title: ASCL1-KO GSI treatment rep2

description:
G523_CA09_G2_R1
G523_CA09_G2_R2

data_processing:
The quality of the sequence data is assessed using FastQC v.0.11.2
Adaptors are trimmed using using Trimmomatic v0.32
The trimmed reads are also screened for presence of rRNA and mtRNA/DNA sequences using FastQ-Screen v.0.4.3
To assess the read distribution and confirm the strandedness of the alignments we use the RseQC package
The raw trimmed reads are aligned to the reference genome using Tophat v. 2.0.11
Tophat alignments are processed to extract raw read counts for genes using htseq-count v.0.6.1p2
Raw gene counts are loaded and sample-normalized using DESeq v.1.18.0
Two-condition differential expression was done with the edgeR R package, v.3.8.6
Genome_build: UCSC hg19
Supplementary_files_format_and_content: htsqct_tmp.txt file contain raw read counts for genes
Supplementary_files_format_and_content: AllData.txt file contains output from EdgeR analysis and includes logFC, logCPM, LR, Pvalue, FDR, and RPKMs for each gene and for each sample

treatment_protocol: 5 μM L-685,458 or DMSO (control)


title: ASCL1-KO GSI treatment rep3

status: Public on Jul 13 2017

type: SRA

city: Toronto

first: Peter

middle: B

last: Dirks

state: ON

address: 686 Bay St

department: Arthur and Sonia Labatt Brain Tumour Research Centre and Division of Neurosurgery

country: Canada

institute: The Hospital for Sick Children

description:
G523_CA09_G3_R1
G523_CA09_G3_R2

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

growth_protocol: Cells were cultured adherently for 7 days

extract_protocol:
Cells were harvested using Accutase and RNA was extracted using RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tumor

value: glioblastoma

tag: derived cell line

tag: genotype


title: Hepatocellular cancer 1

city: Chengdu

first: Dan

last: Xie

state: Sichuan

address: #17 Renmin Road

department: West China Hospital

country: China

institute: Sichuan University

description: 5hmC capture sequencing of cell free DNA

library_source: genomic

data_processing:
bcl-fastq base-calling
bowtie2 2.2.5 alignment
samtools 0.1.19 filtering
bedtools for reads counting and rpkm calculation
N/A
Genome_build: hg19
Supplementary_files_format_and_content: rpkm matrix

molecule: other

source_name: Hepatocellular cancer 1

growth_protocol: not applicable

extract_protocol:
Samples for healthy subjects were obtained from Stanford blood center. HCC and BrCa patients were recruited in a Stanford University Institutional Review Board-approved protocol. LuCa, PaCa, GBM, GaCa and CoCa patients were recruited in a Sichuan University Institutional Review Board-approved protocol. Blood was collected into EDTA-coated Vacutainers. Plasma was collected from the blood samples after centrifugation at 1,600 × g for 10 min at 4 °C and 16,000 × g at 10 min at 4 °C. cfDNA was extracted using the Circulating Nucleic Acid Kit (Qiagen). Whole blood genomic DNA was extracted using the DNA Mini Kit (Qiagen) and fragmented using dsDNA Fragmentase (NEB) into average 300 bp. DNA was quantified by Qubit Fluorometer (Life Technologies). Cell-free RNA was extracted using the Plasma/Serum Circulating and Exosomal RNA Purification Kit (Norgen). The extracted cell-free RNA was further digested using Baseline-ZERO DNases (Epicentre) and depleted using Ribo-Zero rRNA Removal Kit (Epicentre) according to a protocol from Clontech.
cfDNA (10 ng) or fragmented genomic DNA (1 µg) spiked with amplicons (0.001 pg of each amplicon per 10 ng DNA) was end repaired, 3’-adenylated and ligated to DNA Barcodes (Bioo Scientific) using KAPA Hyper Prep Kit (Kapa Biosystems) according to the manufacturer’s instructions. Ligated DNA was incubated in a 25 µl solution containing 50 mM HEPES buffer (pH 8), 25 mM MgCl2, 100 µM UDP-6-N3-Glc (Active Motif), and 12.5 U βGT (Thermo) for 2 hr at 37 °C. After that, 2.5 μL DBCO-PEG4-biotin (Click Chemistry Tools, 20 mM stock in DMSO) was directly added to the reaction mixture and incubated for 2 hr at 37 °C. Next, 10 µg sheared salmon sperm DNA (Life Technologies) was added into the reaction mixture and the DNA was purified by Micro Bio-Spin 30 Column (Bio–Rad). The purified DNA was incubated with 0.5 µL M270 Streptavidin beads (Life Technologies) pre-blocked with salmon sperm DNA in buffer 1 (5 mM Tris pH 7.5, 0.5 mM EDTA, 1 M NaCl and 0.2% Tween 20) for 30 min. The beads were subsequently undergone three 5-min washes each with buffer 1, buffer 2 (buffer 1 without NaCl), buffer 3 (buffer 1 with pH 9) and buffer 4 (buffer 3 without NaCl). All binding and washing were done at room temperature with gentle rotation. Beads were then resuspended in water and amplified with 14 (cfDNA) or 9 (blood genomic DNA) cycles of PCR amplification using Phusion DNA polymerase (NEB). The PCR products were purified using AMPure XP beads. Separate input libraries were made by direct PCR from ligated DNA without labeling and capture. Pair-end 75 bp sequencing was performed on the NextSeq instrument.

treatment_protocol: not applicable

tag: sample name

tag: tissue

value: blood

tag: target molecule

value: cell-free DNA


title: Lung cancer 15

source_name: Lung cancer 15


title: Hepatocellular cancer 14

source_name: Hepatocellular cancer 14


title: ASCL1-KO GSI treatment rep1

description:
G523_CA09_G1_R1
G523_CA09_G1_R2


title: Hepatocellular cancer 3

source_name: Hepatocellular cancer 3


title: ASCL1-KO control treatment rep3

description:
G523_CA09_D3_R1
G523_CA09_D3_R2


title: Prmt5i_1

city: Houston

first: Margarida

last: Almeida Santos

state: Texas

address: 1515 Holcombe Blvd Mail code 1000

department: Epigenetics and Molecular Carcinogenesis

country: USA

institute: UT MD Anderson Cancer Center

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads were mapped to the mouse genome (mm10) by TopHat (version 2.0.10).
The number of fragments in each known gene from RefSeq database (downloaded from UCSC Genome Browser on July 17, 2015) was enumerated using htseq-count from HTSeq package (version 0.6.0).
Genes with less than 10 fragments in all the samples were removed, and then the normalized fragment count for each gene was calculated by R/Bioconductor package DESeq (version 1.16.0).
Genome_build: mm10
Supplementary_files_format_and_content: The first column is gene symbol. The other columns are normalized expression values (estimated by DESeq) for all the samples.

molecule: polyA RNA

organism: Mus musculus

source_name: MLL-ENL/NrasG12D cells

growth_protocol: Mouse MLL-ENL/NrasG12D cells were kindly provided by I. Zuber and were cultured in RPMI-1640 (Gibco-Invitrogen) supplemented with 10% FBS, 100 U/ml penicillin and 100 mg/ml streptomycin.

extract_protocol:
Cells were spun down and washed once with cold PBS, then RNA isolated with a QIAGEN RNeasy kit (Cat# 74104) according to the manufacturer’s protocol.
RNA-Seq sequencing libraries were made from MLL-ENL/RasG12D cells following Illumina TruSeq Stranded mRNA kit according to the manufacturer’s protocol.

treatment_protocol: The PRMT5 inhibitor was dissolved in DMSO at the concentration of 5 mM and the cells were treated with the compound at the final concentration of 5 μM. The cells for control were treated with equal concentration of DMSO. The cells were treated again on Day 2. At the end of each treatment period, cells were counted using the Nexcelom Cellometer and AOPI staining. Relative proliferation rates were calculated by normalizing to the rate of DMSO-treated cells.

tag: cell type

value: MLL-fusion  leukemia cells

tag: treatment

value: PRMT5 inhibitor-treated


title: Lung cancer 14

source_name: Lung cancer 14


title: P_normal

city: Beijing

first: Zongmin

last: Du

address: No. 20, Fengtai Dongdajie Street

institute: Beijing Institute of Microbiology and Epidemiology

data_processing:
Illumina Casava1.7 software used for basecalling.
Data filtering were performed as follows:1 ) Remove reads with adaptor sequences; 2). Remove reads in which the percentage of unknown bases (N) is greater than 10%; 3). Remove low quality reads. If the percentage of the low quality base (base with quality value ≤ 5) is greater than 50% in a read, this read is defined as low quality. No more than 2 mismatches were allowed in the alignment.
Fragments per kilobase of exon per million fragments mapped (FPKM) method is used in calculated expression level (Mortazavi et al., 2008)
BWA (Burrows-Wheeler Aligner) (Li et al., 2009) was used to map clean reads to the mouse reference genome (NCBI37/mm9) and Bowtie1 (Langmead et al., 2009) was used to map clean reads to reference gene.
Genome_build: NCBI37/mm9

source_name: none (uninfected)_spleen

extract_protocol:
Groups of mice infected with strain 201 or EV76 were killed at 12, 48 and 72 hpi, and lungs, liver and spleen of infected mice were collected. Approximately 100 mg of tissue was immediately immersed into 1.5 ml RNAlater solution. Samples were then stored at 4 ºC for RNA isolation experiments. Pools of lungs, liver and spleen tissues containing at least 8 mice per duration of infection were homogenized in homogenizer. TTotal RNA were purified from the lungs, liver and spleen using a TRIzol reagent  and treated with RNAse free DNase I. Agilent 2100 Bioanalyzer and the Agilent RNA 6000 Nano kit were used to detect RNA integrity number, rRNA ratio (28S/18S), and the concentration of the total RNA samples.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Female mice were anesthetized by intraperitoneal injection of 100 μl of 0.2% amobarbital solution, and then 10 μl of suspensions containing 1×10^5 colony form unit (cfu) bacteria were loaded into the mouse nasal cavity using a pipette. Seven groups of mice (n=10 each) were infected with strain 201, EV76, or uninfected.

tag: strain

value: Balb/C

tag: age

value: 6-8 weeks

tag: gender

value: female

tag: infected with

value: none (uninfected)

value: spleen


title: F_normal

source_name: none (uninfected)_lung

value: lung


title: G_normal

source_name: none (uninfected)_liver

value: liver


title: DMSO_2

value: DMSO Control


title: ASCL1-KO control treatment rep2

description:
G523_CA09_D2_R1
G523_CA09_D2_R2


title: ASCL1-KO control treatment rep1

description:
G523_CA09_D1_R1
G523_CA09_D1_R2


title: Lung cancer 11

source_name: Lung cancer 11


title: WT GSI treatment rep3

description:
G523_CC06_G3_R1
G523_CC06_G3_R2

value: wildtype


title: P_EV_12

source_name: Y. pestis strain EV76_12 hpi_spleen

value: fully virulent Yersinia pestis strain EV76

tag: time point

value: 12 hpi


title: WT_Interphase_3

city: Tokyo

first: Yasutaka

last: Kakui

address: 1-21-1 Nishiwaseda, Shinjuku-ku

country: Japan

institute: Waseda Institute for Advanced Study

description: Hi-C

data_processing:
Read Trimming. When present, reads were trimmed to until immediately after the first occurrence of a DpnII site (GATC). Read pairs where either read was shorter than 20bp were discarded.
Alignment. Each read in the pair was independently aligned to build ASM294v2.21 of the Pombe genome using the BWA-mem algorithm (version 0.7.12).
1st Pair Filter. Read pairs were either read was unmapped or had a mapping quality of <10 were discarded.
2nd Pair Filter. Reads pairs that were mapped concordantly, within a 2kb region of the genome, were discarded.
3rd Pair Filter. Duplicate read pairs were discarded. Duplicate read pairs are defined as reads where the mapped read start site, read end site and read strand are identical for each read in the pair.
4th Pair Filter. Read pairs were either read start site was >1kb of the downstream DpnII restriction site were discarded.
Identification of frag-end ligations. Ligation events are defined as occurring between the centre of the downstream DpnII sites of the remaining mapped pairs.
Generation of count matrix. Chromosomes I, II and III were split into equally sized bins of the desired size. Where the chromosome length was not a multiple of the bin size, bases at either end of the chromosome were ignored. A zero-matrix was then generated where each row and column is assigned to an individual bin. Each cell in the matrix therefore represents a ligation event occurring between DpnII sites contained within the column and row bins. The matrix is then completed by adding 1 to the value of each cell covering the observed frag-end ligations.
Normalisation of the count matrices. Count matrices, covering the regions of interest, are extracted. Within bin ligations (self-ligations) are removed by setting the diagonal values to zero. Bins containing a low number of interactions are also set to zero. Where matrices are to be compared, any bins with a low count in any individual matrix is removed from all matrices within the sample sample group. The modified count matrix is then normalised using the iterative correction algorythm described by Imakaev et al, Nature Methods, 2012, 9(10):999-1003.
Genome_build: ASM294v2.21
Supplementary_files_format_and_content: Processed files are gzipped compressed text files containing the normalised count matrices for all samples at X different bin sizes.
Supplementary_files_format_and_content: ----------------------------
Supplementary_files_format_and_content: NGS-8177.2000.Genome.500.noself.normMatrix.gz: sample NGS-8177, bin size 2000, region Chromosome I, II & III, minimum count 500
Supplementary_files_format_and_content: NGS-8177.2000.I_ArmL.500.noself.normMatrix.gz: sample NGS-8177, bin size 2000, region Left arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8177.2000.I_ArmR.500.noself.normMatrix.gz: sample NGS-8177, bin size 2000, region Right arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8177.2000.II_ArmL.500.noself.normMatrix.gz: sample NGS-8177, bin size 2000, region Left arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8177.2000.II_ArmR.500.noself.normMatrix.gz: sample NGS-8177, bin size 2000, region Right arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8177.2000.III_ArmL.500.noself.normMatrix.gz: sample NGS-8177, bin size 2000, region Left arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8177.2000.III_ArmR.500.noself.normMatrix.gz: sample NGS-8177, bin size 2000, region Right arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8177.5000.I_ArmL.1000.noself.normMatrix.gz: sample NGS-8177, bin size 5000, region Left arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8177.5000.I_ArmR.1000.noself.normMatrix.gz: sample NGS-8177, bin size 5000, region Right arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8177.5000.II_ArmL.1000.noself.normMatrix.gz: sample NGS-8177, bin size 5000, region Left arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8177.5000.II_ArmR.1000.noself.normMatrix.gz: sample NGS-8177, bin size 5000, region Right arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8177.5000.III_ArmL.1000.noself.normMatrix.gz: sample NGS-8177, bin size 5000, region Left arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8177.5000.III_ArmR.1000.noself.normMatrix.gz: sample NGS-8177, bin size 5000, region Right arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8178.2000.Genome.500.noself.normMatrix.gz: sample NGS-8178, bin size 2000, region Chromosome I, II & III, minimum count 500
Supplementary_files_format_and_content: NGS-8178.2000.I_ArmL.500.noself.normMatrix.gz: sample NGS-8178, bin size 2000, region Left arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8178.2000.I_ArmR.500.noself.normMatrix.gz: sample NGS-8178, bin size 2000, region Right arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8178.2000.II_ArmL.500.noself.normMatrix.gz: sample NGS-8178, bin size 2000, region Left arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8178.2000.II_ArmR.500.noself.normMatrix.gz: sample NGS-8178, bin size 2000, region Right arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8178.2000.III_ArmL.500.noself.normMatrix.gz: sample NGS-8178, bin size 2000, region Left arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8178.2000.III_ArmR.500.noself.normMatrix.gz: sample NGS-8178, bin size 2000, region Right arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8178.5000.I_ArmL.1000.noself.normMatrix.gz: sample NGS-8178, bin size 5000, region Left arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8178.5000.I_ArmR.1000.noself.normMatrix.gz: sample NGS-8178, bin size 5000, region Right arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8178.5000.II_ArmL.1000.noself.normMatrix.gz: sample NGS-8178, bin size 5000, region Left arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8178.5000.II_ArmR.1000.noself.normMatrix.gz: sample NGS-8178, bin size 5000, region Right arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8178.5000.III_ArmL.1000.noself.normMatrix.gz: sample NGS-8178, bin size 5000, region Left arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8178.5000.III_ArmR.1000.noself.normMatrix.gz: sample NGS-8178, bin size 5000, region Right arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8179.2000.Genome.500.noself.normMatrix.gz: sample NGS-8179, bin size 2000, region Chromosome I, II & III, minimum count 500
Supplementary_files_format_and_content: NGS-8179.2000.I_ArmL.500.noself.normMatrix.gz: sample NGS-8179, bin size 2000, region Left arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8179.2000.I_ArmR.500.noself.normMatrix.gz: sample NGS-8179, bin size 2000, region Right arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8179.2000.II_ArmL.500.noself.normMatrix.gz: sample NGS-8179, bin size 2000, region Left arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8179.2000.II_ArmR.500.noself.normMatrix.gz: sample NGS-8179, bin size 2000, region Right arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8179.2000.III_ArmL.500.noself.normMatrix.gz: sample NGS-8179, bin size 2000, region Left arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8179.2000.III_ArmR.500.noself.normMatrix.gz: sample NGS-8179, bin size 2000, region Right arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8179.5000.I_ArmL.1000.noself.normMatrix.gz: sample NGS-8179, bin size 5000, region Left arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8179.5000.I_ArmR.1000.noself.normMatrix.gz: sample NGS-8179, bin size 5000, region Right arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8179.5000.II_ArmL.1000.noself.normMatrix.gz: sample NGS-8179, bin size 5000, region Left arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8179.5000.II_ArmR.1000.noself.normMatrix.gz: sample NGS-8179, bin size 5000, region Right arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8179.5000.III_ArmL.1000.noself.normMatrix.gz: sample NGS-8179, bin size 5000, region Left arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8179.5000.III_ArmR.1000.noself.normMatrix.gz: sample NGS-8179, bin size 5000, region Right arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8309.2000.Genome.500.noself.normMatrix.gz: sample NGS-8309, bin size 2000, region Chromosome I, II & III, minimum count 500
Supplementary_files_format_and_content: NGS-8309.2000.I_ArmL.500.noself.normMatrix.gz: sample NGS-8309, bin size 2000, region Left arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8309.2000.I_ArmR.500.noself.normMatrix.gz: sample NGS-8309, bin size 2000, region Right arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8309.2000.II_ArmL.500.noself.normMatrix.gz: sample NGS-8309, bin size 2000, region Left arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8309.2000.II_ArmR.500.noself.normMatrix.gz: sample NGS-8309, bin size 2000, region Right arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8309.2000.III_ArmL.500.noself.normMatrix.gz: sample NGS-8309, bin size 2000, region Left arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8309.2000.III_ArmR.500.noself.normMatrix.gz: sample NGS-8309, bin size 2000, region Right arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8309.5000.I_ArmL.1000.noself.normMatrix.gz: sample NGS-8309, bin size 5000, region Left arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8309.5000.I_ArmR.1000.noself.normMatrix.gz: sample NGS-8309, bin size 5000, region Right arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8309.5000.II_ArmL.1000.noself.normMatrix.gz: sample NGS-8309, bin size 5000, region Left arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8309.5000.II_ArmR.1000.noself.normMatrix.gz: sample NGS-8309, bin size 5000, region Right arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8309.5000.III_ArmL.1000.noself.normMatrix.gz: sample NGS-8309, bin size 5000, region Left arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8309.5000.III_ArmR.1000.noself.normMatrix.gz: sample NGS-8309, bin size 5000, region Right arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8310.2000.Genome.500.noself.normMatrix.gz: sample NGS-8310, bin size 2000, region Chromosome I, II & III, minimum count 500
Supplementary_files_format_and_content: NGS-8310.2000.I_ArmL.500.noself.normMatrix.gz: sample NGS-8310, bin size 2000, region Left arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8310.2000.I_ArmR.500.noself.normMatrix.gz: sample NGS-8310, bin size 2000, region Right arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8310.2000.II_ArmL.500.noself.normMatrix.gz: sample NGS-8310, bin size 2000, region Left arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8310.2000.II_ArmR.500.noself.normMatrix.gz: sample NGS-8310, bin size 2000, region Right arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8310.2000.III_ArmL.500.noself.normMatrix.gz: sample NGS-8310, bin size 2000, region Left arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8310.2000.III_ArmR.500.noself.normMatrix.gz: sample NGS-8310, bin size 2000, region Right arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8310.5000.I_ArmL.1000.noself.normMatrix.gz: sample NGS-8310, bin size 5000, region Left arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8310.5000.I_ArmR.1000.noself.normMatrix.gz: sample NGS-8310, bin size 5000, region Right arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8310.5000.II_ArmL.1000.noself.normMatrix.gz: sample NGS-8310, bin size 5000, region Left arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8310.5000.II_ArmR.1000.noself.normMatrix.gz: sample NGS-8310, bin size 5000, region Right arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8310.5000.III_ArmL.1000.noself.normMatrix.gz: sample NGS-8310, bin size 5000, region Left arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8310.5000.III_ArmR.1000.noself.normMatrix.gz: sample NGS-8310, bin size 5000, region Right arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8311.2000.Genome.500.noself.normMatrix.gz: sample NGS-8311, bin size 2000, region Chromosome I, II & III, minimum count 500
Supplementary_files_format_and_content: NGS-8311.2000.I_ArmL.500.noself.normMatrix.gz: sample NGS-8311, bin size 2000, region Left arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8311.2000.I_ArmR.500.noself.normMatrix.gz: sample NGS-8311, bin size 2000, region Right arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8311.2000.II_ArmL.500.noself.normMatrix.gz: sample NGS-8311, bin size 2000, region Left arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8311.2000.II_ArmR.500.noself.normMatrix.gz: sample NGS-8311, bin size 2000, region Right arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8311.2000.III_ArmL.500.noself.normMatrix.gz: sample NGS-8311, bin size 2000, region Left arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8311.2000.III_ArmR.500.noself.normMatrix.gz: sample NGS-8311, bin size 2000, region Right arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8311.5000.I_ArmL.1000.noself.normMatrix.gz: sample NGS-8311, bin size 5000, region Left arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8311.5000.I_ArmR.1000.noself.normMatrix.gz: sample NGS-8311, bin size 5000, region Right arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8311.5000.II_ArmL.1000.noself.normMatrix.gz: sample NGS-8311, bin size 5000, region Left arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8311.5000.II_ArmR.1000.noself.normMatrix.gz: sample NGS-8311, bin size 5000, region Right arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8311.5000.III_ArmL.1000.noself.normMatrix.gz: sample NGS-8311, bin size 5000, region Left arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8311.5000.III_ArmR.1000.noself.normMatrix.gz: sample NGS-8311, bin size 5000, region Right arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8464.2000.Genome.500.noself.normMatrix.gz: sample NGS-8464, bin size 2000, region Chromosome I, II & III, minimum count 500
Supplementary_files_format_and_content: NGS-8464.2000.I_ArmL.500.noself.normMatrix.gz: sample NGS-8464, bin size 2000, region Left arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8464.2000.I_ArmR.500.noself.normMatrix.gz: sample NGS-8464, bin size 2000, region Right arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8464.2000.II_ArmL.500.noself.normMatrix.gz: sample NGS-8464, bin size 2000, region Left arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8464.2000.II_ArmR.500.noself.normMatrix.gz: sample NGS-8464, bin size 2000, region Right arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8464.2000.III_ArmL.500.noself.normMatrix.gz: sample NGS-8464, bin size 2000, region Left arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8464.2000.III_ArmR.500.noself.normMatrix.gz: sample NGS-8464, bin size 2000, region Right arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8464.5000.I_ArmL.1000.noself.normMatrix.gz: sample NGS-8464, bin size 5000, region Left arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8464.5000.I_ArmR.1000.noself.normMatrix.gz: sample NGS-8464, bin size 5000, region Right arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8464.5000.II_ArmL.1000.noself.normMatrix.gz: sample NGS-8464, bin size 5000, region Left arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8464.5000.II_ArmR.1000.noself.normMatrix.gz: sample NGS-8464, bin size 5000, region Right arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8464.5000.III_ArmL.1000.noself.normMatrix.gz: sample NGS-8464, bin size 5000, region Left arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8464.5000.III_ArmR.1000.noself.normMatrix.gz: sample NGS-8464, bin size 5000, region Right arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8465.2000.Genome.500.noself.normMatrix.gz: sample NGS-8465, bin size 2000, region Chromosome I, II & III, minimum count 500
Supplementary_files_format_and_content: NGS-8465.2000.I_ArmL.500.noself.normMatrix.gz: sample NGS-8465, bin size 2000, region Left arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8465.2000.I_ArmR.500.noself.normMatrix.gz: sample NGS-8465, bin size 2000, region Right arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8465.2000.II_ArmL.500.noself.normMatrix.gz: sample NGS-8465, bin size 2000, region Left arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8465.2000.II_ArmR.500.noself.normMatrix.gz: sample NGS-8465, bin size 2000, region Right arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8465.2000.III_ArmL.500.noself.normMatrix.gz: sample NGS-8465, bin size 2000, region Left arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8465.2000.III_ArmR.500.noself.normMatrix.gz: sample NGS-8465, bin size 2000, region Right arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8465.5000.I_ArmL.1000.noself.normMatrix.gz: sample NGS-8465, bin size 5000, region Left arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8465.5000.I_ArmR.1000.noself.normMatrix.gz: sample NGS-8465, bin size 5000, region Right arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8465.5000.II_ArmL.1000.noself.normMatrix.gz: sample NGS-8465, bin size 5000, region Left arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8465.5000.II_ArmR.1000.noself.normMatrix.gz: sample NGS-8465, bin size 5000, region Right arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8465.5000.III_ArmL.1000.noself.normMatrix.gz: sample NGS-8465, bin size 5000, region Left arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8465.5000.III_ArmR.1000.noself.normMatrix.gz: sample NGS-8465, bin size 5000, region Right arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8466.2000.Genome.500.noself.normMatrix.gz: sample NGS-8466, bin size 2000, region Chromosome I, II & III, minimum count 500
Supplementary_files_format_and_content: NGS-8466.2000.I_ArmL.500.noself.normMatrix.gz: sample NGS-8466, bin size 2000, region Left arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8466.2000.I_ArmR.500.noself.normMatrix.gz: sample NGS-8466, bin size 2000, region Right arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8466.2000.II_ArmL.500.noself.normMatrix.gz: sample NGS-8466, bin size 2000, region Left arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8466.2000.II_ArmR.500.noself.normMatrix.gz: sample NGS-8466, bin size 2000, region Right arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8466.2000.III_ArmL.500.noself.normMatrix.gz: sample NGS-8466, bin size 2000, region Left arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8466.2000.III_ArmR.500.noself.normMatrix.gz: sample NGS-8466, bin size 2000, region Right arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8466.5000.I_ArmL.1000.noself.normMatrix.gz: sample NGS-8466, bin size 5000, region Left arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8466.5000.I_ArmR.1000.noself.normMatrix.gz: sample NGS-8466, bin size 5000, region Right arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8466.5000.II_ArmL.1000.noself.normMatrix.gz: sample NGS-8466, bin size 5000, region Left arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8466.5000.II_ArmR.1000.noself.normMatrix.gz: sample NGS-8466, bin size 5000, region Right arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8466.5000.III_ArmL.1000.noself.normMatrix.gz: sample NGS-8466, bin size 5000, region Left arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8466.5000.III_ArmR.1000.noself.normMatrix.gz: sample NGS-8466, bin size 5000, region Right arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8467.2000.Genome.500.noself.normMatrix.gz: sample NGS-8467, bin size 2000, region Chromosome I, II & III, minimum count 500
Supplementary_files_format_and_content: NGS-8467.2000.I_ArmL.500.noself.normMatrix.gz: sample NGS-8467, bin size 2000, region Left arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8467.2000.I_ArmR.500.noself.normMatrix.gz: sample NGS-8467, bin size 2000, region Right arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8467.2000.II_ArmL.500.noself.normMatrix.gz: sample NGS-8467, bin size 2000, region Left arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8467.2000.II_ArmR.500.noself.normMatrix.gz: sample NGS-8467, bin size 2000, region Right arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8467.2000.III_ArmL.500.noself.normMatrix.gz: sample NGS-8467, bin size 2000, region Left arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8467.2000.III_ArmR.500.noself.normMatrix.gz: sample NGS-8467, bin size 2000, region Right arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8467.5000.I_ArmL.1000.noself.normMatrix.gz: sample NGS-8467, bin size 5000, region Left arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8467.5000.I_ArmR.1000.noself.normMatrix.gz: sample NGS-8467, bin size 5000, region Right arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8467.5000.II_ArmL.1000.noself.normMatrix.gz: sample NGS-8467, bin size 5000, region Left arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8467.5000.II_ArmR.1000.noself.normMatrix.gz: sample NGS-8467, bin size 5000, region Right arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8467.5000.III_ArmL.1000.noself.normMatrix.gz: sample NGS-8467, bin size 5000, region Left arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8467.5000.III_ArmR.1000.noself.normMatrix.gz: sample NGS-8467, bin size 5000, region Right arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8468.2000.Genome.500.noself.normMatrix.gz: sample NGS-8468, bin size 2000, region Chromosome I, II & III, minimum count 500
Supplementary_files_format_and_content: NGS-8468.2000.I_ArmL.500.noself.normMatrix.gz: sample NGS-8468, bin size 2000, region Left arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8468.2000.I_ArmR.500.noself.normMatrix.gz: sample NGS-8468, bin size 2000, region Right arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8468.2000.II_ArmL.500.noself.normMatrix.gz: sample NGS-8468, bin size 2000, region Left arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8468.2000.II_ArmR.500.noself.normMatrix.gz: sample NGS-8468, bin size 2000, region Right arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8468.2000.III_ArmL.500.noself.normMatrix.gz: sample NGS-8468, bin size 2000, region Left arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8468.2000.III_ArmR.500.noself.normMatrix.gz: sample NGS-8468, bin size 2000, region Right arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8468.5000.I_ArmL.1000.noself.normMatrix.gz: sample NGS-8468, bin size 5000, region Left arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8468.5000.I_ArmR.1000.noself.normMatrix.gz: sample NGS-8468, bin size 5000, region Right arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8468.5000.II_ArmL.1000.noself.normMatrix.gz: sample NGS-8468, bin size 5000, region Left arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8468.5000.II_ArmR.1000.noself.normMatrix.gz: sample NGS-8468, bin size 5000, region Right arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8468.5000.III_ArmL.1000.noself.normMatrix.gz: sample NGS-8468, bin size 5000, region Left arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8468.5000.III_ArmR.1000.noself.normMatrix.gz: sample NGS-8468, bin size 5000, region Right arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8469.2000.Genome.500.noself.normMatrix.gz: sample NGS-8469, bin size 2000, region Chromosome I, II & III, minimum count 500
Supplementary_files_format_and_content: NGS-8469.2000.I_ArmL.500.noself.normMatrix.gz: sample NGS-8469, bin size 2000, region Left arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8469.2000.I_ArmR.500.noself.normMatrix.gz: sample NGS-8469, bin size 2000, region Right arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8469.2000.II_ArmL.500.noself.normMatrix.gz: sample NGS-8469, bin size 2000, region Left arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8469.2000.II_ArmR.500.noself.normMatrix.gz: sample NGS-8469, bin size 2000, region Right arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8469.2000.III_ArmL.500.noself.normMatrix.gz: sample NGS-8469, bin size 2000, region Left arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8469.2000.III_ArmR.500.noself.normMatrix.gz: sample NGS-8469, bin size 2000, region Right arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8469.5000.I_ArmL.1000.noself.normMatrix.gz: sample NGS-8469, bin size 5000, region Left arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8469.5000.I_ArmR.1000.noself.normMatrix.gz: sample NGS-8469, bin size 5000, region Right arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8469.5000.II_ArmL.1000.noself.normMatrix.gz: sample NGS-8469, bin size 5000, region Left arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8469.5000.II_ArmR.1000.noself.normMatrix.gz: sample NGS-8469, bin size 5000, region Right arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8469.5000.III_ArmL.1000.noself.normMatrix.gz: sample NGS-8469, bin size 5000, region Left arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8469.5000.III_ArmR.1000.noself.normMatrix.gz: sample NGS-8469, bin size 5000, region Right arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8593.2000.Genome.500.noself.normMatrix.gz: sample NGS-8593, bin size 2000, region Chromosome I, II & III, minimum count 500
Supplementary_files_format_and_content: NGS-8593.2000.I_ArmL.500.noself.normMatrix.gz: sample NGS-8593, bin size 2000, region Left arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8593.2000.I_ArmR.500.noself.normMatrix.gz: sample NGS-8593, bin size 2000, region Right arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8593.2000.II_ArmL.500.noself.normMatrix.gz: sample NGS-8593, bin size 2000, region Left arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8593.2000.II_ArmR.500.noself.normMatrix.gz: sample NGS-8593, bin size 2000, region Right arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8593.2000.III_ArmL.500.noself.normMatrix.gz: sample NGS-8593, bin size 2000, region Left arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8593.2000.III_ArmR.500.noself.normMatrix.gz: sample NGS-8593, bin size 2000, region Right arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8593.5000.I_ArmL.1000.noself.normMatrix.gz: sample NGS-8593, bin size 5000, region Left arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8593.5000.I_ArmR.1000.noself.normMatrix.gz: sample NGS-8593, bin size 5000, region Right arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8593.5000.II_ArmL.1000.noself.normMatrix.gz: sample NGS-8593, bin size 5000, region Left arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8593.5000.II_ArmR.1000.noself.normMatrix.gz: sample NGS-8593, bin size 5000, region Right arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8593.5000.III_ArmL.1000.noself.normMatrix.gz: sample NGS-8593, bin size 5000, region Left arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8593.5000.III_ArmR.1000.noself.normMatrix.gz: sample NGS-8593, bin size 5000, region Right arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8594.2000.Genome.500.noself.normMatrix.gz: sample NGS-8594, bin size 2000, region Chromosome I, II & III, minimum count 500
Supplementary_files_format_and_content: NGS-8594.2000.I_ArmL.500.noself.normMatrix.gz: sample NGS-8594, bin size 2000, region Left arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8594.2000.I_ArmR.500.noself.normMatrix.gz: sample NGS-8594, bin size 2000, region Right arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8594.2000.II_ArmL.500.noself.normMatrix.gz: sample NGS-8594, bin size 2000, region Left arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8594.2000.II_ArmR.500.noself.normMatrix.gz: sample NGS-8594, bin size 2000, region Right arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8594.2000.III_ArmL.500.noself.normMatrix.gz: sample NGS-8594, bin size 2000, region Left arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8594.2000.III_ArmR.500.noself.normMatrix.gz: sample NGS-8594, bin size 2000, region Right arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8594.5000.I_ArmL.1000.noself.normMatrix.gz: sample NGS-8594, bin size 5000, region Left arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8594.5000.I_ArmR.1000.noself.normMatrix.gz: sample NGS-8594, bin size 5000, region Right arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8594.5000.II_ArmL.1000.noself.normMatrix.gz: sample NGS-8594, bin size 5000, region Left arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8594.5000.II_ArmR.1000.noself.normMatrix.gz: sample NGS-8594, bin size 5000, region Right arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8594.5000.III_ArmL.1000.noself.normMatrix.gz: sample NGS-8594, bin size 5000, region Left arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8594.5000.III_ArmR.1000.noself.normMatrix.gz: sample NGS-8594, bin size 5000, region Right arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8595.2000.Genome.500.noself.normMatrix.gz: sample NGS-8595, bin size 2000, region Chromosome I, II & III, minimum count 500
Supplementary_files_format_and_content: NGS-8595.2000.I_ArmL.500.noself.normMatrix.gz: sample NGS-8595, bin size 2000, region Left arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8595.2000.I_ArmR.500.noself.normMatrix.gz: sample NGS-8595, bin size 2000, region Right arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8595.2000.II_ArmL.500.noself.normMatrix.gz: sample NGS-8595, bin size 2000, region Left arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8595.2000.II_ArmR.500.noself.normMatrix.gz: sample NGS-8595, bin size 2000, region Right arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8595.2000.III_ArmL.500.noself.normMatrix.gz: sample NGS-8595, bin size 2000, region Left arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8595.2000.III_ArmR.500.noself.normMatrix.gz: sample NGS-8595, bin size 2000, region Right arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8595.5000.I_ArmL.1000.noself.normMatrix.gz: sample NGS-8595, bin size 5000, region Left arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8595.5000.I_ArmR.1000.noself.normMatrix.gz: sample NGS-8595, bin size 5000, region Right arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8595.5000.II_ArmL.1000.noself.normMatrix.gz: sample NGS-8595, bin size 5000, region Left arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8595.5000.II_ArmR.1000.noself.normMatrix.gz: sample NGS-8595, bin size 5000, region Right arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8595.5000.III_ArmL.1000.noself.normMatrix.gz: sample NGS-8595, bin size 5000, region Left arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8595.5000.III_ArmR.1000.noself.normMatrix.gz: sample NGS-8595, bin size 5000, region Right arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8596.2000.Genome.500.noself.normMatrix.gz: sample NGS-8596, bin size 2000, region Chromosome I, II & III, minimum count 500
Supplementary_files_format_and_content: NGS-8596.2000.I_ArmL.500.noself.normMatrix.gz: sample NGS-8596, bin size 2000, region Left arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8596.2000.I_ArmR.500.noself.normMatrix.gz: sample NGS-8596, bin size 2000, region Right arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8596.2000.II_ArmL.500.noself.normMatrix.gz: sample NGS-8596, bin size 2000, region Left arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8596.2000.II_ArmR.500.noself.normMatrix.gz: sample NGS-8596, bin size 2000, region Right arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8596.2000.III_ArmL.500.noself.normMatrix.gz: sample NGS-8596, bin size 2000, region Left arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8596.2000.III_ArmR.500.noself.normMatrix.gz: sample NGS-8596, bin size 2000, region Right arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8596.5000.I_ArmL.1000.noself.normMatrix.gz: sample NGS-8596, bin size 5000, region Left arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8596.5000.I_ArmR.1000.noself.normMatrix.gz: sample NGS-8596, bin size 5000, region Right arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8596.5000.II_ArmL.1000.noself.normMatrix.gz: sample NGS-8596, bin size 5000, region Left arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8596.5000.II_ArmR.1000.noself.normMatrix.gz: sample NGS-8596, bin size 5000, region Right arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8596.5000.III_ArmL.1000.noself.normMatrix.gz: sample NGS-8596, bin size 5000, region Left arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8596.5000.III_ArmR.1000.noself.normMatrix.gz: sample NGS-8596, bin size 5000, region Right arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8597.2000.Genome.500.noself.normMatrix.gz: sample NGS-8597, bin size 2000, region Chromosome I, II & III, minimum count 500
Supplementary_files_format_and_content: NGS-8597.2000.I_ArmL.500.noself.normMatrix.gz: sample NGS-8597, bin size 2000, region Left arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8597.2000.I_ArmR.500.noself.normMatrix.gz: sample NGS-8597, bin size 2000, region Right arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8597.2000.II_ArmL.500.noself.normMatrix.gz: sample NGS-8597, bin size 2000, region Left arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8597.2000.II_ArmR.500.noself.normMatrix.gz: sample NGS-8597, bin size 2000, region Right arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8597.2000.III_ArmL.500.noself.normMatrix.gz: sample NGS-8597, bin size 2000, region Left arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8597.2000.III_ArmR.500.noself.normMatrix.gz: sample NGS-8597, bin size 2000, region Right arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8597.5000.I_ArmL.1000.noself.normMatrix.gz: sample NGS-8597, bin size 5000, region Left arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8597.5000.I_ArmR.1000.noself.normMatrix.gz: sample NGS-8597, bin size 5000, region Right arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8597.5000.II_ArmL.1000.noself.normMatrix.gz: sample NGS-8597, bin size 5000, region Left arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8597.5000.II_ArmR.1000.noself.normMatrix.gz: sample NGS-8597, bin size 5000, region Right arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8597.5000.III_ArmL.1000.noself.normMatrix.gz: sample NGS-8597, bin size 5000, region Left arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8597.5000.III_ArmR.1000.noself.normMatrix.gz: sample NGS-8597, bin size 5000, region Right arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8598.2000.Genome.500.noself.normMatrix.gz: sample NGS-8598, bin size 2000, region Chromosome I, II & III, minimum count 500
Supplementary_files_format_and_content: NGS-8598.2000.I_ArmL.500.noself.normMatrix.gz: sample NGS-8598, bin size 2000, region Left arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8598.2000.I_ArmR.500.noself.normMatrix.gz: sample NGS-8598, bin size 2000, region Right arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-8598.2000.II_ArmL.500.noself.normMatrix.gz: sample NGS-8598, bin size 2000, region Left arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8598.2000.II_ArmR.500.noself.normMatrix.gz: sample NGS-8598, bin size 2000, region Right arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-8598.2000.III_ArmL.500.noself.normMatrix.gz: sample NGS-8598, bin size 2000, region Left arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8598.2000.III_ArmR.500.noself.normMatrix.gz: sample NGS-8598, bin size 2000, region Right arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-8598.5000.I_ArmL.1000.noself.normMatrix.gz: sample NGS-8598, bin size 5000, region Left arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8598.5000.I_ArmR.1000.noself.normMatrix.gz: sample NGS-8598, bin size 5000, region Right arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-8598.5000.II_ArmL.1000.noself.normMatrix.gz: sample NGS-8598, bin size 5000, region Left arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8598.5000.II_ArmR.1000.noself.normMatrix.gz: sample NGS-8598, bin size 5000, region Right arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-8598.5000.III_ArmL.1000.noself.normMatrix.gz: sample NGS-8598, bin size 5000, region Left arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-8598.5000.III_ArmR.1000.noself.normMatrix.gz: sample NGS-8598, bin size 5000, region Right arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-9243.2000.Genome.500.noself.normMatrix.gz: sample NGS-9243, bin size 2000, region Chromosome I, II & III, minimum count 500
Supplementary_files_format_and_content: NGS-9243.2000.I_ArmL.500.noself.normMatrix.gz: sample NGS-9243, bin size 2000, region Left arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-9243.2000.I_ArmR.500.noself.normMatrix.gz: sample NGS-9243, bin size 2000, region Right arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-9243.2000.II_ArmL.500.noself.normMatrix.gz: sample NGS-9243, bin size 2000, region Left arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-9243.2000.II_ArmR.500.noself.normMatrix.gz: sample NGS-9243, bin size 2000, region Right arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-9243.2000.III_ArmL.500.noself.normMatrix.gz: sample NGS-9243, bin size 2000, region Left arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-9243.2000.III_ArmR.500.noself.normMatrix.gz: sample NGS-9243, bin size 2000, region Right arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-9243.5000.I_ArmL.1000.noself.normMatrix.gz: sample NGS-9243, bin size 5000, region Left arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-9243.5000.I_ArmR.1000.noself.normMatrix.gz: sample NGS-9243, bin size 5000, region Right arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-9243.5000.II_ArmL.1000.noself.normMatrix.gz: sample NGS-9243, bin size 5000, region Left arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-9243.5000.II_ArmR.1000.noself.normMatrix.gz: sample NGS-9243, bin size 5000, region Right arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-9243.5000.III_ArmL.1000.noself.normMatrix.gz: sample NGS-9243, bin size 5000, region Left arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-9243.5000.III_ArmR.1000.noself.normMatrix.gz: sample NGS-9243, bin size 5000, region Right arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-9244.2000.Genome.500.noself.normMatrix.gz: sample NGS-9244, bin size 2000, region Chromosome I, II & III, minimum count 500
Supplementary_files_format_and_content: NGS-9244.2000.I_ArmL.500.noself.normMatrix.gz: sample NGS-9244, bin size 2000, region Left arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-9244.2000.I_ArmR.500.noself.normMatrix.gz: sample NGS-9244, bin size 2000, region Right arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-9244.2000.II_ArmL.500.noself.normMatrix.gz: sample NGS-9244, bin size 2000, region Left arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-9244.2000.II_ArmR.500.noself.normMatrix.gz: sample NGS-9244, bin size 2000, region Right arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-9244.2000.III_ArmL.500.noself.normMatrix.gz: sample NGS-9244, bin size 2000, region Left arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-9244.2000.III_ArmR.500.noself.normMatrix.gz: sample NGS-9244, bin size 2000, region Right arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-9244.5000.I_ArmL.1000.noself.normMatrix.gz: sample NGS-9244, bin size 5000, region Left arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-9244.5000.I_ArmR.1000.noself.normMatrix.gz: sample NGS-9244, bin size 5000, region Right arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-9244.5000.II_ArmL.1000.noself.normMatrix.gz: sample NGS-9244, bin size 5000, region Left arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-9244.5000.II_ArmR.1000.noself.normMatrix.gz: sample NGS-9244, bin size 5000, region Right arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-9244.5000.III_ArmL.1000.noself.normMatrix.gz: sample NGS-9244, bin size 5000, region Left arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-9244.5000.III_ArmR.1000.noself.normMatrix.gz: sample NGS-9244, bin size 5000, region Right arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-9245.2000.Genome.500.noself.normMatrix.gz: sample NGS-9245, bin size 2000, region Chromosome I, II & III, minimum count 500
Supplementary_files_format_and_content: NGS-9245.2000.I_ArmL.500.noself.normMatrix.gz: sample NGS-9245, bin size 2000, region Left arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-9245.2000.I_ArmR.500.noself.normMatrix.gz: sample NGS-9245, bin size 2000, region Right arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-9245.2000.II_ArmL.500.noself.normMatrix.gz: sample NGS-9245, bin size 2000, region Left arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-9245.2000.II_ArmR.500.noself.normMatrix.gz: sample NGS-9245, bin size 2000, region Right arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-9245.2000.III_ArmL.500.noself.normMatrix.gz: sample NGS-9245, bin size 2000, region Left arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-9245.2000.III_ArmR.500.noself.normMatrix.gz: sample NGS-9245, bin size 2000, region Right arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-9245.5000.I_ArmL.1000.noself.normMatrix.gz: sample NGS-9245, bin size 5000, region Left arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-9245.5000.I_ArmR.1000.noself.normMatrix.gz: sample NGS-9245, bin size 5000, region Right arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-9245.5000.II_ArmL.1000.noself.normMatrix.gz: sample NGS-9245, bin size 5000, region Left arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-9245.5000.II_ArmR.1000.noself.normMatrix.gz: sample NGS-9245, bin size 5000, region Right arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-9245.5000.III_ArmL.1000.noself.normMatrix.gz: sample NGS-9245, bin size 5000, region Left arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-9245.5000.III_ArmR.1000.noself.normMatrix.gz: sample NGS-9245, bin size 5000, region Right arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-9580.2000.Genome.500.noself.normMatrix.gz: sample NGS-9580, bin size 2000, region Chromosome I, II & III, minimum count 500
Supplementary_files_format_and_content: NGS-9580.2000.I_ArmL.500.noself.normMatrix.gz: sample NGS-9580, bin size 2000, region Left arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-9580.2000.I_ArmR.500.noself.normMatrix.gz: sample NGS-9580, bin size 2000, region Right arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-9580.2000.II_ArmL.500.noself.normMatrix.gz: sample NGS-9580, bin size 2000, region Left arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-9580.2000.II_ArmR.500.noself.normMatrix.gz: sample NGS-9580, bin size 2000, region Right arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-9580.2000.III_ArmL.500.noself.normMatrix.gz: sample NGS-9580, bin size 2000, region Left arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-9580.2000.III_ArmR.500.noself.normMatrix.gz: sample NGS-9580, bin size 2000, region Right arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-9580.5000.I_ArmL.1000.noself.normMatrix.gz: sample NGS-9580, bin size 5000, region Left arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-9580.5000.I_ArmR.1000.noself.normMatrix.gz: sample NGS-9580, bin size 5000, region Right arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-9580.5000.II_ArmL.1000.noself.normMatrix.gz: sample NGS-9580, bin size 5000, region Left arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-9580.5000.II_ArmR.1000.noself.normMatrix.gz: sample NGS-9580, bin size 5000, region Right arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-9580.5000.III_ArmL.1000.noself.normMatrix.gz: sample NGS-9580, bin size 5000, region Left arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-9580.5000.III_ArmR.1000.noself.normMatrix.gz: sample NGS-9580, bin size 5000, region Right arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-9581.2000.Genome.500.noself.normMatrix.gz: sample NGS-9581, bin size 2000, region Chromosome I, II & III, minimum count 500
Supplementary_files_format_and_content: NGS-9581.2000.I_ArmL.500.noself.normMatrix.gz: sample NGS-9581, bin size 2000, region Left arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-9581.2000.I_ArmR.500.noself.normMatrix.gz: sample NGS-9581, bin size 2000, region Right arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-9581.2000.II_ArmL.500.noself.normMatrix.gz: sample NGS-9581, bin size 2000, region Left arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-9581.2000.II_ArmR.500.noself.normMatrix.gz: sample NGS-9581, bin size 2000, region Right arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-9581.2000.III_ArmL.500.noself.normMatrix.gz: sample NGS-9581, bin size 2000, region Left arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-9581.2000.III_ArmR.500.noself.normMatrix.gz: sample NGS-9581, bin size 2000, region Right arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-9581.5000.I_ArmL.1000.noself.normMatrix.gz: sample NGS-9581, bin size 5000, region Left arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-9581.5000.I_ArmR.1000.noself.normMatrix.gz: sample NGS-9581, bin size 5000, region Right arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-9581.5000.II_ArmL.1000.noself.normMatrix.gz: sample NGS-9581, bin size 5000, region Left arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-9581.5000.II_ArmR.1000.noself.normMatrix.gz: sample NGS-9581, bin size 5000, region Right arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-9581.5000.III_ArmL.1000.noself.normMatrix.gz: sample NGS-9581, bin size 5000, region Left arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-9581.5000.III_ArmR.1000.noself.normMatrix.gz: sample NGS-9581, bin size 5000, region Right arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-9582.2000.Genome.500.noself.normMatrix.gz: sample NGS-9582, bin size 2000, region Chromosome I, II & III, minimum count 500
Supplementary_files_format_and_content: NGS-9582.2000.I_ArmL.500.noself.normMatrix.gz: sample NGS-9582, bin size 2000, region Left arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-9582.2000.I_ArmR.500.noself.normMatrix.gz: sample NGS-9582, bin size 2000, region Right arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-9582.2000.II_ArmL.500.noself.normMatrix.gz: sample NGS-9582, bin size 2000, region Left arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-9582.2000.II_ArmR.500.noself.normMatrix.gz: sample NGS-9582, bin size 2000, region Right arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-9582.2000.III_ArmL.500.noself.normMatrix.gz: sample NGS-9582, bin size 2000, region Left arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-9582.2000.III_ArmR.500.noself.normMatrix.gz: sample NGS-9582, bin size 2000, region Right arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-9582.5000.I_ArmL.1000.noself.normMatrix.gz: sample NGS-9582, bin size 5000, region Left arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-9582.5000.I_ArmR.1000.noself.normMatrix.gz: sample NGS-9582, bin size 5000, region Right arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-9582.5000.II_ArmL.1000.noself.normMatrix.gz: sample NGS-9582, bin size 5000, region Left arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-9582.5000.II_ArmR.1000.noself.normMatrix.gz: sample NGS-9582, bin size 5000, region Right arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-9582.5000.III_ArmL.1000.noself.normMatrix.gz: sample NGS-9582, bin size 5000, region Left arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-9582.5000.III_ArmR.1000.noself.normMatrix.gz: sample NGS-9582, bin size 5000, region Right arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-9583.2000.Genome.500.noself.normMatrix.gz: sample NGS-9583, bin size 2000, region Chromosome I, II & III, minimum count 500
Supplementary_files_format_and_content: NGS-9583.2000.I_ArmL.500.noself.normMatrix.gz: sample NGS-9583, bin size 2000, region Left arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-9583.2000.I_ArmR.500.noself.normMatrix.gz: sample NGS-9583, bin size 2000, region Right arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-9583.2000.II_ArmL.500.noself.normMatrix.gz: sample NGS-9583, bin size 2000, region Left arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-9583.2000.II_ArmR.500.noself.normMatrix.gz: sample NGS-9583, bin size 2000, region Right arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-9583.2000.III_ArmL.500.noself.normMatrix.gz: sample NGS-9583, bin size 2000, region Left arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-9583.2000.III_ArmR.500.noself.normMatrix.gz: sample NGS-9583, bin size 2000, region Right arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-9583.5000.I_ArmL.1000.noself.normMatrix.gz: sample NGS-9583, bin size 5000, region Left arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-9583.5000.I_ArmR.1000.noself.normMatrix.gz: sample NGS-9583, bin size 5000, region Right arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-9583.5000.II_ArmL.1000.noself.normMatrix.gz: sample NGS-9583, bin size 5000, region Left arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-9583.5000.II_ArmR.1000.noself.normMatrix.gz: sample NGS-9583, bin size 5000, region Right arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-9583.5000.III_ArmL.1000.noself.normMatrix.gz: sample NGS-9583, bin size 5000, region Left arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-9583.5000.III_ArmR.1000.noself.normMatrix.gz: sample NGS-9583, bin size 5000, region Right arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-9584.2000.Genome.500.noself.normMatrix.gz: sample NGS-9584, bin size 2000, region Chromosome I, II & III, minimum count 500
Supplementary_files_format_and_content: NGS-9584.2000.I_ArmL.500.noself.normMatrix.gz: sample NGS-9584, bin size 2000, region Left arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-9584.2000.I_ArmR.500.noself.normMatrix.gz: sample NGS-9584, bin size 2000, region Right arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-9584.2000.II_ArmL.500.noself.normMatrix.gz: sample NGS-9584, bin size 2000, region Left arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-9584.2000.II_ArmR.500.noself.normMatrix.gz: sample NGS-9584, bin size 2000, region Right arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-9584.2000.III_ArmL.500.noself.normMatrix.gz: sample NGS-9584, bin size 2000, region Left arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-9584.2000.III_ArmR.500.noself.normMatrix.gz: sample NGS-9584, bin size 2000, region Right arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-9584.5000.I_ArmL.1000.noself.normMatrix.gz: sample NGS-9584, bin size 5000, region Left arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-9584.5000.I_ArmR.1000.noself.normMatrix.gz: sample NGS-9584, bin size 5000, region Right arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-9584.5000.II_ArmL.1000.noself.normMatrix.gz: sample NGS-9584, bin size 5000, region Left arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-9584.5000.II_ArmR.1000.noself.normMatrix.gz: sample NGS-9584, bin size 5000, region Right arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-9584.5000.III_ArmL.1000.noself.normMatrix.gz: sample NGS-9584, bin size 5000, region Left arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-9584.5000.III_ArmR.1000.noself.normMatrix.gz: sample NGS-9584, bin size 5000, region Right arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-9585.2000.Genome.500.noself.normMatrix.gz: sample NGS-9585, bin size 2000, region Chromosome I, II & III, minimum count 500
Supplementary_files_format_and_content: NGS-9585.2000.I_ArmL.500.noself.normMatrix.gz: sample NGS-9585, bin size 2000, region Left arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-9585.2000.I_ArmR.500.noself.normMatrix.gz: sample NGS-9585, bin size 2000, region Right arm chromosome I, minimum count 500
Supplementary_files_format_and_content: NGS-9585.2000.II_ArmL.500.noself.normMatrix.gz: sample NGS-9585, bin size 2000, region Left arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-9585.2000.II_ArmR.500.noself.normMatrix.gz: sample NGS-9585, bin size 2000, region Right arm chromosome II, minimum count 500
Supplementary_files_format_and_content: NGS-9585.2000.III_ArmL.500.noself.normMatrix.gz: sample NGS-9585, bin size 2000, region Left arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-9585.2000.III_ArmR.500.noself.normMatrix.gz: sample NGS-9585, bin size 2000, region Right arm chromosome III, minimum count 500
Supplementary_files_format_and_content: NGS-9585.5000.I_ArmL.1000.noself.normMatrix.gz: sample NGS-9585, bin size 5000, region Left arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-9585.5000.I_ArmR.1000.noself.normMatrix.gz: sample NGS-9585, bin size 5000, region Right arm chromosome I, minimum count 1000
Supplementary_files_format_and_content: NGS-9585.5000.II_ArmL.1000.noself.normMatrix.gz: sample NGS-9585, bin size 5000, region Left arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-9585.5000.II_ArmR.1000.noself.normMatrix.gz: sample NGS-9585, bin size 5000, region Right arm chromosome II, minimum count 1000
Supplementary_files_format_and_content: NGS-9585.5000.III_ArmL.1000.noself.normMatrix.gz: sample NGS-9585, bin size 5000, region Left arm chromosome III, minimum count 1000
Supplementary_files_format_and_content: NGS-9585.5000.III_ArmR.1000.noself.normMatrix.gz: sample NGS-9585, bin size 5000, region Right arm chromosome III, minimum count 1000

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: interphase

growth_protocol: Cells were grown in EMM supplemented with glutamate. Culture was separated into interphase sample and mitotic samples. Cells were arrested in mitosis by addition of 5 µg/mL of thiamine with 0.5 mM of NAA, 5 µM of 1NM-PP1, or DMSO.

extract_protocol:
Crosslinked chromatin was digested by DpnII. The sticky ends were filled in by Biotin-14-dATP and the other dNTPs. Proximal ligation was performed in diluted conditions, followed by DNA recovery.
Crosslinked chromatin was immunoprecipitated with anti-HA antibody.
NEBNext Ultra DNA Library Prep kit for Illumina and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) were used for adapter ligation and indexing. Indexed Hi-C library was purified by double selection of SPRI selection beads.

treatment_protocol: Mitotic arrested cells were crosslinked with 0.5 % formaldehyde for 30 minutes at 25 ºC

tag: cell cycle stage

value: interphase

tag: sample group


title: P_EV_48

source_name: Y. pestis strain EV76_48 hpi_spleen

value: 48 hpi


title: WT_Mitosis_3

description: Hi-C

source_name: mitosis

value: mitosis

value: 0.5 mM NAA & 5 ug/mL thiamine


title: Cut14.Inactive_Mitosis_3

description: Hi-C


title: WT GSI treatment rep2

description:
G523_CC06_G2_R1
G523_CC06_G2_R2

value: glioblastoma


title: G_EV_72

source_name: Y. pestis strain EV76_72 hpi_liver

value: 72 hpi


title: Lung cancer 10

source_name: Lung cancer 10

value: blood

value: cell-free DNA


title: Cnd3.Inactive_Mitosis_3

description: Hi-C


title: Cut14.Active_Interphase_3

description: Hi-C


title: Lung cancer 9

source_name: Lung cancer 9


title: Cnd3.Active_Interphase_3

description: Hi-C


title: P_EV_72

source_name: Y. pestis strain EV76_72 hpi_spleen

value: Balb/C

value: 6-8 weeks

value: female


title: Ark1.Active_Interphase_3

description: Hi-C


title: Lung cancer 7

source_name: Lung cancer 7


title: WT control treatment rep2

description:
G523_CC06_D2_R1
G523_CC06_D2_R2


title: F_EV_72

source_name: Y. pestis strain EV76_72 hpi_lung

value: lung


title: WT control treatment rep3

description:
G523_CC06_D3_R1
G523_CC06_D3_R2


title: G_EV_12

source_name: Y. pestis strain EV76_12 hpi_liver

value: liver


title: F_EV_48

source_name: Y. pestis strain EV76_48 hpi_lung


title: Lung cancer 5

source_name: Lung cancer 5


title: F_EV_12

source_name: Y. pestis strain EV76_12 hpi_lung


title: Lung cancer 13

source_name: Lung cancer 13


title: Lung cancer 4

source_name: Lung cancer 4


title: Lung cancer 8

source_name: Lung cancer 8


title: Ark1.Inactive_Mitosis_3

description: Hi-C

source_name: mitosis_ark1 inhibited

value: 5 uM 1NM-PP1 & 5 ug/mL thiamine


title: WT GSI treatment rep1

description:
G523_CC06_G1_R1
G523_CC06_G1_R2

value: wildtype


title: Ark1.Active_Mitosis_3

description: Hi-C

value: DMSO & 5 ug/mL thiamine


title: Lung cancer 12

source_name: Lung cancer 12


title: WT_Mitosis_2

description: Hi-C


title: WT control treatment rep1

description:
G523_CC06_D1_R1
G523_CC06_D1_R2


title: Lung cancer 6

source_name: Lung cancer 6


title: G_122_72

source_name: Y. pestis strain 201_72 hpi_liver

value: fully virulent Yersinia pestis strain 201


title: P_122_48

source_name: Y. pestis strain 201_48 hpi_spleen

value: spleen


title: P_122_72

source_name: Y. pestis strain 201_72 hpi_spleen


title: Lung cancer 3

source_name: Lung cancer 3


title: Lung cancer 2

source_name: Lung cancer 2


title: input of gDNA extracted from healthy control 4 and 5

value: blood-input


title: G_EV_48

source_name: Y. pestis strain EV76_48 hpi_liver

value: fully virulent Yersinia pestis strain EV76

value: 48 hpi


title: Cnd3.InActive_Mitosis_2

description: Hi-C

value: mitosis

value: 0.5 mM NAA & 5 ug/mL thiamine


title: G_122_48

source_name: Y. pestis strain 201_48 hpi_liver


title: Lung cancer 1

source_name: Lung cancer 1

value: blood


title: P_122_12

source_name: Y. pestis strain 201_12 hpi_spleen

value: 12 hpi


title: Cut14.Active_Interphase_2

description: Hi-C

source_name: interphase

value: interphase


title: Cut14.Inactive_Mitosis_2

description: Hi-C


title: WT_Interphase_2

description: Hi-C


title: input from healthy controls

source_name: input from healthy controls

value: input

value: cell-free DNA


title: healthy control 8

source_name: healthy control 8


title: WT_Interphase_1

description: Hi-C


title: F_122_12

source_name: Y. pestis strain 201_12 hpi_lung

value: Balb/C

value: 6-8 weeks

value: female

value: lung


title: Cut14.Active_Interphase_1

description: Hi-C


title: gDNA extracted from healthy control 4 blood cells

value: genomic DNA


title: G_122_12

source_name: Y. pestis strain 201_12 hpi_liver

value: fully virulent Yersinia pestis strain 201

value: liver


title: WT_Mitosis_1

description: Hi-C

source_name: mitosis


title: Cnd3.Inactive_Mitosis_1

description: Hi-C


title: F_122_48

source_name: Y. pestis strain 201_48 hpi_lung


title: F_122_72

source_name: Y. pestis strain 201_72 hpi_lung

value: 72 hpi


title: healthy control 6

source_name: healthy control 6


title: healthy control 7

source_name: healthy control 7


title: healthy control 5 (RNA)

source_name: healthy control 5

value: cell-free RNA


title: Cnd3.Active_Interphase_2

description: Hi-C


title: healthy control 5


title: gDNA extracted from healthy control 5 blood cells


title: Cut14.Inactive_Mitosis_1

description: Hi-C


title: healthy control 4 (RNA)

source_name: healthy control 4


title: healthy control 3

source_name: healthy control 3


title: Ark1.Active_Interphase_2

description: Hi-C


title: Input for Cnd2 ChIP

description:
Control for ChIP-seq
Condensin_peaks.xls

data_processing:
Trimming. Read 1 and read 2 files were trimmed to 50bp
Alignment. Each read in the pair was independently aligned to build ASM294v2.21 of the Pombe genome using the BWA-mem algorithm (version 0.7.12).
Peak identification. Peaks were indentified using Macs2 (version 2.1.0) using the paired input sample as control.
Genome_build: ASM294v2.21
Supplementary_files_format_and_content: An excel spreadsheet summarising parameters and identified ChIP peaks.

growth_protocol: Cells were grown in EMM supplemented with glutamate. Cells were arrested in mitosis by addition of 5 µg/mL of thiamine.

extract_protocol:
Crosslinked chromatin was immunoprecipitated with anti-HA antibody.
NEBNext Ultra DNA Library Prep kit for Illumina and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) were used for adapter ligation and indexing. Indexed Hi-C library was purified by double selection of SPRI selection beads.

value: YUK421 Cnd2-HA

value: 5 µg/mL thiamine


title: Ark1.Inactive_Mitosis_2

description: Hi-C

source_name: mitosis_ark1 inhibited

value: mitosis

value: 5 uM 1NM-PP1 & 5 ug/mL thiamine


title: healthy control 1

source_name: healthy control 1

value: blood


title: Ark1.Active_Mitosis_2

description: Hi-C

value: DMSO & 5 ug/mL thiamine


title: Ark1.Active_Mitosis_1

description: Hi-C


title: healthy control 2

source_name: healthy control 2


title: Ark1.Active_Interphase_1

description: Hi-C

value: interphase


title: Ark1.Inactive_Mitosis_1

description: Hi-C


title: PO_con miRNA-seq 3

city: Qingdao

last: Wang

state: Shandong

address: 106 Nanjing Road

institute: Yellow Sea Fisheries Research Institute, Chinese Academy Fishery Science

data_processing:
Initially, the raw reads were subjected to the Illumina pipeline filter (Solexa 0.3), and the datasets were further processed with an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA), to remove adapter dimers, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats
Subsequently, the remaining clean reads were used to search against miRBase 21.0 (http://www.mirbase.org/search.shtml) for known miRNA prediction. During the alignment, length variation at both the 5’ and 3’ ends and one mismatch inside of the sequence were allowed.
The unmapped sequences were further searched against P. olivaceus genomes using RNAfold software for novel miRNA prediction.
Genome_build: Paralichtys olivaceus genome; https://www.ncbi.nlm.nih.gov/assembly/GCA_001904815.2
Supplementary_files_format_and_content: All expressed miRNAs information

organism: Paralichthys olivaceus

source_name: P. olivaceus_WT_ocular side skin

extract_protocol:
Skins were removed and the total RNAs were extracted using Trizol reagent. Approximately 1 μg RNA of an RNA integrity number (RIN) >7.0 from each sample was used for the subsequent cDNA library construction following the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA). Single-end sequencing (36 bp) was then performed on an Illumina HiSeq 2500 at the LC-BIO (Hangzhou, China) according to the vendor’s recommended protocol.
miRNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: wild type

value: 5 month

value: ocular side skin


title: Cnd3.Active_Interphase_1

description: Hi-C

source_name: interphase


title: PO_alb miRNA-seq 2

source_name: P. olivaceus_albino_ocular side skin

value: albino


title: healthy control 4

value: cell-free DNA


title: PO_alb miRNA-seq 3


title: WT rep3

city: Los Angeles

first: Douglas

middle: L.

last: Black

state: CA

address: 675 Charles E. Young Drive South

department: MIMG

institute: UCLA

data_processing:
Library strategy: RASL-seq
The sequenced 40 bases were mapped to the oligo pool sequences with Blat by allowing 2 mismatch in each of the donor and acceptor sequences.
alternative splicing events with the counts of both isoforms less than 5 were filtered out.
Genome_build: hg18
Supplementary_files_format_and_content: The processed files counts for 2 isoforms of each alternative splicing event and genomic coordinates of oligo probes used for each event.

source_name: Flp-In™ T-REx™ 293 Rbfox2-/- Cell Line

growth_protocol: cells were cultured in DMEM supplemented with 10% fetal bovine serum and L-glutamine. Cells were transfected with plasmids containing Rbfox1 wildtype and its mutant cDNA by BioT according to the manufacturer's instructions

extract_protocol:
Total RNA was extracted from cells using Trizol reagent (Life technologies).
RASL library was constructed according to Li H, et al protocol published Current Protocols in Molecular Biology.

treatment_protocol: 500 ng/ml Doxcycline was added to the cells to induce protein expression for 2 days.

tag: cell line

value: Flp-In(TM) T-REx(TM) 293 Rbfox2-/-

value: Rbfox1 wildtype transfection


title: 10Y rep3

value: Rbfox1 10Y mutant transfection


title: WT rep2


title: FA rep1

value: Rbfox1 FA mutant transfection


title: FA rep3


title: PO_con RNA-seq 3

data_processing:
The clean reads were obtained by removing reads containing adapter, reads containing Poly-N and low quality reads from raw reads
The index of Paralichtys olivaceus genome was built using Bowtie v2.0.6 and clean reads were aligned to Japanese flounder genome using TopHat v2.0.9 for gene mapping and annotation.
The Cufflinks v2.1.1 Reference Annotation Based Transcript (RABT) assembly method was used to construct and identify both known and novel transcripts from TopHat alignment results.
Genome_build: Paralichtys olivaceus genome; https://www.ncbi.nlm.nih.gov/assembly/GCA_001904815.2
Supplementary_files_format_and_content: readcount and normalized readcount for each sample

extract_protocol:
Skins were removed and the total RNAs were extracted using Trizol reagent. A total amount of 3 μg RNA (RIN>7.0) per sample was used for cDNA paired-end libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®. In order to select cDNA fragments of 150-200bp in length, the library fragments were purified with AMPure XP system. 3 μl USER Enzyme was used with size-selected, adaptor-ligated cDNA at 37 oC for 15 min followed by 5 min at 95 oC before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. After cluster generation on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina), the libraries were sequenced on an Illumina Hiseq2000 platform by Novogene Bioinformatics Technology Co. Ltd (Beijing, China) and 100 bp paired-end reads were generated.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: 10Y rep2


title: 10Y rep1


title: FA rep2


title: PO_alb miRNA-seq 1


title: PO_con RNA-seq 2


title: Cnd2 ChIP

description:
ChIP-seq
Condensin_peaks.xls


title: PO_con miRNA-seq 2


title: Ctrl rep3

value: Control


title: PO_con RNA-seq 1


title: Ctrl rep2


title: PO_con miRNA-seq 1


title: Ctrl rep1


title: PO_alb RNA-seq 3


title: PO_alb RNA-seq 2


title: PO_alb RNA-seq 1


title: tdTom_liver_4

status: Public on Jul 12 2017

city: Edinburgh

first: John

middle: Paterson

last: Thomson

address: Crewe Road

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

data_processing:
Paired ends aligned using FASTQ paired-end parser
Quality control and Tophat 2 Alignment
General sequence statistics calculated
Genome_build: mm9
Supplementary_files_format_and_content: .bw

source_name: tdTom p21 over-expressed liver

extract_protocol:
NA extracted using the mirVana™ total RNA isolation protocols (Ambion, Austin, USA).  For RNA quantification, samples were treated with DNase (Ambion) and random hexamer cDNA synthesized by reverse transcription.  Assays-on-demand gene expression TaqMan® MGB 6FAM dye-labeled products (Applied Biosystems) were used for relative quantification of cDNA.
Illumina Tru-seq paired end strand specific sequencing (Illumina, USA) was carried out on a NextSeq-550 sequencer

tag: strain background

value: Male

value: Biliray derived hepatocytes from AAV8-p21 liver


title: SK1 x S288C 6h sample

city: New York

first: Scott

last: Keeney

state: NY

address: 1275 York Ave

department: Molecular Biology Program

institute: Memorial Sloan Kettering Cancer Center

description: Spo11-associated DNA oligonucleotides

data_processing:
Demultiplexing and base calls perfomed using CASAVA v. 1.8.1 (with options--use-bases-mask Y50n,I6n --force) and HiSeq Control Software v.1.4.8 for samples sequenced on Illumina HiSeq 2500
Adapters (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) were clipped from reads using fastx_clipper, part of the FASTX Toolkit 0.0.13.2, with parameters -l 15 -n -v -Q33 -i
First five bases (diffusion primer added in library prep) in each sequence were trimmed and trimmed sequence was recorded in the FASTQ ID tag for downstream tracking
Clipped reads were mapped using SHRiMP 2.1.1b with parameters -N 24 -U -g -1000 -q -1000 -m 10 -i -20 -h 100 -r 50% -n 1 -s 1111111111,11110111101111,1111011100100001111,1111000011001101111 -o 10001 -Q -E --sam-unaligned --strata
Sequences clipped from a read during mapping should be polyC on the 3' end or polyG on the 5' end. If clipped bases were not polyC or polyG the alignment score was corrected by deducting the mismatch score for each non-C,G base in the clipped sequence.
Maps of 5' ends of sequence reads were compiled in R (RStudio version  0.99.893, R version 3.2.4)
Genome_build: Reads were mapped to the SGD assembly released in June 2008, called "sacCer2" by UCSC: http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=340067645
Supplementary_files_format_and_content: wig file includes total unique read count (number of 5' ends of Spo11 oligos that mapped uniquely at a given position) at each non-zero base position in the nuclear genome

organism: Saccharomyces cerevisiae

source_name: meiotic culture

growth_protocol: Synchronized meiotic cultures were prepared in 1% potassium acetate at 30°C by the YPA pre-growth method as described in Lam et al. Methods Mol Bio 1471: 51-98 (2017). Cells were collected at 6 hr after transfer to sporulation medium.

extract_protocol:
As described in Zhu and Keeney, Genetics 201: 525-542 (2015)
As described in Zhu and Keeney, Genetics 201: 525-542 (2015) and Lam et al. Methods Mol Bio 1471: 51-98 (2017).

value: wild type, SPO11-Flag


title: Itbg_mut_liver_4

source_name: Itbg mutant liver

value: Biliray derived hepatocytes from Itgb1 fl/fl liver


title: Itbg_mut_liver_1


title: tdTom_liver_3


title: tdTom_liver_1


title: ductal_cells_3

value: Wild type Bile Ducts


title: ductal_cells_1


title: WT rep1


title: control_hepatocytes_3

source_name: Control mouse hepatocytes

value: Wild type Hepatocytes


title: control_hepatocytes_2


title: met_RHH1648

city: Delhi

first: Debarka

last: Sengupta

state: Delhi

address: IIIT Delhi, Okhla Phase 3

department: Computational Biology and Computer Science

country: India

institute: Indraprastha Institute of Information Technology

description:
Metastatic cancer
PolyA+ RNA
Processed data file: expression.txt

data_processing:
BAM files produced using Tophat-2.1.0.
FPKM obtained using Cuffdiff-2.2.1.
The RefSeq genes are tracked for analysis.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: expression.txt: The tab-delimited text file contains the log2(1+pQ normalized FPKM) expression matrix for all individual cells. For details about pQ normalization, see Sengupta, Debarka, et al. "Fast, scalable and accurate differential expression analysis for single cells." bioRxiv (2016): 049734.

source_name: squamous cell carcinoma, metastatic tumor

extract_protocol:
RNA isolated from cells using the SMARTer Ultra Low RNA Kit for the Fluidigm C1 System (Clontech).
Library construction: In accordance to protocol from Fluidigm describing the use of the C1 system to generate cDNA library for single cell RNA-seq. Briefly, cDNA was synthesized using SMARTer Ultra Low RNA Kit for the Fluidigm C1 System from Clontech; library was constructed using Nextera XT DNA Sample Preparation Kit and Nextera XT DNA Library Preparation Index Kits from Illumina.

tag: disease status

value: squamous cell carcinoma

value: metastatic lymph node tumor

tag: sample type

value: single cell


title: met_RHH1651


title: met_RHH1653


title: met_RHH1658


title: met_RHH1657


title: met_RHH1654


title: met_RHH1647


title: ChIP-seq from embryonic facial prominence (ENCLB710KNT)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR779MSI/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-seq on embryonic 10.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR779MSI
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR682UEM
encode release date: 2016-07-12
lab: Bing Ren, UCSD
library encode accession: ENCLB710KNT
size range: 300-500

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Mus musculus strain B6NCrl embryonic facial prominence tissue mixed sex embryo (10.5 days)

tag: antibody

value: embryonic facial prominence

value: tissue

tag: description

value: Craniofacial prominence from 51 embryonic 10.5 day mice

tag: biosample encode accession

tag: dev stage

value: embryonic

tag: Sex

value: pooled male and female

tag: health state

value: healthy

tag: lab

value: Len Pennacchio, LBNL

tag: link

value: ENCBS199YOQ at ENCODE; https://www.encodeproject.org/ENCBS199YOQ/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from embryonic facial prominence (ENCLB620EIF)

description:
https://www.encodeproject.org/experiments/ENCSR779MSI/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-seq on embryonic 10.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR779MSI
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR682UEM
encode release date: 2016-07-12
lab: Bing Ren, UCSD
library encode accession: ENCLB620EIF
size range: 300-500

value: Craniofacial prominence from 69 embryonic 10.5 day mice

tag: age

value: ENCBS938XWJ at ENCODE; https://www.encodeproject.org/ENCBS938XWJ/


title: met_RHH1645

tag: tissue


title: met_RHH1641


title: met_RHH1640


title: control_hepatocytes_1

tag: gender

value: Male


title: met_RHH1636


title: met_RHH1646


title: Itbg_mut_liver_3

value: Biliray derived hepatocytes from Itgb1 fl/fl liver


title: met_RHH1631


title: met_RHH1628


title: met_RHH1629


title: met_RHH1627


title: met_RHH1626


title: met_RHH1644


title: met_RHH1623


title: met_RHH1619


title: met_RHH1620


title: met_RHH1616


title: met_RHH1615


title: met_RHH1618


title: met_RHH1621


title: met_RHH1624


title: met_RHH1614


title: met_RHH1611


title: met_RHH1617


title: met_RHH1609


title: met_RHH1612


title: met_RHH1610


title: met_RHH1613


title: met_RHH1608


title: met_RHH1607


title: met_RHH1659


title: met_RHH1639


title: met_RHH1622


title: met_RHH1604


title: met_RHH1603


title: met_RHH1605


title: met_RHH1606


title: met_RHH1599


title: met_RHH1597


title: met_RHH1596


title: met_RHH1600


title: met_RHH1590


title: met_RHH1594


title: met_RHH1592


title: met_RHH1593


title: met_RHH1595


title: met_RHH1588


title: met_RHH1591


title: met_RHH1585


title: met_RHH1584


title: met_RHH1587


title: met_RHH1583


title: met_RHH1582


title: met_RHH1581


title: met_RHH1575


title: met_RHH1576


title: met_RHH1574


title: met_RHH1580


title: met_RHH1572


title: hHep-HCV

first: yi

last: wang

address: 27(9) Taiping Road

institute: Beijing Institute of Transfusion Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Paired-end reads were  mapped against the UCSC GRCh38 reference by Tophat with stringent parameters: --coverage-search --microexon-search --b2-very-sensitive. Only unique mapping reads were retained for normalization purposes. Read counts of each gene were summarized using HTSeq version 0.6.1p1. DESeq2 was used to normalize read counts.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include read counts of each gene for each sample

source_name: induced hHep-HCV

growth_protocol: hESC H9 cells were passaged and grown for 1 day in MTeSR (Stem Cell), then cultured in KM (23) with Activin A (100 ng/ml) and Wnt3a (50 ng/ml) for 4 days to induce cells to definitive endoderm (DE) cells. The DE cells were differentiated in HM, Wnt3a (50 ng/ml), FGF4 (30 ng/ml), retinoic acid (RA, 0.1 μM) for 6 days to achieve lineage restrictions to hHpSCs. The hHBs were obtained by treating the hHpSCs with the HM, FGF4 (30 ng/ml), BMP4 (25 ng/ml) and HGF (25 ng/ml) for another 6 days. Finally differentiation to hepatocytes was achieved with HM with HGF (25 ng/ml), OSM (10 ng/ml) and dexamethasone (Dex, 0.1 μM).

extract_protocol:
total RNA (Qiagen, Cat#: 74004) were extracted according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.The library was sequenced using Illumina HiSeq X ten.

treatment_protocol: infected with HCVcc

tag: cell type

value: hESCs-derived hepatic lineage cells


title: met_RHH1571

value: squamous cell carcinoma


title: met_RHH1569

value: metastatic lymph node tumor


title: hHep

source_name: induced hHep


title: PreHep

source_name: induced PreHep


title: PreHep-HCV

source_name: induced PreHep-HCV


title: met_RHH1568

value: single cell


title: HS-HCV

source_name: induced hHpSC-HCV


title: HB

source_name: induced hHB


title: HS

source_name: induced hHpSC


title: primary_RHH1565

description:
Primary cancer
PolyA+ RNA
Processed data file: expression.txt

source_name: squamous cell carcinoma, primary tumor

value: primary tumor


title: met_RHH1566


title: HB-HCV

source_name: induced hHB-HCV


title: primary_RHH1563


title: ductal_cells_4

tag: genotype/variation

value: Wild type Bile Ducts


title: met_RHH1586


title: primary_RHH1564


title: primary_RHH1560


title: primary_RHH1556


title: total RNA-seq from G1E (ENCLB338BVM)

description:
https://www.encodeproject.org/experiments/ENCSR475TDY/
***************
biological replicate number: 2
technical replicate number: 1
description: PSU mouse G1E 100ng rRNA-depeleted RNA-seq via ScriptSeq
experiment encode accession: ENCSR475TDY
assay title: total RNA-seq
assembly: mm10
encode release date: 2017-01-04
lab: Ross Hardison, PennState
library encode accession: ENCLB338BVM
size range: 200-1000
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

source_name: Mus musculus strain C57BL/6J G1E immortalized cell line

tag: line

value: immortalized cell line

value: Gata1- erythroid progenitor

value: postnatal

value: Ross Hardison, PennState

value: 0 day

value: male

value: ENCBS503ARZ at ENCODE; https://www.encodeproject.org/ENCBS503ARZ/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: total RNA-seq from granulocyte monocyte progenitor cell (ENCLB975GRJ)

description:
https://www.encodeproject.org/experiments/ENCSR277DPB/
***************
biological replicate number: 2
technical replicate number: 1
description: PSU mouse GMP 100ng rRNA-depleted RNA-seq via ScriptSeq
experiment encode accession: ENCSR277DPB
assay title: total RNA-seq
assembly: mm10
encode release date: 2017-01-04
lab: Ross Hardison, PennState
library encode accession: ENCLB975GRJ
size range: 200-1000
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

source_name: Mus musculus strain C57BL/6J granulocyte monocyte progenitor primary cell male adult (5-6 weeks)

value: granulocyte monocyte progenitor cell

value: primary cell

value: granulocyte monocyte progenitor

value: adult

value: 5-6 week

value: unknown

value: ENCBS581UFA at ENCODE; https://www.encodeproject.org/ENCBS581UFA/


title: total RNA-seq from G1E (ENCLB924EVD)

description:
https://www.encodeproject.org/experiments/ENCSR475TDY/
***************
biological replicate number: 1
technical replicate number: 1
description: PSU mouse G1E 100ng rRNA-depeleted RNA-seq via ScriptSeq
experiment encode accession: ENCSR475TDY
assay title: total RNA-seq
assembly: mm10
encode release date: 2017-01-04
lab: Ross Hardison, PennState
library encode accession: ENCLB924EVD
size range: 200-1000
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

value: ENCBS159ZTO at ENCODE; https://www.encodeproject.org/ENCBS159ZTO/