuclear RNA was extracted and fragmented, and biotinylated RNA was purified with strepavidin magnetic beads, which was followed by 3' adaptor ligation, 5' repair, 5' adaptor ligation, reverse transcription, and PCR full-scale amplification.
Briefly, 20 million nuclei were used for each run-on assay. In vitro nuclear run-on assays were carried out in the presence of 375 uM biotinylated NTPs and 0.5% Sarkosyl at 30°C for 3 min on the day of nuclei isolation. Total nuclear RNA was isolated by Trizol extraction and ethanol precipitation, and RNA pellets were kept in 75% ethanol at -80°C. On the next day, RNA was resuspended and hydrolyzed with 0.2 N NaOH, and biotinylated RNA was purified by streptavidin bead binding. Following adaptor ligation, RNA was reverse transcribed and PCR amplified. DNA libraries were PAGE purified and submitted for sequencing.

tag: strain background

tag: genotype/variation

value: Hdac3 KO

value: day 14

value: liver

tag: molecule subtype

value: nuclear RNA


title: PRO-seq WT rep1 [YZ-1]

description:
3178-YZ-1
processed data file:
PROseq-pp_gb_normalized_counts.txt
Enhancer.txt

source_name: PRO-seq WT_liver

value: wild type


title: PRO-seq Hdac3-KO rep1 [YZ-3]

description:
3178-YZ-3
processed data file:
PROseq-pp_gb_normalized_counts.txt
Enhancer.txt


title: PRO-seq WT rep2 [YZ-2]

description:
3178-YZ-2
processed data file:
PROseq-pp_gb_normalized_counts.txt
Enhancer.txt


title: LUC/LUC_Clone_1

description:
Sample 22
RNA-seq in WT MEFs

value: NIH/3T3 fibroblast cell line


title: PEO1_Clone18

status: Public on Jul 28 2018

city: Cleveland

first: Hyunmin

last: Kim

state: Ohio

address: 10900 Euclid Ave.

department: Department of Genetics and Genome Sciences

institute: Case Western Reserve University

description:
C18
Olaparib resistant  cells cultured in 2uM olaparib

data_processing:
[Hisat2 (version 2.1.0)] Used to map reads to human genome GRCh37
[bedtools] Used to assemble transcripts
[edgeR] Used to identify differenentially expressed genes
[filtering] Genes with zero expression in all samples were excluded
Genome_build: GRCH37/hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized expression values

source_name: PEO1 olaparib-resistant C18 cells

extract_protocol:
RNeasy kit (Qiagen)
RNAlibraries were prepared for sequencing using TruSEQ RNA Sample Prep v4 using standard Illumina protocols.

tag: phenotype

value: Olaparib-resistant


title: PEO1_Clone4

description:
C4
Olaparib resistant  cells cultured in 2uM olaparib

source_name: PEO1 olaparib-resistant C4 cells


title: ChIPseq_3T3_CHD4

description:
Sample 1
NuRD subunit ChIP
PeakCoverageAnnotation.txt
NuRD_H3_ref_eachLevel.txt

value: CHD4 (Abcam, ab70469)


title: PEO1_Clone10

description:
C10
Olaparib resistant  cells cultured in 2uM olaparib

source_name: PEO1 olaparib-resistant C10 cells


title: scMNase-seq_mESC_haploid_GB400770

status: Public on Jul 23 2018

description: scMNase-seq

data_processing:
Basecalls performed using RTA 1.7 or Illumina Casava1.7
Paired-end sequencing reads for 48 scMNase-seq datasets were mapped to mouse genome (mm9) using Bowtie2. Reads with mapping quality (MAPQ) ≤ 10 were removed from further analysis. Discordantly aligned pairs were removed and paired reads were concatenated into fragments. Redundant fragments that mapped to the same location (both ends of fragments) were further removed.
We selected the longest fragments (140-180 bp) as nucleosomes and the shortest (≤80 bp) as subnucleosome-sized particles.
The midpoints of nucleosomes/subnucleosomes-sized particles were defined as their positions.
Genome_build: mm9
Supplementary_files_format_and_content: Plan text file. Non-redundant fragment position. Each line is one fragment. The six columns are chrom, start position, end position, length, alignment score and strand.

source_name: mouse embryonic stem cells

growth_protocol: For growing AN3-12 haploid ES cells, we use cell culture-treated dishes coated with gelatin. Cells were cultured in ES cell media containing LIF (ESGRO, Millipore ESG1107) + 1.5M GSK3i (CHIR9901, Stemgent Inc. S1263)

extract_protocol:
For Micrococcal Nuclease (MNase) digestion, 8 ml diluted MNase (1:3000 in lysis buffer) was added to the sorted single cells and incubated at 37°C for 5 min. The reaction was stopped by addition of 80 ml of Stop Buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 0.15% SDS, 10mM EGTA), 1 ml of 20mg/ml Proteinase K and 5 ml of 6ng/ml circular carrier DNA. Following incubation at 55°C for 1 hour, DNA was purified by Phenol-chloroform extraction and precipitation with ethanol in the presence of glycogen.
Universal adaptors were then ligated to the DNA ends as described by Jin et al (Nature 2015) . The libraries were amplified using indexed primers with the PCR condition: 98°C, 10”; 67°C, 30”; 72°C, 30” for 23 cycles. The fragments between 200bp to 300bp were isolated on E-gel and subjected to paired-end sequencing on Illumina HiSeq2500.

treatment_protocol: Haploid ES cells were FACS sorted using Hoechst 33342 (Sigma B2261) to maintain haploid. Single live cells were sorted by flow cytometer and deposited directly into each tubes of a PCR strip-tube, which containing 32 ml of cell lysis buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 3mM CaCl2, 0.1% Triton X-100).

value: AN3-12 mouse embryonic haploid stem cells

tag: cell number

value: Single cell


title: scMNase-seq_mESC_haploid_GB400767

description: scMNase-seq

tag: cell line


title: PEO1_Clone5

description:
C5
Olaparib resistant  cells cultured in 2uM olaparib

source_name: PEO1 olaparib-resistant C5 cells


title: scMNase-seq_mESC_haploid_GB400763

description: scMNase-seq


title: scMNase-seq_mESC_haploid_GB400761

description: scMNase-seq


title: scMNase-seq_mESC_haploid_GB400772

description: scMNase-seq


title: scMNase-seq_mESC_haploid_GB400751

description: scMNase-seq


title: scMNase-seq_NIH3T3_MNase2.4U_GB4007119

description: scMNase-seq

source_name: NIH/3T3 tet-on 3G cells

growth_protocol: NIH/3T3 cells were maintained in culture medium DMEM (Invitrogen cat# 10566-016) supplemented with 10% FBS (Sigma cat# F4135-500ML) and 100U/ml Penicillin-Streptomycin (Invitrogen cat# 15140-122).

extract_protocol:
2.4 units of MNase was added to 5 million of NIH/3T3 cells in 1ml of cell lysis buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 3mM CaCl2, 0.1% Triton X-100) and incubated at 37°C for 5 min. The reaction was stopped by adding 5mM of EDTA and spin down. Wash once with FACS buffer. Single cell were sorted by flow cytometer into 100ul of Stop Buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 0.15% SDS, 10mM EGTA) includ 1 µl of 20mg/ml Proteinase K. Following incubation at 65°C for overnight, DNA was purified by Phenol-chloroform extraction and precipitation with ethanol in the presence of glycogen.
Universal adaptors were then ligated to the DNA ends as described by Jin et al (Nature 2015) . The libraries were amplified using indexed primers with the PCR condition: 98°C, 10”; 67°C, 30”; 72°C, 30” for 23 cycles. The fragments between 200bp to 300bp were isolated on E-gel and subjected to paired-end sequencing on Illumina HiSeq2500.

treatment_protocol: Cells were cross-linked with 1% of Formaldehyde in RPMI complete medium.


title: scMNase-seq_NIH3T3_MNase2.4U_GB4007120

description: scMNase-seq


title: scMNase-seq_mESC_haploid_GB400749

description: scMNase-seq


title: scMNase-seq_mESC_haploid_GB400753

description: scMNase-seq


title: scMNase-seq_NIH3T3_MNase2.4U_GB4007115

description: scMNase-seq


title: scMNase-seq_NIH3T3_MNase2.4U_GB4007114

description: scMNase-seq


title: scMNase-seq_NIH3T3_MNase2.4U_GB4007116

description: scMNase-seq


title: scMNase-seq_mESC_haploid_GB400762

description: scMNase-seq


title: scMNase-seq_NIH3T3_MNase2.4U_GB4007113

description: scMNase-seq


title: scMNase-seq_NIH3T3_MNase2.4U_GB4007117

description: scMNase-seq


title: scMNase-seq_NIH3T3_MNase2.4U_GB4007112

description: scMNase-seq


title: scMNase-seq_NIH3T3_MNase2.4U_GB4007111

description: scMNase-seq

extract_protocol:
0.6 units of MNase was added to 5 million of NIH/3T3 cells in 1ml of cell lysis buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 3mM CaCl2, 0.1% Triton X-100) and incubated at 37°C for 5 min. The reaction was stopped by adding 5mM of EDTA and spin down. Wash once with FACS buffer. Single cell were sorted by flow cytometer into 100ul of Stop Buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 0.15% SDS, 10mM EGTA) includ 1 µl of 20mg/ml Proteinase K. Following incubation at 65°C for overnight, DNA was purified by Phenol-chloroform extraction and precipitation with ethanol in the presence of glycogen.
Universal adaptors were then ligated to the DNA ends as described by Jin et al (Nature 2015) . The libraries were amplified using indexed primers with the PCR condition: 98°C, 10”; 67°C, 30”; 72°C, 30” for 23 cycles. The fragments between 200bp to 300bp were isolated on E-gel and subjected to paired-end sequencing on Illumina HiSeq2500.


title: scMNase-seq_NIH3T3_MNase0.6U_GB4007103

description: scMNase-seq


title: scMNase-seq_mESC_haploid_GB400769

description: scMNase-seq


title: scMNase-seq_NIH3T3_MNase0.6U_GB4007100

description: scMNase-seq


title: scMNase-seq_mESC_haploid_GB400765

description: scMNase-seq


title: scMNase-seq_mESC_haploid_GB400764

description: scMNase-seq


title: scMNase-seq_NIH3T3_MNase0.6U_GB4007097

description: scMNase-seq


title: scMNase-seq_NIH3T3_MNase0.6U_GB4007098

description: scMNase-seq


title: scMNase-seq_NIH3T3_MNase0.6U_GB4007090

description: scMNase-seq

tag: mnase concentration

value: 0.1 unit per 1 million cells


title: scMNase-seq_NIH3T3_MNase0.6U_GB4007102

description: scMNase-seq


title: scMNase-seq_NIH3T3_MNase0.1U_GB4007082

description: scMNase-seq

extract_protocol:
0.1 units of MNase was added to 5 million of NIH/3T3 cells in 1ml of cell lysis buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 3mM CaCl2, 0.1% Triton X-100) and incubated at 37°C for 5 min. The reaction was stopped by adding 5mM of EDTA and spin down. Wash once with FACS buffer. Single cell were sorted by flow cytometer into 100ul of Stop Buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 0.15% SDS, 10mM EGTA) includ 1 µl of 20mg/ml Proteinase K. Following incubation at 65°C for overnight, DNA was purified by Phenol-chloroform extraction and precipitation with ethanol in the presence of glycogen.
Universal adaptors were then ligated to the DNA ends as described by Jin et al (Nature 2015) . The libraries were amplified using indexed primers with the PCR condition: 98°C, 10”; 67°C, 30”; 72°C, 30” for 23 cycles. The fragments between 200bp to 300bp were isolated on E-gel and subjected to paired-end sequencing on Illumina HiSeq2500.


title: scMNase-seq_NIH3T3_MNase0.1U_GB4007075

description: scMNase-seq

value: 0.1 unit MNase per 1 million cells


title: scMNase-seq_NIH3T3_MNase0.1U_GB4007079

description: scMNase-seq


title: scMNase-seq_NIH3T3_MNase0.1U_GB4007076

description: scMNase-seq


title: scMNase-seq_NIH3T3_MNase0.1U_GB4007080

description: scMNase-seq


title: scMNase-seq_NIH3T3_MNase0.6U_GB4007089

description: scMNase-seq


title: scMNase-seq_NIH3T3_MNase0.1U_GB4007078

description: scMNase-seq


title: scMNase-seq_NIH3T3_MNase0.6U_GB4007101

description: scMNase-seq


title: scMNase-seq_NIH3T3_MNase0.1U_GB4007074

description: scMNase-seq


title: MNase-seq_mESC_rep2

description: MNase-seq

data_processing:
Basecalls performed using RTA 1.7 or Illumina Casava1.7
Paired-end sequencing reads for 48 scMNase-seq datasets were mapped to mouse genome (mm9) using Bowtie2. Reads with mapping quality (MAPQ) ≤ 10 were removed from further analysis. Discordantly aligned pairs were removed and paired reads were concatenated into fragments. Redundant fragments that mapped to the same location (both ends of fragments) were further removed.
We selected the longest fragments (³140 bp) as nucleosomes and the shortest (≤78 bp) as subnucleosome-sized particles.
The midpoints of nucleosomes/subnucleosomes-sized particles were defined as their positions.
Genome_build: mm9
Supplementary_files_format_and_content: Bed: plain text file. Each line is one fragment. The six columns are chrom, start position, end position, length, alignment score and strand.

growth_protocol: Mouse Naïve CD4+ T cell were isolated from B6 lymph nodes by Mouse Naïve CD4+ T Cell Isolation Kit (STEMCELL TECHNOLOGIES Cat#19765A).  Mouse R1 ES cells were maintained in culture medium DMEM (Invitrogen cat# 10566-016) supplemented with 20% FBS (ATCC Cat#SCRR-30-2020) and ESGRO® (LIF) (MILLIPORE Cat#ESG1107) on EmbryoMax® Primary Mouse Embryo Fibroblasts (MILLIPORE Cat#PMEF-N).

treatment_protocol: For scMNase-seq, single live cells were sorted by flow cytometer and deposited directly into each tubes of a PCR strip-tube, which containing 32 ml of cell lysis buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 3mM CaCl2, 0.1% Triton X-100).

value: R1 mouse ES cells

tag: cell type

value: mouse embryonic stem cells

value: bulk cells


title: scMNase-seq_NIH3T3_MNase0.1U_GB4007073

description: scMNase-seq


title: scMNase-seq_NIH3T3_MNase0.6U_GB4007096

description: scMNase-seq


title: scMNase-seq_NIH3T3_MNase0.6U_GB4007099

description: scMNase-seq


title: scMNase-seq_mESC_GB4405

description: scMNase-seq

treatment_protocol:
single live cells were sorted by flow cytometer and deposited directly into each tubes of a PCR strip-tube, which containing 32 ml of cell lysis buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 3mM CaCl2, 0.1% Triton X-100).
For scMNase-seq, single live cells were sorted by flow cytometer and deposited directly into each tubes of a PCR strip-tube, which containing 32 ml of cell lysis buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 3mM CaCl2, 0.1% Triton X-100).


title: MNase-seq_mESC_rep1

description: MNase-seq


title: scMNase-seq_mESC_GB4406

description: scMNase-seq


title: scMNase-seq_mESC_GB4407

description: scMNase-seq


title: scMNase-seq_mESC_GB4404

description: scMNase-seq


title: scMNase-seq_mESC_GB4403

description: scMNase-seq


title: scMNase-seq_mESC_GB4402

description: scMNase-seq


title: scMNase-seq_NIH3T3_MNase0.1U_GB4007077

description: scMNase-seq


title: scMNase-seq_NIH3T3_MNase0.1U_GB4007081

description: scMNase-seq


title: scMNase-seq_mESC_GB4399

description: scMNase-seq


title: scMNase-seq_mESC_GB4398

description: scMNase-seq


title: scMNase-seq_mESC_GB4400

description: scMNase-seq


title: scMNase-seq_mESC_GB4397

description: scMNase-seq


title: MNase-seq_T_rep1

description: MNase-seq

source_name: naïve CD4 T cells

value: lymph nodes

value: naive CD4 T cells


title: scMNase-seq_mESC_GB4396

description: scMNase-seq


title: scMNase-seq_mESC_GB4393

description: scMNase-seq


title: scMNase-seq_mESC_GB4392

description: scMNase-seq


title: scMNase-seq_mESC_GB4394

description: scMNase-seq


title: MNase-seq_T_rep2

description: MNase-seq


title: scMNase-seq_mESC_GB4390

description: scMNase-seq


title: scMNase-seq_mESC_GB4391

description: scMNase-seq


title: scMNase-seq_mESC_GB4389

description: scMNase-seq


title: scMNase-seq_mESC_GB4386

description: scMNase-seq


title: scMNase-seq_mESC_GB4387

description: scMNase-seq


title: scMNase-seq_mESC_GB4401

description: scMNase-seq


title: scMNase-seq_NIH3T3_MNase2.4U_GB4007118

description: scMNase-seq


title: scMNase-seq_mESC_GB4388

description: scMNase-seq


title: scMNase-seq_mESC_GB4395

description: scMNase-seq


title: scMNase-seq_mESC_GB4384

description: scMNase-seq


title: scMNase-seq_mESC_GB4385

description: scMNase-seq


title: scMNase-seq_mESC_GB4381

description: scMNase-seq


title: scMNase-seq_mESC_GB4382

description: scMNase-seq


title: scMNase-seq_mESC_GB4380

description: scMNase-seq


title: scMNase-seq_mESC_GB4378

description: scMNase-seq


title: scMNase-seq_mESC_GB4375

description: scMNase-seq


title: scMNase-seq_mESC_GB4379

description: scMNase-seq


title: scMNase-seq_mESC_GB4383

description: scMNase-seq


title: scMNase-seq_mESC_GB4374

description: scMNase-seq


title: scMNase-seq_mESC_GB4377

description: scMNase-seq


title: scMNase-seq_mESC_GB2622

description: scMNase-seq


title: scMNase-seq_mESC_GB2623

description: scMNase-seq


title: scMNase-seq_mESC_GB4372

description: scMNase-seq


title: scMNase-seq_mESC_GB2621

description: scMNase-seq


title: scMNase-seq_mESC_GB2619

description: scMNase-seq


title: scMNase-seq_mESC_GB2620

description: scMNase-seq


title: scMNase-seq_mESC_GB2618

description: scMNase-seq


title: scMNase-seq_mESC_GB2617

description: scMNase-seq


title: scMNase-seq_mESC_GB2615

description: scMNase-seq


title: scMNase-seq_mESC_GB2611

description: scMNase-seq


title: scMNase-seq_mESC_GB2616

description: scMNase-seq


title: scMNase-seq_mESC_GB2614

description: scMNase-seq


title: scMNase-seq_mESC_GB2613

description: scMNase-seq


title: scMNase-seq_mESC_GB2612

description: scMNase-seq


title: scMNase-seq_mESC_GB2609

description: scMNase-seq


title: scMNase-seq_mESC_GB4376

description: scMNase-seq


title: scMNase-seq_mESC_GB2610

description: scMNase-seq


title: scMNase-seq_mESC_GB4373

description: scMNase-seq


title: scMNase-seq_mESC_GB2607

description: scMNase-seq


title: scMNase-seq_mESC_GB2603

description: scMNase-seq


title: scMNase-seq_mESC_GB2605

description: scMNase-seq


title: scMNase-seq_mESC_GB2606

description: scMNase-seq


title: scMNase-seq_mESC_GB3789

description: scMNase-seq


title: scMNase-seq_mESC_GB2600

description: scMNase-seq


title: scMNase-seq_mESC_GB3791

description: scMNase-seq


title: scMNase-seq_mESC_GB3787

description: scMNase-seq


title: scMNase-seq_mESC_GB3790

description: scMNase-seq


title: scMNase-seq_mESC_GB3786

description: scMNase-seq


title: scMNase-seq_mESC_GB3785

description: scMNase-seq


title: scMNase-seq_mESC_GB3788

description: scMNase-seq


title: scMNase-seq_mESC_GB3783

description: scMNase-seq


title: scMNase-seq_mESC_GB3782

description: scMNase-seq


title: scMNase-seq_mESC_GB3784

description: scMNase-seq


title: scMNase-seq_mESC_GB3774

description: scMNase-seq


title: scMNase-seq_mESC_GB3780

description: scMNase-seq


title: scMNase-seq_mESC_GB3775

description: scMNase-seq


title: scMNase-seq_mESC_GB3778

description: scMNase-seq


title: scMNase-seq_mESC_GB3779

description: scMNase-seq


title: scMNase-seq_mESC_GB3777

description: scMNase-seq


title: scMNase-seq_mESC_GB3773

description: scMNase-seq


title: scMNase-seq_mESC_GB2608

description: scMNase-seq


title: scMNase-seq_mESC_GB3781

description: scMNase-seq


title: scMNase-seq_mESC_GB3776

description: scMNase-seq


title: scMNase-seq_mESC_GB2602

description: scMNase-seq


title: scMNase-seq_mESC_GB3772

description: scMNase-seq


title: scMNase-seq_mESC_GB3769

description: scMNase-seq


title: scMNase-seq_mESC_GB2604

description: scMNase-seq


title: scMNase-seq_mESC_GB3770

description: scMNase-seq


title: scMNase-seq_mESC_GB3771

description: scMNase-seq


title: scMNase-seq_mESC_GB3767

description: scMNase-seq


title: scMNase-seq_mESC_GB3768

description: scMNase-seq


title: scMNase-seq_mESC_GB3763

description: scMNase-seq


title: scMNase-seq_mESC_GB3765

description: scMNase-seq


title: scMNase-seq_mESC_GB3766

description: scMNase-seq


title: scMNase-seq_mESC_GB3764

description: scMNase-seq


title: scMNase-seq_mESC_GB3761

description: scMNase-seq


title: scMNase-seq_mESC_GB3762

description: scMNase-seq


title: scMNase-seq_mESC_GB3760

description: scMNase-seq


title: scMNase-seq_mESC_GB3756-2

description: scMNase-seq


title: scMNase-seq_mESC_GB3749

description: scMNase-seq


title: scMNase-seq_mESC_GB3751

description: scMNase-seq


title: scMNase-seq_mESC_GB3747

description: scMNase-seq


title: scMNase-seq_mESC_GB3750

description: scMNase-seq


title: scMNase-seq_mESC_GB3756

description: scMNase-seq


title: scMNase-seq_mESC_GB3743

description: scMNase-seq


title: scMNase-seq_mESC_GB3742

description: scMNase-seq


title: scMNase-seq_mESC_GB3755

description: scMNase-seq


title: scMNase-seq_mESC_GB3744

description: scMNase-seq


title: scMNase-seq_mESC_GB3752

description: scMNase-seq


title: scMNase-seq_mESC_GB3741

description: scMNase-seq


title: scMNase-seq_mESC_GB3739

description: scMNase-seq


title: scMNase-seq_mESC_GB3748

description: scMNase-seq


title: scMNase-seq_mESC_GB3746

description: scMNase-seq


title: scMNase-seq_mESC_GB3745

description: scMNase-seq


title: scMNase-seq_mESC_GB3758

description: scMNase-seq


title: scMNase-seq_mESC_GB3759

description: scMNase-seq


title: scMNase-seq_mESC_GB3757

description: scMNase-seq


title: scMNase-seq_mESC_GB3753

description: scMNase-seq


title: scMNase-seq_mESC_GB3738

description: scMNase-seq


title: scMNase-seq_mESC_GB3734

description: scMNase-seq


title: scMNase-seq_mESC_GB3735

description: scMNase-seq


title: scMNase-seq_mESC_GB2601

description: scMNase-seq


title: scMNase-seq_mESC_GB3736

description: scMNase-seq


title: scMNase-seq_mESC_GB3754

description: scMNase-seq


title: scMNase-seq_mESC_GB3731

description: scMNase-seq


title: scMNase-seq_mESC_GB3740

description: scMNase-seq


title: scMNase-seq_mESC_GB3730

description: scMNase-seq


title: scMNase-seq_mESC_GB3737

description: scMNase-seq


title: scMNase-seq_mESC_GB3727

description: scMNase-seq


title: scMNase-seq_mESC_GB3725

description: scMNase-seq


title: scMNase-seq_mESC_GB3724

description: scMNase-seq


title: scMNase-seq_mESC_GB3728

description: scMNase-seq


title: scMNase-seq_mESC_GB3718

description: scMNase-seq


title: scMNase-seq_mESC_GB3717

description: scMNase-seq


title: scMNase-seq_mESC_GB3719

description: scMNase-seq


title: scMNase-seq_mESC_GB3721

description: scMNase-seq


title: scMNase-seq_mESC_GB3716

description: scMNase-seq


title: scMNase-seq_mESC_GB3729

description: scMNase-seq


title: scMNase-seq_mESC_GB3714

description: scMNase-seq


title: scMNase-seq_mESC_GB3715

description: scMNase-seq


title: scMNase-seq_mESC_GB3733

description: scMNase-seq


title: scMNase-seq_mESC_GB3713

description: scMNase-seq


title: scMNase-seq_mESC_GB3712

description: scMNase-seq


title: scMNase-seq_mESC_GB3732

description: scMNase-seq


title: scMNase-seq_mESC_GB3711

description: scMNase-seq


title: scMNase-seq_mESC_GB3720

description: scMNase-seq


title: scMNase-seq_mESC_GB3709

description: scMNase-seq


title: scMNase-seq_mESC_GB3706

description: scMNase-seq


title: scMNase-seq_mESC_GB3708

description: scMNase-seq


title: scMNase-seq_mESC_GB3726

description: scMNase-seq


title: scMNase-seq_mESC_GB3707

description: scMNase-seq


title: scMNase-seq_mESC_GB3710

description: scMNase-seq


title: scMNase-seq_mESC_GB3722

description: scMNase-seq


title: scMNase-seq_mESC_GB3723

description: scMNase-seq


title: scMNase-seq_mESC_GB3703

description: scMNase-seq


title: scMNase-seq_mESC_GB3702

description: scMNase-seq


title: scMNase-seq_mESC_GB3704

description: scMNase-seq


title: scMNase-seq_mESC_GB3701

description: scMNase-seq


title: scMNase-seq_mESC_GB3700

description: scMNase-seq


title: scMNase-seq_mESC_GB3697

description: scMNase-seq


title: scMNase-seq_mESC_GB3696

description: scMNase-seq


title: scMNase-seq_mESC_GB3694

description: scMNase-seq


title: scMNase-seq_mESC_GB3695

description: scMNase-seq


title: scMNase-seq_mESC_GB3692

description: scMNase-seq


title: scMNase-seq_mESC_GB3705

description: scMNase-seq


title: scMNase-seq_mESC_GB3693

description: scMNase-seq


title: scMNase-seq_mESC_GB3699

description: scMNase-seq


title: scMNase-seq_mESC_GB3691

description: scMNase-seq


title: scMNase-seq_mESC_GB3690

description: scMNase-seq


title: scMNase-seq_mESC_GB3689

description: scMNase-seq


title: scMNase-seq_mESC_GB3687

description: scMNase-seq


title: scMNase-seq_mESC_GB3688

description: scMNase-seq


title: scMNase-seq_mESC_GB3685

description: scMNase-seq


title: scMNase-seq_mESC_GB3683

description: scMNase-seq


title: scMNase-seq_mESC_GB3686

description: scMNase-seq


title: scMNase-seq_mESC_GB3682

description: scMNase-seq


title: scMNase-seq_mESC_GB3679

description: scMNase-seq


title: scMNase-seq_mESC_GB3684

description: scMNase-seq


title: scMNase-seq_mESC_GB3681

description: scMNase-seq


title: scMNase-seq_mESC_GB3676

description: scMNase-seq


title: scMNase-seq_mESC_GB3677

description: scMNase-seq


title: scMNase-seq_mESC_GB3680

description: scMNase-seq


title: scMNase-seq_mESC_GB3678

description: scMNase-seq


title: scMNase-seq_mESC_GB3674

description: scMNase-seq


title: scMNase-seq_mESC_GB3698

description: scMNase-seq


title: scMNase-seq_mESC_GB3673

description: scMNase-seq


title: scMNase-seq_mESC_GB3672

description: scMNase-seq


title: scMNase-seq_mESC_GB3671

description: scMNase-seq


title: scMNase-seq_mESC_GB3668

description: scMNase-seq


title: scMNase-seq_mESC_GB3669

description: scMNase-seq


title: scMNase-seq_mESC_GB3675

description: scMNase-seq


title: scMNase-seq_mESC_GB3666

description: scMNase-seq


title: scMNase-seq_mESC_GB3670

description: scMNase-seq


title: scMNase-seq_mESC_GB3664

description: scMNase-seq


title: scMNase-seq_mESC_GB3663

description: scMNase-seq


title: scMNase-seq_mESC_GB3661

description: scMNase-seq


title: scMNase-seq_mESC_GB3662

description: scMNase-seq


title: scMNase-seq_mESC_GB3660

description: scMNase-seq


title: scMNase-seq_mESC_GB3659

description: scMNase-seq


title: scMNase-seq_mESC_GB3658

description: scMNase-seq


title: scMNase-seq_mESC_GB3654

description: scMNase-seq


title: scMNase-seq_mESC_GB3651

description: scMNase-seq


title: scMNase-seq_mESC_GB3653

description: scMNase-seq


title: scMNase-seq_mESC_GB3655

description: scMNase-seq


title: scMNase-seq_mESC_GB3650

description: scMNase-seq


title: scMNase-seq_mESC_GB3652

description: scMNase-seq


title: scMNase-seq_mESC_GB3649

description: scMNase-seq


title: scMNase-seq_T_GB4371

description: scMNase-seq


title: scMNase-seq_T_GB4367

description: scMNase-seq


title: scMNase-seq_T_GB4369

description: scMNase-seq


title: scMNase-seq_mESC_GB3667

description: scMNase-seq


title: scMNase-seq_mESC_GB3665

description: scMNase-seq


title: scMNase-seq_T_GB4366

description: scMNase-seq


title: scMNase-seq_T_GB4365

description: scMNase-seq


title: scMNase-seq_T_GB4370

description: scMNase-seq


title: scMNase-seq_T_GB4363

description: scMNase-seq


title: scMNase-seq_T_GB4368

description: scMNase-seq


title: scMNase-seq_T_GB4359

description: scMNase-seq


title: scMNase-seq_T_GB4364

description: scMNase-seq


title: scMNase-seq_T_GB4360

description: scMNase-seq


title: scMNase-seq_T_GB4362

description: scMNase-seq


title: scMNase-seq_T_GB4358

description: scMNase-seq


title: scMNase-seq_mESC_GB3656

description: scMNase-seq


title: scMNase-seq_T_GB4357

description: scMNase-seq


title: scMNase-seq_mESC_GB3657

description: scMNase-seq


title: scMNase-seq_T_GB4356

description: scMNase-seq


title: scMNase-seq_T_GB4354

description: scMNase-seq


title: scMNase-seq_T_GB4353

description: scMNase-seq


title: scMNase-seq_T_GB4361

description: scMNase-seq


title: scMNase-seq_T_GB4351

description: scMNase-seq


title: scMNase-seq_T_GB4349

description: scMNase-seq


title: scMNase-seq_T_GB4352

description: scMNase-seq


title: scMNase-seq_T_GB4347

description: scMNase-seq


title: scMNase-seq_T_GB4345

description: scMNase-seq


title: scMNase-seq_T_GB4346

description: scMNase-seq


title: scMNase-seq_T_GB4344

description: scMNase-seq


title: scMNase-seq_T_GB4341

description: scMNase-seq


title: scMNase-seq_T_GB4342

description: scMNase-seq


title: scMNase-seq_T_GB4350

description: scMNase-seq


title: scMNase-seq_T_GB4339

description: scMNase-seq


title: scMNase-seq_T_GB4343

description: scMNase-seq


title: scMNase-seq_T_GB4340

description: scMNase-seq


title: scMNase-seq_T_GB4336

description: scMNase-seq


title: scMNase-seq_T_GB4334

description: scMNase-seq


title: scMNase-seq_T_GB4335

description: scMNase-seq


title: scMNase-seq_T_GB4355

description: scMNase-seq


title: scMNase-seq_T_GB4337

description: scMNase-seq


title: scMNase-seq_T_GB4348

description: scMNase-seq


title: scMNase-seq_T_GB4328

description: scMNase-seq


title: scMNase-seq_T_GB4325

description: scMNase-seq


title: scMNase-seq_T_GB4327

description: scMNase-seq


title: scMNase-seq_T_GB4329

description: scMNase-seq


title: scMNase-seq_T_GB4330

description: scMNase-seq


title: scMNase-seq_T_GB4332

description: scMNase-seq


title: scMNase-seq_T_GB4326

description: scMNase-seq


title: scMNase-seq_T_GB4331

description: scMNase-seq


title: scMNase-seq_T_GB4333

description: scMNase-seq


title: scMNase-seq_T_GB4324

description: scMNase-seq


title: scMNase-seq_T_GB4323

description: scMNase-seq


title: scMNase-seq_T_GB4321

description: scMNase-seq


title: scMNase-seq_T_GB4322

description: scMNase-seq


title: scMNase-seq_T_GB4338

description: scMNase-seq


title: scMNase-seq_T_GB4319

description: scMNase-seq


title: scMNase-seq_T_GB4320

description: scMNase-seq


title: scMNase-seq_T_GB4316

description: scMNase-seq


title: scMNase-seq_T_GB4318

description: scMNase-seq


title: scMNase-seq_T_GB4317

description: scMNase-seq


title: scMNase-seq_T_GB4314

description: scMNase-seq


title: scMNase-seq_T_GB4313

description: scMNase-seq


title: scMNase-seq_T_GB4315

description: scMNase-seq


title: scMNase-seq_T_GB4312

description: scMNase-seq


title: scMNase-seq_T_GB4310

description: scMNase-seq


title: scMNase-seq_T_GB4309

description: scMNase-seq


title: scMNase-seq_T_GB4311

description: scMNase-seq


title: scMNase-seq_T_GB4306

description: scMNase-seq


title: scMNase-seq_T_GB4308

description: scMNase-seq


title: scMNase-seq_T_GB4307

description: scMNase-seq


title: scMNase-seq_T_GB4305

description: scMNase-seq


title: scMNase-seq_T_GB4302

description: scMNase-seq


title: scMNase-seq_T_GB4303

description: scMNase-seq


title: scMNase-seq_T_GB4304

description: scMNase-seq


title: scMNase-seq_T_GB4301

description: scMNase-seq


title: scMNase-seq_T_GB4300

description: scMNase-seq


title: scMNase-seq_T_GB3648

description: scMNase-seq


title: scMNase-seq_T_GB3646

description: scMNase-seq


title: scMNase-seq_T_GB3647

description: scMNase-seq


title: scMNase-seq_T_GB3642

description: scMNase-seq


title: scMNase-seq_T_GB3643

description: scMNase-seq


title: scMNase-seq_T_GB3638

description: scMNase-seq


title: scMNase-seq_T_GB3639

description: scMNase-seq


title: scMNase-seq_T_GB3641

description: scMNase-seq


title: scMNase-seq_T_GB3645

description: scMNase-seq


title: scMNase-seq_T_GB3640

description: scMNase-seq


title: scMNase-seq_T_GB3637

description: scMNase-seq


title: scMNase-seq_T_GB3635

description: scMNase-seq


title: scMNase-seq_T_GB3636

description: scMNase-seq


title: scMNase-seq_T_GB3633

description: scMNase-seq


title: scMNase-seq_T_GB3632

description: scMNase-seq


title: scMNase-seq_T_GB3630

description: scMNase-seq


title: scMNase-seq_T_GB3628

description: scMNase-seq


title: scMNase-seq_T_GB3627

description: scMNase-seq


title: scMNase-seq_T_GB3625

description: scMNase-seq


title: scMNase-seq_T_GB3626

description: scMNase-seq


title: scMNase-seq_T_GB3620

description: scMNase-seq


title: scMNase-seq_T_GB3623

description: scMNase-seq


title: scMNase-seq_T_GB3621

description: scMNase-seq


title: scMNase-seq_T_GB3624

description: scMNase-seq


title: scMNase-seq_T_GB3618

description: scMNase-seq


title: scMNase-seq_T_GB3619

description: scMNase-seq


title: scMNase-seq_T_GB3622

description: scMNase-seq


title: scMNase-seq_T_GB3644

description: scMNase-seq


title: scMNase-seq_T_GB3616

description: scMNase-seq


title: scMNase-seq_T_GB3614

description: scMNase-seq


title: scMNase-seq_T_GB3613

description: scMNase-seq


title: scMNase-seq_T_GB3634

description: scMNase-seq


title: scMNase-seq_T_GB3610

description: scMNase-seq


title: scMNase-seq_T_GB3611

description: scMNase-seq


title: scMNase-seq_T_GB3612

description: scMNase-seq


title: scMNase-seq_T_GB3615

description: scMNase-seq


title: scMNase-seq_T_GB3608

description: scMNase-seq


title: scMNase-seq_T_GB3606

description: scMNase-seq


title: scMNase-seq_T_GB3629

description: scMNase-seq


title: scMNase-seq_T_GB3604

description: scMNase-seq


title: scMNase-seq_T_GB3605

description: scMNase-seq


title: scMNase-seq_T_GB3609

description: scMNase-seq


title: scMNase-seq_T_GB3631

description: scMNase-seq


title: scMNase-seq_T_GB3607

description: scMNase-seq


title: scMNase-seq_T_GB3601

description: scMNase-seq


title: scMNase-seq_T_GB3603

description: scMNase-seq


title: scMNase-seq_T_GB3602

description: scMNase-seq


title: scMNase-seq_T_GB3600

description: scMNase-seq


title: scMNase-seq_T_GB3617

description: scMNase-seq


title: scMNase-seq_T_GB3595

description: scMNase-seq


title: scMNase-seq_T_GB3598

description: scMNase-seq


title: scMNase-seq_T_GB3596

description: scMNase-seq


title: scMNase-seq_T_GB3597

description: scMNase-seq


title: scMNase-seq_T_GB3594

description: scMNase-seq


title: scMNase-seq_T_GB3587

description: scMNase-seq


title: scMNase-seq_T_GB3588

description: scMNase-seq


title: scMNase-seq_T_GB3590

description: scMNase-seq


title: scMNase-seq_T_GB3593

description: scMNase-seq


title: scMNase-seq_T_GB3585

description: scMNase-seq


title: scMNase-seq_T_GB3589

description: scMNase-seq


title: scMNase-seq_T_GB3581

description: scMNase-seq


title: scMNase-seq_T_GB3591

description: scMNase-seq


title: scMNase-seq_T_GB3584

description: scMNase-seq


title: scMNase-seq_T_GB3578

description: scMNase-seq


title: scMNase-seq_T_GB3592

description: scMNase-seq


title: scMNase-seq_T_GB3580

description: scMNase-seq


title: scMNase-seq_T_GB3577

description: scMNase-seq


title: scMNase-seq_T_GB3582

description: scMNase-seq


title: scMNase-seq_T_GB3579

description: scMNase-seq


title: scMNase-seq_T_GB3575

description: scMNase-seq


title: scMNase-seq_T_GB3583

description: scMNase-seq


title: scMNase-seq_T_GB3599

description: scMNase-seq


title: scMNase-seq_T_GB3574

description: scMNase-seq


title: scMNase-seq_T_GB3573

description: scMNase-seq


title: scMNase-seq_T_GB3576

description: scMNase-seq


title: scMNase-seq_T_GB3571

description: scMNase-seq


title: scMNase-seq_T_GB3570

description: scMNase-seq


title: scMNase-seq_T_GB3568

description: scMNase-seq


title: scMNase-seq_T_GB3567

description: scMNase-seq


title: scMNase-seq_T_GB3566

description: scMNase-seq


title: scMNase-seq_T_GB3569

description: scMNase-seq


title: scMNase-seq_T_GB3565

description: scMNase-seq


title: scMNase-seq_T_GB3586

description: scMNase-seq


title: scMNase-seq_T_GB3562

description: scMNase-seq


title: scMNase-seq_T_GB3560

description: scMNase-seq


title: scMNase-seq_T_GB3557

description: scMNase-seq


title: scMNase-seq_T_GB3558

description: scMNase-seq


title: scMNase-seq_T_GB3561

description: scMNase-seq


title: scMNase-seq_T_GB3554

description: scMNase-seq


title: scMNase-seq_T_GB3564

description: scMNase-seq


title: scMNase-seq_T_GB3548

description: scMNase-seq


title: scMNase-seq_T_GB3552

description: scMNase-seq


title: scMNase-seq_T_GB3551

description: scMNase-seq


title: scMNase-seq_T_GB3550

description: scMNase-seq


title: scMNase-seq_T_GB3549

description: scMNase-seq


title: scMNase-seq_T_GB3553

description: scMNase-seq


title: scMNase-seq_T_GB3556

description: scMNase-seq


title: scMNase-seq_T_GB3572

description: scMNase-seq


title: scMNase-seq_T_GB3544

description: scMNase-seq


title: scMNase-seq_T_GB3545

description: scMNase-seq


title: scMNase-seq_T_GB3547

description: scMNase-seq


title: scMNase-seq_T_GB3543

description: scMNase-seq


title: scMNase-seq_T_GB3542

description: scMNase-seq


title: scMNase-seq_T_GB3540

description: scMNase-seq


title: scMNase-seq_T_GB3541

description: scMNase-seq


title: scMNase-seq_T_GB3539

description: scMNase-seq


title: scMNase-seq_T_GB3563

description: scMNase-seq


title: scMNase-seq_T_GB3538

description: scMNase-seq


title: scMNase-seq_T_GB3559

description: scMNase-seq


title: scMNase-seq_T_GB3536

description: scMNase-seq


title: scMNase-seq_T_GB3555

description: scMNase-seq


title: scMNase-seq_T_GB3534

description: scMNase-seq


title: scMNase-seq_T_GB3535

description: scMNase-seq


title: scMNase-seq_T_GB3546

description: scMNase-seq


title: scMNase-seq_T_GB3532

description: scMNase-seq


title: scMNase-seq_T_GB3531

description: scMNase-seq


title: scMNase-seq_T_GB3529

description: scMNase-seq


title: scMNase-seq_T_GB3530

description: scMNase-seq


title: scMNase-seq_T_GB3528

description: scMNase-seq


title: scMNase-seq_T_GB3524

description: scMNase-seq


title: scMNase-seq_T_GB3533

description: scMNase-seq


title: scMNase-seq_T_GB3527

description: scMNase-seq


title: scMNase-seq_T_GB3523

description: scMNase-seq


title: scMNase-seq_T_GB3522

description: scMNase-seq


title: scMNase-seq_T_GB3520

description: scMNase-seq


title: scMNase-seq_T_GB3525

description: scMNase-seq


title: scMNase-seq_T_GB3521

description: scMNase-seq


title: scMNase-seq_T_GB3526

description: scMNase-seq


title: scMNase-seq_T_GB3518

description: scMNase-seq


title: scMNase-seq_T_GB3519

description: scMNase-seq


title: scMNase-seq_T_GB3537

description: scMNase-seq


title: scMNase-seq_T_GB3517

description: scMNase-seq


title: scMNase-seq_T_GB3516

description: scMNase-seq


title: scMNase-seq_T_GB3515

description: scMNase-seq


title: scMNase-seq_T_GB3510

description: scMNase-seq


title: scMNase-seq_T_GB3512

description: scMNase-seq


title: scMNase-seq_T_GB3511

description: scMNase-seq


title: scMNase-seq_T_GB3509

description: scMNase-seq


title: scMNase-seq_T_GB3508

description: scMNase-seq


title: scMNase-seq_T_GB3507

description: scMNase-seq


title: scMNase-seq_T_GB3502

description: scMNase-seq


title: scMNase-seq_T_GB3505

description: scMNase-seq


title: scMNase-seq_T_GB3503

description: scMNase-seq


title: scMNase-seq_T_GB3504

description: scMNase-seq


title: scMNase-seq_T_GB3491

description: scMNase-seq


title: scMNase-seq_T_GB3498

description: scMNase-seq


title: scMNase-seq_T_GB3513

description: scMNase-seq


title: scMNase-seq_T_GB3496

description: scMNase-seq


title: scMNase-seq_T_GB3493

description: scMNase-seq


title: scMNase-seq_T_GB3488

description: scMNase-seq


title: scMNase-seq_T_GB3485

description: scMNase-seq


title: scMNase-seq_T_GB3486

description: scMNase-seq


title: scMNase-seq_T_GB3495

description: scMNase-seq


title: scMNase-seq_T_GB3497

description: scMNase-seq


title: scMNase-seq_T_GB3489

description: scMNase-seq


title: scMNase-seq_T_GB3492

description: scMNase-seq


title: scMNase-seq_T_GB3494

description: scMNase-seq


title: scMNase-seq_T_GB3490

description: scMNase-seq


title: scMNase-seq_T_GB3514

description: scMNase-seq


title: scMNase-seq_T_GB3483

description: scMNase-seq


title: scMNase-seq_T_GB3482

description: scMNase-seq


title: scMNase-seq_T_GB3481

description: scMNase-seq


title: scMNase-seq_T_GB3487

description: scMNase-seq


title: scMNase-seq_T_GB3480

description: scMNase-seq


title: scMNase-seq_T_GB3506

description: scMNase-seq


title: scMNase-seq_T_GB3501

description: scMNase-seq


title: scMNase-seq_T_GB3484

description: scMNase-seq


title: scMNase-seq_T_GB3500

description: scMNase-seq


title: scMNase-seq_T_GB3499

description: scMNase-seq


title: scMNase-seq_T_GB3476

description: scMNase-seq


title: scMNase-seq_T_GB3477

description: scMNase-seq


title: scMNase-seq_T_GB3478

description: scMNase-seq


title: scMNase-seq_T_GB3473

description: scMNase-seq


title: scMNase-seq_T_GB3472

description: scMNase-seq


title: scMNase-seq_T_GB3471

description: scMNase-seq


title: scMNase-seq_T_GB3470

description: scMNase-seq


title: scMNase-seq_T_GB3469

description: scMNase-seq


title: scMNase-seq_T_GB3474

description: scMNase-seq


title: scMNase-seq_T_GB1875

description: scMNase-seq


title: scMNase-seq_T_GB1876

description: scMNase-seq


title: scMNase-seq_T_GB1868

description: scMNase-seq


title: scMNase-seq_T_GB1869

description: scMNase-seq


title: scMNase-seq_T_GB1873

description: scMNase-seq


title: scMNase-seq_T_GB1865

description: scMNase-seq


title: scMNase-seq_T_GB1872

description: scMNase-seq


title: scMNase-seq_T_GB1863

description: scMNase-seq


title: scMNase-seq_T_GB1862

description: scMNase-seq


title: scMNase-seq_T_GB1870

description: scMNase-seq


title: scMNase-seq_T_GB1859

description: scMNase-seq


title: scMNase-seq_T_GB1871

description: scMNase-seq


title: scMNase-seq_T_GB3479

description: scMNase-seq


title: scMNase-seq_T_GB1867

description: scMNase-seq


title: scMNase-seq_T_GB1860

description: scMNase-seq


title: scMNase-seq_T_GB1861

description: scMNase-seq


title: scMNase-seq_T_GB1857

description: scMNase-seq


title: scMNase-seq_T_GB3475

description: scMNase-seq


title: scMNase-seq_T_GB1858

description: scMNase-seq


title: scMNase-seq_T_GB1874

description: scMNase-seq


title: scMNase-seq_T_GB1856

description: scMNase-seq


title: scMNase-seq_T_GB1855

description: scMNase-seq


title: scMNase-seq_T_GB1853

description: scMNase-seq


title: scMNase-seq_T_GB1864

description: scMNase-seq


title: scMNase-seq_T_GB1852

description: scMNase-seq


title: scMNase-seq_T_GB1849

description: scMNase-seq


title: scMNase-seq_T_GB1848

description: scMNase-seq


title: scMNase-seq_T_GB1851

description: scMNase-seq


title: scMNase-seq_T_GB1854

description: scMNase-seq


title: scMNase-seq_T_GB1866

description: scMNase-seq


title: scMNase-seq_T_GB1850

description: scMNase-seq


title: scMNase-seq_T_GB1847

description: scMNase-seq


title: scMNase-seq_T_GB1846

description: scMNase-seq


title: scMNase-seq_T_GB1845

description: scMNase-seq


title: scMNase-seq_T_GB1844

description: scMNase-seq


title: scMNase-seq_T_GB1843

description: scMNase-seq


title: scMNase-seq_T_GB1841

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA9232

description: scMNase-seq

extract_protocol:
For Micrococcal Nuclease (MNase) digestion, 8 ml diluted MNase (1:3000 in lysis buffer) was added to the sorted single cells and incubated at 37°C for 5 min. The reaction was stopped by addition of 80 ml of Stop Buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 0.15% SDS, 10mM EGTA), 1 ml of 20mg/ml Proteinase K and 5 ml of 6ng/ml circular carrier DNA. Following incubation at 55°C for 1 hour, DNA was purified by Phenol-chloroform extraction and precipitation with ethanol in the presence of glycogen.
Universal adaptors were then ligated to the DNA ends as described by Jin et al (Nature 2015) . The libraries were amplified using indexed primers with the PCR condition: 98°C, 10”; 67°C, 30”; 72°C, 30” for 23 cycles. The fragments between 160bp to 300bp were isolated on E-gel and subjected to paired-end sequencing on Illumina HiSeq2500.

treatment_protocol: Single live cells were sorted by flow cytometer and deposited directly into each tubes of a PCR strip-tube, which containing 32 ml of cell lysis buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 3mM CaCl2, 0.1% Triton X-100).

value: fibroblast cell line


title: scMNase-seq_NIH3T3_GA9226

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA9231

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA9225

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA9227

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA9228

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA9222

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA9223

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA9224

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA9221

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA9220

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA9218

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA9216

description: scMNase-seq


title: scMNase-seq_NIH3T3_GA9215

description: scMNase-seq