title: iNeuron_TDGdegron_dTAG_PBseq_rep2

first: Wei

last: Wu

state: Shanghai

address: 320 yueyang road

department: Center for Excellence in Molecular Cell Science

data_processing:
SAR-seq, END-seq and SEAL reads were aligned to the reference genome (hg19 for human i3Neuron and mm10 for mouse macrophage cells using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1 for END-seq and -n 2 -l 50 -m 1 for the rest. RNA-seq reads were aligned by STAR (v2.7.6a). PB-seq was mapped by BSMAP (v2.90) with parameters -p 10 -w 2 -v 0 -q 30. Functions “view” and “sort” of samtools (v1.11) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools (v2.29.2) bamToBed command. Mitochondrial reads were removed in SAR-seq for intensity comparisons.
Assembly: hg19 for human, mm10 for mourse.
Library strategy: PB-seq

source_name: iNeuron

growth_protocol: For neuronal differentiation, 20–25 million iPSCs were plated on day 0 onto a 15-cm plate in N2 medium (knockout Dulbecco’s modified Eagle’s medium (DMEM)/F12 medium; Life Technologies Corporation, cat. no. 12660012) with N2 supplement (Life Technologies, cat. no. 17502048), 1× GlutaMAX (Thermofisher Scientific, cat. no. 35050061), 1× MEM nonessential amino acids (NEAA) (Thermofisher Scientific, cat. no. 11140050), 10 μM ROCK inhibitor (Y-27632; Selleckchem, cat. no. S1049), and 2 μg/ml doxycycline (Clontech, cat. no. 631311). N2 medium was changed once a day for two more days. On day 3, cells were replated onto freshly prepared dishes coated with freshly prepared poly-L-ornithine (PLO; 0.1 mg/ml; Sigma, cat. no. P3655-10MG). Pre-neuron cells were cultured in i3Neuron Culture Media: BrainPhys media (Stemcell Technologies, cat. no. 05790) supplemented with 1× B27 Plus Supplement (ThermoFisher Scientific, cat. no. A3582801), 10 ng ml−1 BDNF (PeproTech, cat. no. 450-02), 10 ng ml−1 NT-3 (PeproTech, cat. no. 450-03), 1 μg ml−1 mouse laminin (Sigma, cat. no. L2020-1MG), and 2 μg ml−1 doxycycline (Clontech, cat. no. 631311). i3Neurons were then fed by half media change on day 6 and then, collected on day 7. For iMacrophage transdifferentiation, 10 million C10 cells were induced to reprogram by the addition of 100 nM of β-estradiol (Sigma-Aldrich; Cat. #E8875) and grown with 10 ng/ml of IL-3 (Peprotech; Cat. #213-13), CSF-1 (Peprotech; Cat. #315-02) and 350 nM Ascorbic acid (Sigma-Aldrich; Cat. # A8960) and then collected on day 2.

extract_protocol:
Genomic DNA was extracted from day 7 i3Neurons and day 2 C/EBPα-induced Macrophages using DNeasy® Blood & Tissue (QIAGEN; Cat. #69504) following manufacturer’s instructions.
100 ng genomic DNA was used in a 50-μl reaction containing 600 mM sodium acetate solution (3M, pH = 4.3) (Quality Biological, 351-309-101) and 1 M pyridine borane (Alfa Aesar, L13178-09),  and incubated for 16 h at 37°C in a Eppendorf ThermoMixer shaking at 850 rpm. The product was purified by QIAquick Nucleotide Removal Kit (QIAGEN; Cat. # 28306). 4 primer pairs, covering 26 CpGs within neuronal enhancer regions were designed using BiSearch Web (http://bisearch.enzim.hu). Amplicons were between 200-250 base pairs. We also designed 3 primer pairs, which cover 19 CpGs within macrophage enhancer regions. The PCR amplicons were generated using the PyroMark PCR kit (QIAGEN; Cat. # 978703) and quantified using Qubit assays (Invitrogen). PCR amplicons were pooled, then library preparation steps were performed as described (PMID: 33767446). The final libraries were quantified using the KAPA library quantification kit for Illumina (KAPA Biosystems) and sequenced on Illumina Miseq (150 bp, paired end).

tag: harvested day

value: TDGdegron

value: dTAG


title: iNeuron_TDGdegron_dTAG_PBseq_rep3

status: Public on Dec 01 2022

type: SRA

city: Shanghai

country: China

institute: Center for Excellence in Molecular Cell Science

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: genotype

tag: treatment


title: iNeuron_TDGdegron_NT_Pbseq_rep3

value: NT


title: iNeuron_WT_controlfor_sgTDG_PBseq_rep2

value: WT


title: iNeuron_WT_controlfor_sgTDG_PBseq_rep3


title: iNeuron_TDGdegron_NT_Pbseq_rep1


title: HAP1 cells, Control-1

city: Middlebury College

first: Amanda

last: Crocker

state: Vermont

address: 276 Bicentennial Way

department: Neuroscience

country: USA

institute: Middlebury College

description:
DNBseq Platform
RawHTseqCounts_ALL.txt
NormCountsDeseq2HTseqCountsStrict.txt

library_source: transcriptomic

data_processing:
SOAPnuke v.1.5.2 was used to filter reads with adapters, reads with unknown bases more than 10%, low quality reads (the percentage of base which quality is lesser than 15 is greater than 50% in a read)
HiSat2 used for allignment using hg38 build and Homo Sapien GRCh38 NCBI GTF file. Htseq-Counts was used for gene counts. Deseq2 was used for normalization and differential expression analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited files containing either raw counts from Htseq-Counts or normalized counts from DESeq2

molecule: polyA RNA

growth_protocol: Wild type or gene-edited HAP1 cells (SLC25A1 and SLC25A4) were grown in IMDM supplemented with 10% FBS and 100 µg/ml penicillin and streptomycin at 37°C in a 10% CO2 incubator. Cells were grown on 10cm tissue culture dishes to 85% confluency. Cells were placed on ice, washed 3 times with ice cold PBS (Corning, 21-040), and then incubated with PBS with 10mM EDTA for 30 minutes at 4°C. Mechanical agitation with a 10ml pipette was used to remove cells from plates. The collected cells were then centrifuged at 800xg for 5 minutes at 4°C. Following centrifugation, the supernatant was removed and the pellet was washed with ice cold PBS. The resuspended pellet was then spun at 16,100 x g for 5 minutes. The supernatant was aspirated away and the remaining pellet was flash frozen on dry ice for at least 5 minutes and stored at -80°C until further use.

extract_protocol:
The poly-A containing mRNA molecules were purified using poly-T oligo attached magnetic beads.
Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the DNBseq platform for the following data analysis study. For this step, the DNBseq platform combines the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method.

treatment_protocol: No treatments were applied

tag: cell line

tag: cell type

value: C631 (RRID:CVCL_Y019)

value: Parental Wildtype Line


title: iNeuron_WT_controlfor_sgTDG_PBseq_rep1


title: iNeuron_sgTDG_PBseq_rep3

value: TDG CRISPRi


title: HAP1 cells, C11-2

value: HZGHC000778c011 (RRID:CVCL_TM45)

value: SLC25A4 KO

value: CRISPR/Cas9-Edited Knockout Cell Line


title: iNeuron_sgTDG_PBseq_rep2


title: iNeuron_sgTDG_PBseq_rep1


title: iNeuron_TDGdegron_NT_Pbseq_rep2


title: NORAD Doxocyclin Control replicate1

city: Edinburgh

first: Grzegorz

last: Kudla

address: Crewe Road

department: MRC HGU

country: United Kingdom

institute: University of Edinburgh

data_processing:
Library strategy: COMRADES
After obtaining sequencing data in fastq format, we removed sequencing adapters (cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --minimum-length 10), merged paired-end reads using pear with default settings, collapsed identical reads (bash uniq -c), extracted the 6-nt Unique Molecular Identifier (UMI) from 3'ends of reads, and saved the reads in a deduplicated fasta file, where the number of duplicates and number of UMIs observed for every sequence was encoded in the read ID.
To call chimeric reads, we used hyb (Travis et al. 2014) with bowtie2 mapping to a human transcriptome database (Helwak et al. 2013) that consisted of spliced mRNAs, tRNAs and other noncoding RNAs, supplemented with the human NORAD sequence (nucleotides 1-5339 from gene NR_027451.1).
Supplementary_files_format_and_content: Processed data column headers:
column 1: read_id
column 2: read_sequence
column 3: folding_energy
column 4: arm_1_gene_id
column 5: arm_1_start_coordinate_in_read
column 6: arm_1_end_coordinate_in_read
column 7: arm_1_start_coordinate_in_gene
column 8: arm_1_end_coordinate_in_gene
column 9: arm_1_mapping_score
column 10: arm_2_gene_id
column 11: arm_2_start_coordinate_in_read
column 12: arm_2_end_coordinate_in_read
column 13: arm_2_start_coordinate_in_gene
column 14: arm_2_end_coordinate_in_gene
column 15: arm_2_mapping_score

molecule: total RNA

source_name: Large intestine; Colon

growth_protocol: HCT116 cells were cultured in McCoy's 5a Medium supplemented with 10% fetal bovine serum (FBS) and 100 U of penicillin/0.1 mg mL−1 streptomycin. Cells were maintained at 37°C in a humidified incubator with 5% CO2. and were routinely examined to rule out mycoplasma contamination.

extract_protocol:
Cells were lysed using RNeasy lysis buffer (QIAGEN) supplemented with DTT and proteins were degraded using proteinase K (NEB). Total cellular RNA was purified using the RNeasy maxi kit (QIAGEN) and quantified using Qubit RNA BR assay kit.
Library preparation was done as described in (Ziv et al., 2018, doi.org/10.1038/s41592-018-0121-0), using 6N unique molecular identifiers to eliminate PCR biases. Pre-adenylated adapters were used and all ligation reactions were carried without ATP to reduce ligation artifacts. Libraries were PCR amplified using KAPA HiFi HotStart Ready Mix (KAPA Biosystems). PCR products were size-selected on a 1.8% agarose gel before loading on a HiSeq 1500 sequencer (Illumina) for paired-end 100nt runs

treatment_protocol: Ar treated HCT116 cells were supplemented with 20 mM Sodium Arsenite and maintained for 1 hour under growth conditions. Dox treated HCT116 cells were supplemented with 1 uM Doxorubicin and were maintained for 24 hours under growth conditions. Cells were washed 3 times with HANKS buffer and were incubated with 0.7 mg/ml Psoralen-triethylene glycol azide (psoralen-TEG azide, Berry & Associates) diluted in PBS and supplemented with OptiMEM I (Gibco) without phenol red for 20 minutes. Subsequently, cells were irradiated with 50 KJ/m2 365 nm UVA on ice using a CL-1000 crosslinker (UVP).

value: HCT 116

value: Doxocyclin Control

tag: molecule subtype

value: NORAD enriched RNA


title: NORAD Doxocyclin Control replicate2


title: NORAD Arsenite Control replicate2

value: Arsenite Control


title: NORAD Arsenite Control replicate3


title: NORAD Control replicate2

value: control


title: NORAD Control replicate1


title: NORAD replicate3


title: NORAD Doxocyclin replicate2

value: Doxocyclin


title: NORAD Arsenite Control replicate1


title: NORAD Doxocyclin replicate1


title: NORAD Arsenite replicate3

value: Arsenite


title: dglyGCC rep3

status: Public on Dec 02 2022

city: Ploen

first: Jenna

last: Gallie

address: August-Thienemann Strasse 2

country: Germany

description: mature tRNA

data_processing:
Sorted into 24 samples using the unique, 6-bp Illumina indices. 0 mismatches allowed.
Per sample: reads between 80 and 151 bp were extracted (in Geneious v11.1.4)
Per sample: 80-151 bp reads were aligned to a set of 42 reference tRNA sequences (all unique primary sequences predicted in the SBW25 genome by GtRNAdb). This was done using Geneious version 11.1.4 (assembly parameters: up to 10% mismatches or gaps of <3 bp per read, up to 5 ambiguities per read, no assignment of reads that map equally well to more than one reference sequence, and no iterations)
Per sample: read numbers for the 42 contigs were used in pairwise comparisons with DESeq2 (in R version 3.6.0)
Genome_build: The 42 tRNA sequence reference file was derived from the SBW25 genome sequence (NCBI accession number: NC_012660.1) using GtRNAdb (http://gtrnadb.ucsc.edu/GtRNAdb2/genomes/bacteria/Pseu_fluo_SBW25/pseuFluo_SBW25-tRNAs.fa)
Supplementary_files_format_and_content: 24 text files: the raw read numbers aligned to the 42 reference sequences. One file per sample.
Supplementary_files_format_and_content: Two excel workbooks. "aligned_reads_multicopy.xlsx" contains a summary of the data for all 24 samples, plus a spreadsheet for each of the 8 strains listing the of the number of reads aligned to each reference sequence in each replicate. "deseq2_comparisons_multicopy.xlsx"  contains the DESeq2 output for pairwise comparisons between strains of interest.

organism: Pseudomonas fluorescens

source_name: liquid cell culture

growth_protocol: Samples were grown from single colonies in liquid culture overnight (28˚C, shaking). A small volume of grown culture was inoculated into fresh medium and grown to mid-exponential phase (approx. 5-7 hours, 28˚C, shaking).

extract_protocol:
Per sample: 1.5 ml aliquots of mid-exponential phase culture were taken, and total RNA extracted (TRIzol Max Bacterial RNA isolation kit; Life Technologies).
The YAMAT-seq method is an adaptation of that published for human cell lines (Shigematsu et al., 2017; doi:10.1093/nar/gkx005 ) and adapted for use in Pseudomonas fluorescens in (Ayan et al., 2020; doi:10.7554/eLife.57947).  Briefly, for each sample, 5 ug total RNA was subjected to tRNA deacylation treatment by exposure to hydrochloric acid. Hybrid DNA/RNA Y-shaped adapters (Eurofins) were ligated to exposed 5'-CCA-3' tRNA ends using T4 RNA ligase 2 (New England Biolabs). Ligation products were reverse transcribed into cDNA (SuperScript III reverse transcriptase; Thermo Fisher), and amplified PCR (Phusion; Thermo Fisher). One of 24 sample-specific indices (Illumina) was added to each of the 24 reactions. The quality and quantity of each PCR product was checked using an Agilent DNA 7500 kit on a Bioanalyzer (Agilent), and samples combined in equimolar amounts into a single tube. The mixture was run on a 5 % polyacrylaminde gel (Bio-Rad Laboratories), and the group of bands ranging between ~180 bp and ~250 bp excised. DNA was extracted in deionized water overnight, and agarose removed by centrifugation through filter paper. DNA quality and quantity was checked with a Quant-iT dsDNA BR Assay kit (Invitrogen) on a Fluorescence Nanodrop. High throughput sequencing was performed at the Max Planck Institute for Evolutionary Biology (Ploen, Germany). Single-end, 150 bp reads were generated with a NextSeq 550 Output v2.5 kit (Illumina).

tag: strain type

value: engineered

value: {delta}glyGCC

tag: evolution day


title: iNeuron_TDGdegron_dTAG_PBseq_rep1

value: TDGdegron

value: dTAG


title: NORAD Arsenite replicate2


title: NORAD Control replicate3


title: HAP1 cells, C3-1

value: HZGHC001753c010 (RRID:CVCL_TM05)

value: SLC25A1 KO


title: NORAD Arsenite replicate1


title: NORAD replicate1


title: NORAD replicate2


title: 202242410179_R04C01 [PPH0306UC_FU]

type: genomic

city: Atlanta

first: Suresh

last: Venkateswaran

state: Georgia

address: 1760 Haygood Drive, HSRB, Room No: E-250

department: Pediatrics

institute: Emory University

description: HumanMethylationEPIC BeadChip - standard protocol

hyb_protocol: HumanMethylationEPIC BeadChip

scan_protocol: BeadStudio

data_processing: Average Beta (non-normalized, background subtracted)

label: Cy3, Cy5

source_name: Rectal biopsies

label_protocol: HumanMethylationEPIC BeadChip

extract_protocol:
bisulfite conversion protocol: EZ DNA Methylation-GoldTM Kit (Zymo Research, Irvine, CA)
AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA)

tag: tissue

value: Rectal biopsy

tag: gender

value: Female

tag: race

value: Caucasian

tag: age

tag: disease status

value: UC

tag: time point

value: 104wk FU


title: 202184990178_R04C01 [PHP3640UC_FU]

value: Male


title: 202232290094_R01C01 [PPH0197UC_FU]


title: 202242410179_R01C01 [PCN2877UC_FU]


title: 202242410058_R03C01 [PGA0653UC_FU]

value: African American


title: 202226400052_R08C01 [PCT4047UC_FU]

value: 78wk FU


title: 202229250249_R08C01 [PON0261UC_FU]


title: 202242400144_R02C01 [PON0233UC_FU]


title: 202226400028_R07C01 [PCT4325UC_FU]


title: 4C-rDNA-new primers rep2

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

country: Russia

institute: Engelhardt Institute of Molecular Biology

description:
Library strategy: 4C-seq
Replica 2
4C_hg19_new_intersect.bedGraph

data_processing:
Base calling and quality control were performed in real time with standard Illumina analysis pipeline using a phiX control.
Sequenced reads were trimmed for adaptor sequences and low quality sequences by cutadapt v. 1.16 using the following options: --trim-n --times=5 --minimum-length 20 -q 26 --trimmed-only -g AAAAGAAGCTCAAGTACATCTAATCTAATCCCTTACCAAGGCCT -g TTCGCCTACGGATTTCTAGAAAATAAGATGT -a AGGCCTTGGTAAGGGATTAGATTAGATGTACTTGAGCTTCTTTT -a ACATCTTATTTTCTAGAAATCCGTAGGCGAA
Trimmed reads were mapped to hg19p13 by bwa 0.7.12-r1039 using the mem algorithm. All non-aligned reads were removed from resulting alignment file by samtools 1.6: -b -S -F 4 -@ 10 allalign.sam > aligned.bam
Mapping and alignment results were converted to resulting tables using samtools 1.6 and ad hoc Perl scripts.
Each replica results table was converted to bedGraph file for further processing using reads amount as data value. Intersection file was built by bedtools v. 2.27.1 with the following command line: bedtools intersect -a 4C_hg19_new_rep1.bedGraph -b 4C_hg19_new_rep2.bedGraph -wb. Ad hoc Perl script was used to convert bedtools output file back to bedGraph file with summing up in the overlapped regions.
Genome_build: Homo Sapiens hg19/GRCh37.p13 genome with included to chr14 from address 1 Human ribosomal DNA U13369
Supplementary_files_format_and_content: Tab-delimited text file include the following features of each mapping: begin, end, length, coverage, number of reads, sequence. bedGraph files for each replica and intersection are supplied too.

growth_protocol: HEK293T cells were grown in DMEM with 10% FBS in a humidified incubator at 37°C and 5% CO2 to 80% confluency.

extract_protocol: DNA samples were prepared as described before (Dekker et al., 2002; Osborne et al., 2004; http://www.protocol-online.org/cgi-bin/prot/view_cache.cgi?ID=3978).  Cross-linking  To suspension containing about 20x106 HEK293T cells in 40 ml of DMEM formaldehyde solution was added to final concentration 1.5%. After mixing incubation of cell suspension was performed for 10 min at room temperature with mixing. The quenching with 2.75 ml of 2M glycin (final concentration 0.125M) was performed. After incubation at room temperature for 5 min the suspension was cooled for 15 min in ice bath and then cells were collected by centrifugation for 15 min at 3500 rpm at +2°C.  Lysis   The pellet of cells was resuspended at °C in 1ml of buffer containing 10 mM tris-HCl buffer, pH 8, 10 mM NaCl, 0.2% NP-40 and freshly added protease inhibitors – 0.1 mM PMSF and 1:500 protease inhibitor cocktail (Sigma). After incubation for 15 min cells were homogenized by passing through insulin syringe about 50 times into Eppendorf. Then nuclei were spin down by centrifugation for 5 min at 5000 rpm in Eppendorf centrifuge 5415 R at +2°C.  Digestion with EcoRI  The nuclei pellet was resuspended in 756 l of solution containing 40 mM tris-HCl buffer, pH 7.4, 50 mM NaCl, 10 mM MgCl2 and 10 mM 2-mercaptoethanol. Then 20% SDS was added to final concentration 0.3% and incubation with shaking was performed for 1 h at +37°C. To sequester SDS 180 l of 10% Triton X-100 was added and the incubation for 1 h at +37°C was performed. Before digestion 1 l of BSA (5 mg/ml) was added with mixing. Then 50 l of EcoRI (10 u/l) was added and after mixing digestion was performed overnight at +37°C.   Ligation  To inactivate the restriction enzyme, 35l of 20% SDS was added (final concentration 0.7%) and the probe was heated to 65°C for 30 min. Then the mixture was transferred into 15 ml Nunc tube and consequently 375 l of 20% Triton X-100 (to final concentration 1%), 750 l of 10x ligase buffer, 7,5l of BSA (5 mg/ml), 80l of 100 mM ATP, and 5241l of milliQ water  were added and the final 7.5 ml solution was well mixed. Then 10 l of T4 DNA ligase (200 u/l) was added and after mixing incubation was performed for 5 h at +16°C and then for 30 min at room temperature. Usually during ligation DNA concentration was equal to 2 ng/l.    DNA purification  For isolation of DNA 50l of proteinase K (10 mg/ml) was added (final concentration 50 g/ml) and after mixing incubation was performed at 55°C B1overnight. For RNA digestion 40l of RNase A (10 mg/ml) was added (final concentration 0.5 g/ml) and after mixing incubation was performed for 30 min at +37°C. After extensive extraction with phenol-chloroform extraction (three times with 7 ml each) DNA was precipitated by 2.5 vol. of ethanol after addition of 40 l 10 mg/ml glycogen and 175 l 4M NaCl. The final DNA pellet was washed twice with 70% ethanol and then dissolved in 0.1xTE.   Digestion with FaeI  About 15 g of DNA was digested in 250l solution with 75 u of FaeI overnight at +37°C. Then the enzyme was inactivated by heating at 65°C for 30 min. DNA was isolated after phenol-chloroform extraction, precipitated by ethanol and dissolved in 100l of 0.1xTE.   Ligation  For circularization 15g of DNA was incubated in 8 ml of T4 DNA ligase buffer containing 400 u of T4 DNA ligase for 5 h at +16°C. DNA was isolated after phenol-chloroform extraction, precipitated by ethanol and dissolved in 50l of 0.1xTE.   PCR and library preparation  One or two rounds of PCR were used as described below. There are about 300-400 copies of rDNA. That is why a single round of PCR (with up to 35 cycles) was found to be sufficient. DNA concentration was titrated and finally about 30 ng of DNA was used for PCR with primers   5’ TCTTTGAAAAAAATCCCAGAAGTGGT 3’ and 5’ AAGTCCAGAAATCAACTCGCCAGT 3’ (for PCR-1), and 5’ GCCTAAGCCTGCTGAGAACTTTC 3’ and 5’ CAGCATTCTGTAGGGAGATCAAATC 3’ (for PCR-2). After separation in 2% agarose gels two DNA fractions (200-400 bp and higher 400 bp) were eluted using QIAqiuck gel extraction kit (Quigen). The libraries were prepared using TruSeq RNA Sample Preparation Kit v2 (Illumina) using adapter AR006 for 200-400 bp DNA fraction and adapter R007 for DNA fraction higher 400 bp. The samples were sequenced using MiSeq (Illumina).

tag: strain

value: kidney

value: wild type


title: 202242400132_R07C01 [PCT4180UC_FU]

value: 52wk FU


title: 4C-rDNA-new primers rep1

description:
Library strategy: 4C-seq
Replica 1
4C_hg19_new_intersect.bedGraph


title: 202226320167_R06C01 [PCT4431UC_FU]


title: 202226400029_R08C01 [PWI7409UC_FU]


title: 202242410187_R07C01 [PRI0150UC_FU]


title: 202226400093_R02C01 [POH0331UC_FU]


title: 202242410060_R07C01 [PUP0136UC_FU]


title: 202229250154_R04C01 [PCT4697UC_FU]


title: 202242410058_R06C01 [PBU2630UC_FU]


title: 202226400037_R05C01 [PTO0049UC_FU]


title: 202229250129_R05C01 [PON0021UC_FU]


title: 202226320146_R04C01 [PTO6861UC_FU]

value: Asian


title: 202229250128_R03C01 [PCT4554UC_FU]


title: 202226320146_R01C01 [POH0490UC_FU]


title: 202242410230_R02C01 [PPH0098UC_FU]


title: 202229250128_R01C01 [PCT4228UC_FU]


title: 202242410122_R08C01 [PUP0150UC_FU]


title: 202226400002_R07C01 [PBU2498UC_FU]


title: 202242410109_R08C01 [PGA0732UC_FU]


title: 202226320187_R02C01 [PPT5566UC_FU]


title: 202242410059_R08C01 [PBO2303UC_FU]


title: 202226320126_R03C01 [POH0759UC_FU]


title: 202229250152_R04C01 [PHP3896UC_FU]


title: 202184990178_R01C01 [PBU2674UC_FU]


title: 202226320187_R08C01 [PCN2866UC_FU]


title: 202226400037_R01C01 [PGA0645UC_FU]


title: 202226400002_R01C01 [PPH4010UC_FU]


title: 202226320051_R03C01 [POH0370UC_FU]


title: 202242410188_R04C01 [POH0136UC_FU]


title: 202226400054_R05C01 [PCT4729UC_FU]


title: 202226400038_R07C01 [PCT4340UC_FU]


title: 202242410111_R08C01 [PPT5415UC_FU]

value: 39wk FU


title: 202226400091_R02C01 [PSF0240UC_FU]


title: 202226320051_R06C01 [PBU2642UC_FU]


title: 202226400088_R02C01 [PPT5654UC_FU]


title: 202226400040_R03C01 [PCT4601UC_FU]


title: 202242410111_R02C01 [PBU2465UC_FU]


title: 202242410239_R08C01 [POH0578UC_FU]


title: 202229250264_R05C01 [PGA4096UC_FU]


title: 202226400021_R01C01 [PPT5698UC_FU]


title: 202242400132_R02C01 [PON0150UC_FU]


title: 202226400088_R07C01 [PCT4079UC_FU]


title: 202226320167_R07C01 [PPT5520UC_FU]


title: 202242410239_R02C01 [PGA0830UC_FU]

value: 26wk FU


title: 202226400038_R05C01 [PWI0082UC_FU]


title: 202226400063_R02C01 [PON5318UC_FU]


title: 202226400093_R03C01 [PNJ4263UC_FU]


title: 202229250175_R02C01 [PON0294UC_FU]


title: 202226400091_R03C01 [PNJ4274UC_FU]


title: 202226400054_R03C01 [POH0434UC_FU]


title: 202229250175_R08C01 [POH0408UC_FU]


title: 202242410109_R05C01 [PCT4386UC_FU]


title: 202242420021_R04C01 [PHP4096UC_FU]


title: 202184990149_R02C01 [POH5102UC_FU]


title: 202226400028_R02C01 [POH0815UC_FU]


title: 202226400052_R04C01 [PPT0258UC_FU]


title: 202242410122_R05C01 [POH0150UC_FU]

value: 12wk FU


title: 202816900102_R06C01 [PON0122UC_FU]

value: 8wk FU


title: 202226400058_R03C01 [POH0327UC_FU]


title: 202226400063_R06C01 [PBU2543UC_FU]


title: 202226400058_R05C01 [PBO2125UC_Base]

value: Screening/Baseline


title: 202242400132_R08C01 [PCT4180UC_Base]

value: Rectal biopsy


title: 202232290123_R02C01 [PCN4152UC_Base]


title: 202242420095_R05C01 [PBO2248UC_Base]

value: Female


title: 202816900147_R02C01 [PSF0054UC_FU]

value: Caucasian


title: 202242410187_R04C01 [PCT3018UC_Base]

value: UC


title: 202226400009_R04C01 [PPT0503UC_Base]


title: 202242410240_R07C01 [PHP3907UC_Base]


title: 202226400029_R07C01 [PWI7409UC_Base]


title: 202229250249_R05C01 [PBO2161UC_Base]


title: 202242410239_R05C01 [PCT4614UC_Base]


title: 202226320187_R07C01 [PCN2866UC_Base]


title: 202242400144_R06C01 [PON0355UC_FU]


title: 202226320167_R05C01 [PCT4431UC_Base]


title: 202242410187_R08C01 [PRI0150UC_Base]


title: 202184990178_R07C01 [PRI5995UC_Base]


title: 202242410122_R03C01 [PCT4757UC_Base]


title: 202229250129_R03C01 [PGA4068UC_Base]


title: 202242400142_R08C01 [PNY4598UC_FU]


title: 202229250264_R03C01 [PRI0054UC_FU]


title: 202242420095_R01C01 [PIN4035UC_Base]


title: 202242420021_R02C01 [PRI0612UC_Base]


title: 202229250128_R05C01 [PUT7081UC_Base]


title: 202242410059_R03C01 [PTO6825UC_Base]


title: 202242410110_R08C01 [PCT4582UC_Base]


title: 202242410239_R01C01 [PGA0830UC_Base]


title: 202226320146_R02C01 [POH0490UC_Base]


title: 202226400029_R06C01 [PSF6052UC_Base]


title: 202229250129_R06C01 [PON0021UC_Base]


title: 202229250154_R03C01 [PCT4697UC_Base]


title: 202226400040_R01C01 [PTO6763UC_Base]


title: 202226400099_R05C01 [PCN2959UC_Base]


title: 202242410188_R02C01 [PNY4576UC_Base]


title: 202229250154_R02C01 [PBO2158UC_Base]


title: 202229250154_R01C01 [PCT4394UC_Base]


title: 202229250152_R06C01 [PON5285UC_Base]


title: 202229250129_R02C01 [PTO6679UC_Base]


title: 202226400099_R08C01 [PON5241UC_Base]


title: 202229250249_R01C01 [PNY4549UC_Base]


title: 202226400037_R06C01 [PTO0049UC_Base]


title: 202229250154_R07C01 [PCN2905UC_Base]


title: 202229250189_R05C01 [PON0370UC_FU]


title: 202242410058_R05C01 [PBU2630UC_Base]


title: 202226400052_R02C01 [POH4945UC_Base]


title: 202242400142_R03C01 [PON0462UC_Base]


title: 202226400052_R06C01 [PNC1276UC_Base]


title: 202242410060_R08C01 [PUP0136UC_Base]


title: 202242410230_R08C01 [PMN0065UC_Base]


title: 202816900102_R03C01 [PPH0240UC_Base]


title: 202226400093_R01C01 [POH0331UC_Base]


title: 202229250249_R07C01 [PON0261UC_Base]


title: 202226400058_R08C01 [PTO6647UC_Base]


title: 202232290094_R02C01 [PPH0197UC_Base]


title: 202226400058_R06C01 [PTX1811UC_Base]


title: 202226400028_R08C01 [PCT4325UC_Base]


title: 202242410058_R02C01 [PTO0054UC_Base]


title: 202242410109_R04C01 [PCT4500UC_Base]


title: 202229250128_R04C01 [PCT4554UC_Base]


title: 202232290123_R01C01 [PON0388UC_Base]


title: 202226400091_R05C01 [PLA0910UC_Base]


title: 202242410110_R06C01 [PHP3713UC_Base]


title: 202226320187_R05C01 [PBO2133UC_Base]


title: 202242410230_R01C01 [PPH0098UC_Base]


title: 202242410059_R02C01 [PMD1748UC_Base]


title: 202816900147_R01C01 [PSF0054UC_Base]


title: 202226400058_R02C01 [PNY4708UC_Base]


title: 202226320146_R03C01 [PTO6861UC_Base]


title: 202232290123_R03C01 [PBO2324UC_Base]


title: 202226320187_R01C01 [PPT5566UC_Base]


title: 202229250128_R02C01 [PCT4228UC_Base]


title: 202816900102_R07C01 [PTO0122UC_Base]


title: 202232290123_R07C01 [PON5196UC_Base]


title: 202229250189_R04C01 [PTX1824UC_Base]


title: 202226400038_R06C01 [PWI0082UC_Base]


title: 202242410240_R06C01 [PTO6872UC_Base]


title: 202816900147_R07C01 [PGA0620UC_Base]


title: 202242410122_R07C01 [PUP0150UC_Base]


title: 202226320051_R02C01 [PTO6789UC_Base]


title: 202226400091_R08C01 [PRI0343UC_Base]


title: 202242410122_R01C01 [PCT4111UC_Base]


title: 202229250249_R03C01 [PCT4636UC_Base]


title: 202184990178_R03C01 [PHP3640UC_Base]


title: 202226400054_R07C01 [PCT3253UC_Base]


title: 202242410109_R07C01 [PGA0732UC_Base]


title: 202816900147_R04C01 [PBU2628UC_Base]


title: 202242420095_R04C01 [PRI0604UC_Base]


title: 202226400002_R05C01 [PBU2607UC_Base]


title: 202226400002_R06C01 [PUP0037UC_Base]


title: 202229250129_R07C01 [PON0049UC_Base]


title: 202242410240_R04C01 [POH0209UC_Base]


title: 202242420021_R06C01 [PHP3737UC_Base]


title: 202242410179_R07C01 [PBU2656UC_Base]


title: 202242410188_R01C01 [PWI0169UC_Base]


title: 202226400002_R08C01 [PBU2498UC_Base]


title: 202226320126_R01C01 [PNC1237UC_Base]


title: 202232290094_R06C01 [PCT3204UC_Base]


title: 202226320146_R05C01 [PON0136UC_Base]


title: 202226400029_R01C01 [PCT4333UC_Base]


title: 202242410060_R04C01 [PTO6696UC_Base]


title: 202226320126_R04C01 [POH0759UC_Base]


title: 202229250152_R03C01 [PHP3896UC_Base]


title: 202226400099_R03C01 [PPT0524UC_Base]


title: 202229250152_R07C01 [PWI7374UC_Base]


title: 202242400142_R06C01 [POH4904UC_Base]


title: 202226400091_R06C01 [PHP3617UC_Base]


title: 202242410060_R06C01 [PIN4047UC_Base]


title: 202242410059_R07C01 [PBO2303UC_Base]


title: 202242410059_R01C01 [PCH0054UC_Base]


title: 202242410240_R02C01 [PGA0793UC_Base]


title: 202229250175_R01C01 [PON0294UC_Base]


title: 202226400063_R08C01 [PTO0082UC_Base]


title: 202242400144_R05C01 [PON0355UC_Base]


title: 202242410059_R06C01 [PNS0331UC_Base]


title: 202232290094_R04C01 [PHP3686UC_Base]


title: 202226400009_R02C01 [PGA0889UC_Base]


title: 202226320126_R07C01 [PSF0272UC_Base]


title: 202226320051_R07C01 [PUT7038UC_Base]


title: 202242410110_R04C01 [PON0013UC_Base]


title: 202242410111_R07C01 [PPT5415UC_Base]


title: 202816900102_R05C01 [PON0122UC_Base]


title: 202242400132_R03C01 [PIN3989UC_Base]


title: 202226400028_R03C01 [POH4844UC_Base]


title: 202242410230_R04C01 [PGA4023UC_Base]


title: 202226400091_R07C01 [PHP4178UC_Base]


title: 202226400093_R05C01 [POH0462UC_Base]


title: 202242410187_R01C01 [PON0169UC_Base]


title: 202242410240_R05C01 [PTO6900UC_Base]


title: 202816900147_R03C01 [PON5208UC_Base]


title: 202229250129_R08C01 [PBU2689UC_Base]


title: 202242420095_R07C01 [PCT4576UC_Base]


title: 202242400142_R05C01 [PON0490UC_Base]


title: 202226400054_R04C01 [POH0434UC_Base]


title: 202242400144_R03C01 [PGA4139UC_Base]


title: 202229250249_R04C01 [POH0416UC_Base]


title: 202242400142_R04C01 [PON5407UC_Base]


title: 202226400099_R02C01 [POH0760UC_Base]


title: 202242410230_R05C01 [PIN4195UC_Base]


title: 202229250128_R07C01 [PTO6707UC_Base]


title: 202242400144_R01C01 [PON0233UC_Base]


title: 202184990149_R07C01 [PRI0258UC_Base]


title: 202226400037_R07C01 [PON0416UC_Base]


title: 202229250175_R07C01 [POH0408UC_Base]


title: 202242410122_R06C01 [POH0150UC_Base]


title: 202229250129_R01C01 [PCT4622UC_Base]


title: 202226400052_R07C01 [PCT4047UC_Base]


title: 202226400028_R05C01 [PNJ4289UC_Base]


title: 202229250264_R07C01 [PRI0331UC_Base]


title: 202242410239_R07C01 [POH0578UC_Base]


title: 202226400041_R04C01 [PGA4124UC_Base]


title: 202242410060_R02C01 [PRI0098UC_Base]


title: 202226400091_R01C01 [PSF0240UC_Base]


title: 202226400091_R04C01 [PNJ4274UC_Base]


title: 202242410060_R05C01 [PTX1880UC_Base]


title: 202226320051_R05C01 [PBU2642UC_Base]


title: 202229250264_R06C01 [PGA4096UC_Base]


title: 202184990178_R02C01 [PBU2674UC_Base]


title: 202242410109_R06C01 [PCT4386UC_Base]


title: 202226400088_R01C01 [PPT5654UC_Base]


title: 202229250264_R04C01 [PRI0054UC_Base]


title: 202226400063_R04C01 [PRI0122UC_Base]


title: 202226400028_R01C01 [POH0815UC_Base]


title: 202226400088_R08C01 [PCT4079UC_Base]


title: 202226400093_R08C01 [PHP3765UC_Base]


title: 202226400038_R03C01 [PPH4111UC_Base]


title: 202242410239_R04C01 [PIN4051UC_Base]


title: 202229250175_R04C01 [PON0209UC_Base]


title: 202242420021_R03C01 [PHP4096UC_Base]


title: 202229250189_R07C01 [PCN4124UC_Base]


title: 202226320187_R03C01 [PUT6949UC_Base]


title: 202226320126_R02C01 [PON0319UC_Base]


title: 202226320167_R04C01 [PTX1895UC_Base]


title: 202226400063_R05C01 [PBU2543UC_Base]


title: 202226400058_R04C01 [POH0327UC_Base]


title: 202242400132_R01C01 [PON0150UC_Base]


title: 202226400063_R01C01 [PON5318UC_Base]


title: 202226400088_R06C01 [PPH0148UC_Base]


title: 202229250154_R06C01 [PGA0828UC_Base]


title: 202226400093_R04C01 [PNJ4263UC_Base]


title: 202226400099_R06C01 [PON0331UC_Base]


title: 202226400040_R04C01 [PCT4601UC_Base]


title: 202226400037_R02C01 [PGA0645UC_Base]


title: 202242410179_R03C01 [PPH0306UC_Base]


title: 202226400054_R06C01 [PCT4729UC_Base]


title: 202242410240_R03C01 [PNJ4394UC_Base]


title: 202226400002_R02C01 [PPH4010UC_Base]


title: 202226320051_R04C01 [POH0370UC_Base]


title: 202226400038_R08C01 [PCT4340UC_Base]


title: 202242410179_R02C01 [PCN2877UC_Base]


title: 202242410111_R01C01 [PBU2465UC_Base]


title: 202226320167_R08C01 [PPT5520UC_Base]


title: 202226400052_R03C01 [PPT0258UC_Base]


title: 202229250175_R03C01 [PHP3884UC_Base]


title: 202226400021_R02C01 [PPT5698UC_Base]


title: 202226320146_R07C01 [PNJ4230UC_Base]


title: 202184990149_R01C01 [POH5102UC_Base]


title: 202242420095_R02C01 [PGA0705UC_Base]


title: 202226400099_R04C01 [PLA1072UC_Base]


title: 202242400144_R08C01 [PBO2346UC_Base]


title: 202184990149_R08C01 [RS06086UC_Base]


title: 202229250189_R03C01 [PON0225UC_Base]


title: 202242410058_R04C01 [PGA0653UC_Base]


title: 202226400041_R02C01 [RS04040UC_Base]


title: 202226400021_R04C01 [PNJ4291UC_Base]


title: 202232290123_R04C01 [RS07049UC_Base]


title: 202226320167_R02C01 [RS11063UC_Base]


title: 202226400054_R01C01 [RS23017UC_Base]


title: 202226400088_R03C01 [RS13084UC_Base]

value: South/East Asian


title: 202226400021_R06C01 [RS05142UC_Base]

value: Male


title: 202226400037_R03C01 [RS06071UC_Base]


title: 202229250128_R06C01 [RS21021UC_Base]


title: 202242410188_R03C01 [POH0136UC_Base]


title: 202229250152_R05C01 [RS06070UC_Base]


title: 202226400099_R07C01 [RS03116NotIBD]

value: Not IBD


title: 202242400142_R07C01 [PNY4598UC_Base]


title: 202242410058_R07C01 [RS03168NotIBD]


title: 202229250189_R06C01 [PON0370UC_Base]


title: 202226400002_R04C01 [RS03152NotIBD]


title: 202226320167_R03C01 [RS21007NotIBD]


title: 202226400041_R03C01 [RS03098NotIBD]


title: 202232290094_R07C01 [RS23005NotIBD]


title: 202242420021_R05C01 [RS27010NotIBD]


title: 202242410059_R04C01 [RS11056NotIBD]


title: 202242410179_R05C01 [RS13078NotIBD]


title: 202242410059_R05C01 [RS27029NotIBD]


title: 202226400021_R03C01 [RS27046NotIBD]


title: 202226400028_R04C01 [RS06085NotIBD]


title: 202242400132_R05C01 [RS06073UC_Base]


title: 202226400063_R03C01 [RS03161NotIBD]


title: 202242400132_R04C01 [RS03089NotIBD]


title: 202229250189_R02C01 [RS08013NotIBD]


title: 202229250175_R05C01 [RS11053NotIBD]


title: 202242410111_R05C01 [RS27020UC_Base]


title: 202226400038_R01C01 [RS13154NotIBD]


title: 202242400142_R01C01 [RS07058NotIBD]


title: 202242410179_R06C01 [RS29013NotIBD]


title: 202184990178_R05C01 [RS27033NotIBD]


title: 202229250129_R04C01 [RS09036NotIBD]


title: 202226400037_R04C01 [RS24010NotIBD]


title: 202226400040_R05C01 [RS08043NotIBD]

value: African American


title: 202229250189_R01C01 [RS05131NotIBD]


title: 202226400093_R06C01 [RS03155NotIBD]


title: 202184990178_R06C01 [RS05104NotIBD]


title: 202226400058_R01C01 [RS27031NotIBD]


title: 202242410110_R05C01 [RS29007NotIBD]


title: 202229250249_R02C01 [RS27040NotIBD]


title: 202242410188_R08C01 [RS27007NotIBD]


title: 202226320146_R08C01 [RS03158NotIBD]


title: 202242400142_R02C01 [RS08023NotIBD]


title: 202229250249_R06C01 [RS07051NotIBD]


title: 202226400029_R04C01 [RS03097NotIBD]


title: 202226400021_R05C01 [RS03144NotIBD]


title: 202242400144_R04C01 [RS03111NotIBD]


title: 202226320146_R06C01 [RS29003NotIBD]


title: 202242410060_R01C01 [RS08055NotIBD]


title: 202226400088_R04C01 [RS23008NotIBD]


title: 202226400093_R07C01 [RS24008NotIBD]


title: 202242410239_R03C01 [RS13137NotIBD]


title: 202242410187_R03C01 [RS03171NotIBD]


title: 202226400009_R05C01 [RS20008NotIBD]


title: 202226400009_R03C01 [RS01109NotIBD]


title: 202229250264_R01C01 [RS29036NotIBD]


title: 202242420021_R08C01 [RS03076NotIBD]


title: 202242410240_R01C01 [RS06095NotIBD]


title: 202242420095_R06C01 [RS01082NotIBD]


title: 202242410111_R03C01 [RS08056NotIBD]


title: 202226400099_R01C01 [RS13081NotIBD]


title: 202226320187_R04C01 [RS03056NotIBD]


title: 202226400038_R02C01 [RS11040NotIBD]


title: 202242410058_R01C01 [RS21020NotIBD]


title: 202242410188_R07C01 [RS09057NotIBD]


title: 202242420095_R03C01 [RS08027NotIBD]


title: 202226400029_R03C01 [RS08039NotIBD]


title: 202226400037_R08C01 [RS15013NotIBD]


title: 202816900102_R04C01 [RS03189NotIBD]


title: 202242410060_R03C01 [RS06091NotIBD]


title: 202226320126_R05C01 [RS03075NotIBD]


title: 202242410122_R02C01 [RS03182NotIBD]


title: 202226400058_R07C01 [RS27035NotIBD]


title: 202226320126_R06C01 [RS27038NotIBD]


title: 202242410109_R03C01 [RS29033NotIBD]


title: 202226400041_R01C01 [RS03187NotIBD]


title: 202184990149_R06C01 [RS03132NotIBD]


title: 202229250264_R08C01 [RS08058NotIBD]


title: 202226400002_R03C01 [RS14017NotIBD]


title: 202226400040_R02C01 [RS23018NotIBD]


title: 202242410109_R01C01 [RS05135NotIBD]


title: 202242400144_R07C01 [RS04075NotIBD]


title: 202226320051_R08C01 [RS03178NotIBD]


title: 202229250152_R01C01 [RS05108NotIBD]


title: 202226400063_R07C01 [RS03060NotIBD]


title: 202242400132_R06C01 [RS03193NotIBD]


title: 202229250128_R08C01 [RS03057NotIBD]


title: 202229250152_R08C01 [RS12026NotIBD]


title: 202226400088_R05C01 [RS24016NotIBD]


title: 202226400054_R02C01 [RS05100NotIBD]


title: 202232290094_R03C01 [RS09043NotIBD]


title: 202232290123_R06C01 [RS11028NotIBD]


title: 202242410230_R06C01 [RS06060NotIBD]


title: 202229250154_R08C01 [RS14025NotIBD]


title: 202242410122_R04C01 [RS03119NotIBD]


title: 202242410110_R03C01 [RS06063NotIBD]


title: CleftProband_893

city: Iowa City

first: J.

middle: Robert

last: Manak

state: Iowa

address: 455 Biology Building, 129 East Jefferson Street

department: Biology and Pediatrics

institute: The University of Iowa

hyb_protocol: Approximately 5-10 ug of each labeled DNA was co-hybridized to an Agilent human whole genome tiling microarray (SurePrint G3 Human CGH Microarray Kit 1x1M)

scan_protocol: Arrays were scanned on an Agilent microarray scanner.

data_processing:
Tif files were aligned with the design file and their fluorescence was measured Agilent Feature extraction software to create .txt files. The .txt files were processed using Agilent Cytogenomics software to generate .xls files and using Nexus 7 Software to generate .bed files, then the .xls and .bed files were compared using BEDTOOLS 50% reciprocal overlap function. Only calls which shared a reciprocal overlap of 50% or greater were retained for further analysis.
BioDiscovery’s FASST2 Segmentation Algorithm, a Hidden Markov Model (HMM) based approach, was the algorithm used to make copy number calls using Nexus 7 Software. The significance threshold for segmentation was set at 1.0E-6 also requiring a minimum of 3 probes per segment and a maximum probe spacing of 1000 between adjacent probes before breaking a segment. The log ratio thresholds for single copy gain and single copy loss were set at 0.3 and -0.3, respectively. A 3:1 sex chromosome gain threshold was set to 1.2 and a 4:1 sex chromosome gain threshold was set to 1.7. Agilent's CytoGenomics ADM-2 algorithm, was used as a second algorithm for all copy number calls after data extraction. Default parameters were used with the exception of setting the minimum segment difference to 0.3 and requiring a minimum of 3 probes per segment.

source_name: genomic DNA from whole blood

label_protocol: 0.5 ug of case DNA was labeled with Cy3-coupled nonamers and 0.5 ug of control DNA (from an unaffected male of European ancestry) was labeled with Cy5-coupled nonamers.

extract_protocol: DNA was extracted from whole blood samples using the Quickgene610L.

tag: Sex

value: male

tag: syndromic versus non-syndromic

value: non-syndromic

tag: cleft type

value: cleft lip and cleft palate

tag: cleft laterality

value: not applicable

source_name: DNA from an unaffected male of European ancestry

value: unaffected


title: CleftProband_889


title: CleftProband_890


title: CleftProband_892

value: female


title: CleftProband_891


title: CleftProband_888


title: CleftProband_885


title: CleftProband_883


title: CleftProband_887


title: CleftProband_881


title: CleftProband_877


title: CleftProband_878


title: CleftProband_884


title: CleftProband_880


title: CleftProband_882


title: CleftProband_879

value: cleft palate only


title: CleftProband_873


title: CleftProband_872


title: CleftProband_874


title: CleftProband_875


title: CleftProband_870


title: CleftProband_871


title: CleftProband_1106

value: bilateral


title: CleftProband_1107

value: right


title: CleftProband_1104


title: CleftProband_1105


title: CleftProband_1108


title: CleftProband_1103


title: CleftProband_886


title: CleftProband_1100

value: left


title: CleftProband_1102


title: CleftProband_1101


title: CleftProband_876


title: CleftProband_1098


title: CleftProband_1097

value: unknown


title: CleftProband_1096


title: CleftProband_1094


title: CleftProband_1093


title: CleftProband_1092


title: CleftProband_1095


title: CleftProband_1089


title: CleftProband_1085


title: CleftProband_1083


title: CleftProband_1087


title: CleftProband_1084


title: CleftProband_1086


title: CleftProband_1082


title: CleftProband_1080


title: CleftProband_1078


title: CleftProband_1091


title: CleftProband_1077


title: CleftProband_1079


title: CleftProband_1076


title: CleftProband_1075


title: CleftProband_1099


title: CleftProband_1074


title: CleftProband_1070


title: CleftProband_1073


title: CleftProband_1072


title: CleftProband_1068


title: CleftProband_1067


title: CleftProband_1088


title: CleftProband_1066


title: CleftProband_1065


title: CleftProband_1063


title: CleftProband_1058


title: CleftProband_1061


title: CleftProband_1060


title: CleftProband_1059


title: CleftProband_1064


title: CleftProband_1057


title: CleftProband_1081


title: CleftProband_1055


title: CleftProband_1056


title: CleftProband_1054


title: CleftProband_1052


title: CleftProband_1090


title: CleftProband_1053


title: CleftProband_1071


title: CleftProband_1051


title: CleftProband_1050


title: CleftProband_1069


title: CleftProband_1049


title: CleftProband_1047


title: CleftProband_1048


title: CleftProband_1045


title: CleftProband_1046


title: CleftProband_1062


title: CleftProband_1043


title: CleftProband_1041


title: CleftProband_1040

value: cleft lip only


title: CleftProband_1039


title: CleftProband_1042

value: syndromic


title: CleftProband_1038


title: CleftProband_1037


title: CleftProband_1032


title: CleftProband_1031


title: CleftProband_1036


title: CleftProband_1034


title: CleftProband_1035


title: CleftProband_1033


title: CleftProband_1028


title: CleftProband_1029


title: CleftProband_1027


title: CleftProband_1026


title: CleftProband_1022


title: CleftProband_1023


title: CleftProband_1025


title: CleftProband_1044


title: CleftProband_1020


title: CleftProband_1021


title: CleftProband_1019


title: CleftProband_1015


title: CleftProband_1024


title: CleftProband_1014


title: CleftProband_1018


title: CleftProband_1017


title: CleftProband_1013


title: CleftProband_1012


title: CleftProband_1011


title: CleftProband_1009


title: CleftProband_1016


title: CleftProband_1010


title: CleftProband_1008


title: CleftProband_1007


title: CleftProband_1004


title: CleftProband_1006


title: CleftProband_1002


title: CleftProband_1005


title: CleftProband_1003


title: CleftProband_1000


title: CleftProband_998

value: Microform


title: CleftProband_999


title: CleftProband_997


title: CleftProband_993


title: CleftProband_992


title: CleftProband_994


title: CleftProband_991


title: CleftProband_996


title: CleftProband_989


title: CleftProband_990


title: CleftProband_1030


title: CleftProband_987


title: CleftProband_986


title: CleftProband_988


title: CleftProband_984


title: CleftProband_983


title: CleftProband_985


title: CleftProband_981


title: CleftProband_982


title: CleftProband_979


title: CleftProband_978


title: CleftProband_1001


title: CleftProband_980


title: CleftProband_977


title: CleftProband_976


title: CleftProband_974


title: CleftProband_973


title: CleftProband_995


title: CleftProband_971


title: CleftProband_969


title: CleftProband_966


title: CleftProband_967


title: CleftProband_968


title: CleftProband_964


title: CleftProband_965


title: CleftProband_959


title: CleftProband_962


title: CleftProband_963


title: CleftProband_960


title: CleftProband_957


title: CleftProband_961


title: CleftProband_956


title: CleftProband_953


title: CleftProband_975


title: CleftProband_958


title: CleftProband_955


title: CleftProband_949


title: CleftProband_951


title: CleftProband_947


title: CleftProband_954


title: CleftProband_972


title: CleftProband_948


title: CleftProband_945


title: CleftProband_946


title: CleftProband_950


title: CleftProband_970


title: CleftProband_940


title: CleftProband_942


title: CleftProband_941


title: CleftProband_939


title: CleftProband_937


title: CleftProband_938


title: CleftProband_944


title: CleftProband_935


title: CleftProband_952


title: CleftProband_932


title: CleftProband_934


title: CleftProband_931


title: CleftProband_933


title: CleftProband_927


title: CleftProband_930


title: CleftProband_928


title: CleftProband_923


title: CleftProband_925


title: CleftProband_926


title: CleftProband_924


title: CleftProband_921


title: CleftProband_920


title: CleftProband_918


title: CleftProband_917


title: CleftProband_929


title: CleftProband_922


title: CleftProband_916


title: CleftProband_943


title: CleftProband_915


title: CleftProband_913


title: CleftProband_912


title: CleftProband_936


title: CleftProband_911


title: CleftProband_909


title: CleftProband_908


title: CleftProband_907


title: CleftProband_906


title: CleftProband_905


title: CleftProband_919


title: CleftProband_903


title: CleftProband_902


title: CleftProband_901


title: CleftProband_895


title: CleftProband_896


title: CleftProband_900


title: CleftProband_898


title: CleftProband_897


title: CleftProband_914


title: CleftProband_899


title: CleftProband_910


title: CleftProband_904


title: Hussain_57_34434_(HuGene-1_0-st-v1)

type: RNA

city: Bethesda

first: Hussain

last: Perwez

state: MD

address: 37 Convent Drive

department: CCR

institute: NIH/NCI

description: Gene expression data from PDAC tumor and non-tumor

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Partek

label: biotin

source_name: human pancreatic Non-tumor tissue sample 16

label_protocol: standard Affymetrix protocol

extract_protocol: none provided by the submitter

value: adjacent non-tumor

tag: grading

tag: Stage

value: IV

tag: resection margin

tag: survival months

tag: survival status


title: Hussain_44_31262_(HuGene-1_0-st-v1)

source_name: human pancreatic Non-tumor tissue sample 12

value: IIB


title: CleftProband_894

value: male


title: Hussain_50_32175_(HuGene-1_0-st-v1)

source_name: human pancreatic tumor tissue sample 38

value: Tumor

value: IIA


title: Hussain_45_31263_(HuGene-1_0-st-v1)

source_name: human pancreatic tumor tissue sample 35


title: Hussain_49_32019_(HuGene-1_0-st-v1)

source_name: human pancreatic Non-tumor tissue sample 14

value: Gx

value: >IIB


title: Hussain_48_32018_(HuGene-1_0-st-v1)

source_name: human pancreatic tumor tissue sample 37


title: Hussain_55_34244_(HuGene-1_0-st-v1)

source_name: human pancreatic Non-tumor tissue sample 15

value: IB


title: Hussain_43_29827_(HuGene-1_0-st-v1)

source_name: human pancreatic tumor tissue sample 34


title: Hussain_41_29819_(HuGene-1_0-st-v1)

source_name: human pancreatic Non-tumor tissue sample 10


title: Hussain_46_31392_(HuGene-1_0-st-v1)

source_name: human pancreatic Non-tumor tissue sample 13


title: Hussain_40_29818_(HuGene-1_0-st-v1)

source_name: human pancreatic tumor tissue sample 33


title: Hussain_42_29826_(HuGene-1_0-st-v1)

source_name: human pancreatic Non-tumor tissue sample 11


title: Hussain_58_34435_(HuGene-1_0-st-v1)

source_name: human pancreatic tumor tissue sample 40


title: Hussain_39_29261_(HuGene-1_0-st-v1)

source_name: human pancreatic tumor tissue sample 32


title: Hussain_56_34245_(HuGene-1_0-st-v1)

source_name: human pancreatic tumor tissue sample 39


title: Hussain_32_27880_(HuGene-1_0-st-v1)

source_name: human pancreatic Non-tumor tissue sample 8


title: Hussain_30_26576_(HuGene-1_0-st-v1)

source_name: human pancreatic tumor tissue sample 27


title: Hussain_38_29164_(HuGene-1_0-st-v1)

source_name: human pancreatic tumor tissue sample 31


title: Hussain_31_27775_(HuGene-1_0-st-v1)

source_name: human pancreatic tumor tissue sample 28


title: Hussain_28_26172_(HuGene-1_0-st-v1)

source_name: human pancreatic tumor tissue sample 26

value: III


title: Hussain_47_31393_(HuGene-1_0-st-v1)

source_name: human pancreatic tumor tissue sample 36


title: Hussain_37_29163_(HuGene-1_0-st-v1)

source_name: human pancreatic Non-tumor tissue sample 9


title: Hussain_24_22505_(HuGene-1_0-st-v1)

source_name: human pancreatic Non-tumor tissue sample 6


title: Hussain_25_22506_(HuGene-1_0-st-v1)

source_name: human pancreatic tumor tissue sample 25


title: Hussain_21_19927_(HuGene-1_0-st-v1)

source_name: human pancreatic tumor tissue sample 24


title: Hussain_33_27881_(HuGene-1_0-st-v1)

source_name: human pancreatic tumor tissue sample 29


title: Hussain_36_29102_(HuGene-1_0-st-v1)

source_name: human pancreatic tumor tissue sample 30


title: Hussain_20_19926_(HuGene-1_0-st-v1)

source_name: human pancreatic Non-tumor tissue sample 5


title: Hussain_29_26171_(HuGene-1_0-st-v1)

source_name: human pancreatic Non-tumor tissue sample 7


title: Hussain_16_17798_(HuGene-1_0-st-v1)

source_name: human pancreatic tumor tissue sample 22


title: Hussain_10_13693_(HuGene-1_0-st-v1)

source_name: huamn normal pancreas 244

value: Normal pancreas


title: Hussain_12_17529_(HuGene-1_0-st-v1)

source_name: human pancreatic tumor tissue sample 20


title: Hussain_15_17797_(HuGene-1_0-st-v1)

source_name: human pancreatic Non-tumor tissue sample 4


title: Hussain_14_17531_(HuGene-1_0-st-v1)

source_name: human pancreatic tumor tissue sample 21


title: E780N

source_name: human pancreatic Non-tumor tissue sample 146


title: Hussain_05_9233_(HuGene-1_0-st-v1)

source_name: human pancreatic tumor tissue sample 17


title: Hussain_13_17530_(HuGene-1_0-st-v1)

source_name: human pancreatic Non-tumor tissue sample 3


title: Hussain_01_3759_(HuGene-1_0-st-v1)

source_name: huamn normal pancreas 242


title: E780T

source_name: human pancreatic tumor tissue sample 173


title: Hussain_09_9728_(HuGene-1_0-st-v1)

source_name: human pancreatic tumor tissue sample 18


title: E671N

source_name: human pancreatic Non-tumor tissue sample 133


title: E770N

source_name: human pancreatic Non-tumor tissue sample 145


title: Hussain_17_18590_(HuGene-1_0-st-v1)

source_name: human pancreatic tumor tissue sample 23


title: Hussain_02_6376_(HuGene-1_0-st-v1)

source_name: human pancreatic Non-tumor tissue sample 1


title: E674N

source_name: human pancreatic Non-tumor tissue sample 144


title: E656T

source_name: human pancreatic tumor tissue sample 153


title: E671T

source_name: human pancreatic tumor tissue sample 169


title: E674T

source_name: human pancreatic tumor tissue sample 170


title: Hussain_08_9727_(HuGene-1_0-st-v1)

source_name: human pancreatic Non-tumor tissue sample 2


title: E99Tp1

source_name: human pancreatic tumor tissue sample 174


title: E739T

source_name: human pancreatic tumor tissue sample 171


title: Hussain_11_14694_(HuGene-1_0-st-v1)

source_name: human pancreatic tumor tissue sample 19


title: Hussain_04_6483_(HuGene-1_0-st-v1)

source_name: huamn normal pancreas 243


title: E636T

source_name: human pancreatic tumor tissue sample 166


title: E770T

source_name: human pancreatic tumor tissue sample 154


title: E639T

source_name: human pancreatic tumor tissue sample 167


title: E762T

source_name: human pancreatic tumor tissue sample 172


title: E655T

source_name: human pancreatic tumor tissue sample 168


title: E656N

source_name: human pancreatic Non-tumor tissue sample 143


title: E636N

source_name: human pancreatic Non-tumor tissue sample 142


title: E604N

source_name: human pancreatic Non-tumor tissue sample 140


title: E626T

source_name: human pancreatic tumor tissue sample 165


title: E530T

source_name: human pancreatic tumor tissue sample 158


title: E623N

source_name: human pancreatic Non-tumor tissue sample 141


title: E623T

source_name: human pancreatic tumor tissue sample 164


title: E604T

source_name: human pancreatic tumor tissue sample 163


title: E577N

source_name: human pancreatic Non-tumor tissue sample 138


title: E523T

source_name: human pancreatic tumor tissue sample 157


title: E593T

source_name: human pancreatic tumor tissue sample 161


title: E577T

source_name: human pancreatic tumor tissue sample 152


title: E580N

source_name: human pancreatic Non-tumor tissue sample 139


title: E505T

source_name: human pancreatic tumor tissue sample 156


title: E523N

source_name: human pancreatic Non-tumor tissue sample 132


title: E532T

source_name: human pancreatic tumor tissue sample 159


title: E527N

source_name: human pancreatic Non-tumor tissue sample 136


title: E505N

source_name: human pancreatic Non-tumor tissue sample 135


title: E580T

source_name: human pancreatic tumor tissue sample 160


title: E504T

source_name: human pancreatic tumor tissue sample 149


title: E530N

source_name: human pancreatic Non-tumor tissue sample 137


title: E504N

source_name: human pancreatic Non-tumor tissue sample 134


title: E527T

source_name: human pancreatic tumor tissue sample 151


title: E387T

source_name: human pancreatic tumor tissue sample 147


title: E480N

source_name: human pancreatic Non-tumor tissue sample 131


title: 90_E234-Tn7_N

source_name: human pancreatic Non-tumor tissue sample 85


title: E480T

source_name: human pancreatic tumor tissue sample 148


title: E599T

source_name: human pancreatic tumor tissue sample 162


title: E494T

source_name: human pancreatic tumor tissue sample 155


title: E520T

source_name: human pancreatic tumor tissue sample 150


title: 9_E33-Tc7_T

source_name: human pancreatic tumor tissue sample 130


title: 88_E229-Tn7_N

source_name: human pancreatic Non-tumor tissue sample 83


title: 87_E229-Tp1_T

source_name: human pancreatic tumor tissue sample 128


title: 83_E250-Tp1_T

source_name: human pancreatic tumor tissue sample 126


title: 89_E234-Tp1_T

source_name: human pancreatic tumor tissue sample 129


title: 76_E218-Tn7_N

source_name: human pancreatic Non-tumor tissue sample 77


title: 84_E250-Tn7_N

source_name: human pancreatic Non-tumor tissue sample 81


title: 85_E220-Tp1_T

source_name: human pancreatic tumor tissue sample 127


title: 8_E122_Tn13

source_name: human pancreatic Non-tumor tissue sample 199


title: 8_E28-Tn16_N

source_name: human pancreatic Non-tumor tissue sample 84


title: 75_E218-Tp1_T

source_name: human pancreatic tumor tissue sample 121


title: 71_E421_T

source_name: human pancreatic tumor tissue sample 240


title: 78_E245-Tn7_N

source_name: human pancreatic Non-tumor tissue sample 78


title: 77_E245-Tp1_T

source_name: human pancreatic tumor tissue sample 122


title: 71_E208-Tp1_T

source_name: human pancreatic tumor tissue sample 119


title: 72_E208-Tn8_N

source_name: human pancreatic Non-tumor tissue sample 75


title: 82_E249-Tn7_N

source_name: human pancreatic Non-tumor tissue sample 80


title: 7_E28-Tp1_T

source_name: human pancreatic tumor tissue sample 124


title: 86_E220-Tn7_N

source_name: human pancreatic Non-tumor tissue sample 82


title: 80_E246-Tn7_N

source_name: human pancreatic Non-tumor tissue sample 79


title: 79_E246-Tp1_T

source_name: human pancreatic tumor tissue sample 123


title: 68_E501_N

source_name: human pancreatic Non-tumor tissue sample 197


title: 70_E203-Tn7_N

source_name: human pancreatic Non-tumor tissue sample 74


title: 73_E209-Tp2_T

source_name: human pancreatic tumor tissue sample 120


title: 70_E420_T_2

source_name: human pancreatic tumor tissue sample 239


title: 7_E122_Tn8

source_name: human pancreatic tumor tissue sample 241


title: 81_E249-Tp1_T

source_name: human pancreatic tumor tissue sample 125


title: 68_E186-Tn7_N

source_name: human pancreatic Non-tumor tissue sample 72


title: 74_E209-Tn8_N

source_name: human pancreatic Non-tumor tissue sample 76


title: 69_E401_T

source_name: human pancreatic tumor tissue sample 238


title: 69_E203-Tp1_T

source_name: human pancreatic tumor tissue sample 118


title: 67_E501_T

source_name: human pancreatic tumor tissue sample 237


title: 66_E182-Tn7_N

source_name: human pancreatic Non-tumor tissue sample 71


title: 65_E182-Tp2_T

source_name: human pancreatic tumor tissue sample 116


title: 62_E409_N_R

source_name: human pancreatic Non-tumor tissue sample 194


title: 66_E499_N_R

source_name: human pancreatic Non-tumor tissue sample 196


title: 65_E499_T

source_name: human pancreatic tumor tissue sample 236


title: 64_E415_N

source_name: human pancreatic Non-tumor tissue sample 195


title: 64_E181-Tn8_N

source_name: human pancreatic Non-tumor tissue sample 70


title: 60_E405_N

source_name: human pancreatic Non-tumor tissue sample 193


title: 58_E165-Tn7_N

source_name: human pancreatic Non-tumor tissue sample 67


title: 60_E178-Tn7_N

source_name: human pancreatic Non-tumor tissue sample 68


title: 54_E152-Tn7_N

source_name: human pancreatic Non-tumor tissue sample 65


title: 63_E415_T

source_name: human pancreatic tumor tissue sample 235


title: 55_E400_T

source_name: human pancreatic tumor tissue sample 230


title: 6_E21-Tn16_N

source_name: human pancreatic Non-tumor tissue sample 73


title: 61_E409_T

source_name: human pancreatic tumor tissue sample 234


title: 6_E205_Tn7

source_name: human pancreatic Non-tumor tissue sample 198


title: 54_E394_N

source_name: human pancreatic Non-tumor tissue sample 190


title: 56_E400_N

source_name: human pancreatic Non-tumor tissue sample 191


title: 57_E403_T

source_name: human pancreatic tumor tissue sample 231


title: 57_E165-Tp1_T

source_name: human pancreatic tumor tissue sample 111


title: 55_E162-Tp1_T

source_name: human pancreatic tumor tissue sample 110


title: 58_E403_N

source_name: human pancreatic Non-tumor tissue sample 192


title: 67_E186-Tp2_T

source_name: human pancreatic tumor tissue sample 117


title: 59_E178-Tp1_T

source_name: human pancreatic tumor tissue sample 112


title: 59_E405_T

source_name: human pancreatic tumor tissue sample 232


title: 63_E181-Tp1_T

source_name: human pancreatic tumor tissue sample 115


title: 61_E179-Tp1_T

source_name: human pancreatic tumor tissue sample 114


title: 62_E179-Tn7_N

source_name: human pancreatic Non-tumor tissue sample 69


title: 53_E394_T

source_name: human pancreatic tumor tissue sample 229


title: 56_E162-Tn9_N

source_name: human pancreatic Non-tumor tissue sample 66


title: 53_E152-Tc5_T

source_name: human pancreatic tumor tissue sample 109


title: 52_E388_N

source_name: human pancreatic Non-tumor tissue sample 189


title: 52_E139-Tn13_N

source_name: human pancreatic Non-tumor tissue sample 64


title: 51_E388_T

source_name: human pancreatic tumor tissue sample 228


title: 51_E139-Tp1_T

source_name: human pancreatic tumor tissue sample 108


title: 50_E488_N

source_name: human pancreatic Non-tumor tissue sample 188


title: 50_E138-Tn14_N

source_name: human pancreatic Non-tumor tissue sample 63


title: 48_E136-Tn13_N

source_name: human pancreatic Non-tumor tissue sample 61


title: 47_E136-Tp1_T

source_name: human pancreatic tumor tissue sample 106


title: 49_E138-Tp1_T

source_name: human pancreatic tumor tissue sample 107


title: 47_E482_T

source_name: human pancreatic tumor tissue sample 226


title: 42_E365_N

source_name: human pancreatic Non-tumor tissue sample 183


title: 48_E482_N

source_name: human pancreatic Non-tumor tissue sample 186


title: 5_E205_Tp3

source_name: human pancreatic tumor tissue sample 233


title: 41_E365_T

source_name: human pancreatic tumor tissue sample 224


title: 46_E133-Tn15_N

source_name: human pancreatic Non-tumor tissue sample 60


title: 43_E130-Tp1_T

source_name: human pancreatic tumor tissue sample 104


title: 44_E130-Tn13_N

source_name: human pancreatic Non-tumor tissue sample 59


title: 49_E488_T

source_name: human pancreatic tumor tissue sample 227


title: 40_E120-Tn13_N

source_name: human pancreatic Non-tumor tissue sample 57


title: 44_E368_N_R

source_name: human pancreatic Non-tumor tissue sample 184


title: 45_E370_T

source_name: human pancreatic tumor tissue sample 225


title: 4_E151_Tn8

source_name: human pancreatic Non-tumor tissue sample 187


title: 40_E465_N

source_name: human pancreatic Non-tumor tissue sample 182


title: 41_E123-Tc7_T

source_name: human pancreatic tumor tissue sample 103


title: 4_E12-Tn15_N

source_name: human pancreatic Non-tumor tissue sample 62


title: 5_E21-Tc8_T

source_name: human pancreatic tumor tissue sample 113


title: 46_E370_N

source_name: human pancreatic Non-tumor tissue sample 185


title: 39_E465_T

source_name: human pancreatic tumor tissue sample 222


title: 39_E120-Tc7_T

source_name: human pancreatic tumor tissue sample 101


title: 45_E133-Tp4_T

source_name: human pancreatic tumor tissue sample 105


title: 38_E119-Tn13_N

source_name: human pancreatic Non-tumor tissue sample 56


title: 42_E123-Tn13_N

source_name: human pancreatic Non-tumor tissue sample 58


title: 38_E445_N

source_name: human pancreatic Non-tumor tissue sample 181


title: 37_E445_T

source_name: human pancreatic tumor tissue sample 221


title: 37_E119-Tc7_T

source_name: human pancreatic tumor tissue sample 100


title: 36_E440_N

source_name: human pancreatic Non-tumor tissue sample 180


title: 35_E440_T

source_name: human pancreatic tumor tissue sample 220


title: 36_E109-Tn13_N

source_name: human pancreatic Non-tumor tissue sample 55


title: 34_E419_Tp1

source_name: human pancreatic tumor tissue sample 219


title: 35_E109Tp1_T

source_name: human pancreatic tumor tissue sample 99


title: 33_E94-Tc7_T

source_name: human pancreatic tumor tissue sample 98


title: 32_E88-Tn13_N

source_name: human pancreatic Non-tumor tissue sample 53


title: 28_E197_Tp2

source_name: human pancreatic tumor tissue sample 213


title: 32_E169_Tp1

source_name: human pancreatic tumor tissue sample 217


title: 28_E82-Tn13_N

source_name: human pancreatic Non-tumor tissue sample 50

value: IVB


title: 29_E86-Tc8_T

source_name: human pancreatic tumor tissue sample 96


title: 3_E12-Tp2_T

source_name: human pancreatic tumor tissue sample 102


title: 29_E221_Tp1

source_name: human pancreatic tumor tissue sample 214


title: 33_E174_Tp1

source_name: human pancreatic tumor tissue sample 218


title: 34_E94-Tn13_N

source_name: human pancreatic Non-tumor tissue sample 54


title: 3_E151_Tp2

source_name: human pancreatic tumor tissue sample 223


title: 31_E157_Tp1_R

source_name: human pancreatic tumor tissue sample 216


title: 25_E73-Tc7_T

source_name: human pancreatic tumor tissue sample 94


title: 23_E193_Tp2_R

source_name: human pancreatic tumor tissue sample 210


title: 25_E194_Tp1

source_name: human pancreatic tumor tissue sample 211


title: 24_E64-Tn16_N

source_name: human pancreatic Non-tumor tissue sample 48

value: IVA


title: 27_E172_Tp1

source_name: human pancreatic tumor tissue sample 212


title: 31_E88-Tc7_T

source_name: human pancreatic tumor tissue sample 97


title: 23_E64-Tp3_T

source_name: human pancreatic tumor tissue sample 93


title: 27_E82-Tp1_T

source_name: human pancreatic tumor tissue sample 95


title: 21_E58-Tc7_T

source_name: human pancreatic tumor tissue sample 92


title: 22_E58-Tn13_N

source_name: human pancreatic Non-tumor tissue sample 47


title: 20_E253_Tn7

source_name: human pancreatic Non-tumor tissue sample 176


title: 30_E86-Tn13_N

source_name: human pancreatic Non-tumor tissue sample 52


title: 22_E164_Tn7_R

source_name: human pancreatic Non-tumor tissue sample 177


title: 20_E52-Tn15_N

source_name: human pancreatic Non-tumor tissue sample 46


title: 30_E223_Tp1_R

source_name: human pancreatic tumor tissue sample 215


title: 26_E194_Tn7_R

source_name: human pancreatic Non-tumor tissue sample 178


title: 2_E74_Tn15

source_name: human pancreatic Non-tumor tissue sample 179


title: 26_E73-Tn13_N

source_name: human pancreatic Non-tumor tissue sample 49


title: 19_E52-Tc7_T

source_name: human pancreatic tumor tissue sample 90


title: 2_E5-Tn14_N

source_name: human pancreatic Non-tumor tissue sample 51


title: 16_E45-Tn14_N

source_name: human pancreatic Non-tumor tissue sample 44


title: 18_E48-Tn13_N

source_name: human pancreatic Non-tumor tissue sample 45


title: 14_E42-Tn14_N

source_name: human pancreatic Non-tumor tissue sample 43


title: 19_E253_Tp1

source_name: human pancreatic tumor tissue sample 207


title: 15_E45-Tc7_T

source_name: human pancreatic tumor tissue sample 88


title: 15_E260_Tp1

source_name: human pancreatic tumor tissue sample 204


title: 16_E262_Tp1

source_name: human pancreatic tumor tissue sample 205

value: G?


title: 21_E164_Tp1

source_name: human pancreatic tumor tissue sample 209


title: 17_E251_Tp1

source_name: human pancreatic tumor tissue sample 206


title: 14_E202_Tp1

source_name: human pancreatic tumor tissue sample 203


title: 11_E29_Tp1

source_name: human pancreatic tumor tissue sample 201


title: 10_E33-Tn13_N

source_name: human pancreatic Non-tumor tissue sample 41


title: 10_E225_Tp1

source_name: human pancreatic tumor tissue sample 200


title: 1_E74_Tp4

source_name: human pancreatic tumor tissue sample 208

value: IA


title: 17_E48-Tc7_T

source_name: human pancreatic tumor tissue sample 89


title: 11_E41-Tc7_T

source_name: human pancreatic tumor tissue sample 86


title: 12_E41-Tn13_N

source_name: human pancreatic Non-tumor tissue sample 42


title: 12_E60_Tp1

source_name: human pancreatic tumor tissue sample 202


title: 13_E42-Tc10_T

source_name: human pancreatic tumor tissue sample 87


title: 18_E251_Tn7

source_name: human pancreatic Non-tumor tissue sample 175


title: SAMPLE 24: IL_IUGR_226_228742_IUGR_HFCS_M_kid

city: Winston-Salem

first: Laura

last: Cox

state: NC

address: One Medical Center Blvd

department: Internal Medicine

institute: Wake Forest School of Medicine

hyb_protocol: cRNA samples were then hybridized to HumanHT-12 v3 Expression BeadChips (Illumina, Inc.) as specified by the Illumina™ TotalPrep™-96 RNA Amplification Kit protocol.

scan_protocol: Illumina GenomeStudio software, Illumina BeadStation 500GX

data_processing: Gene expression data were extracted and log2-transformed using GenomeStudio software (Illumina, Inc.) and subsequently analyzed using Partek® Genomics Suite (Partek®, St. Louis, MO). Signal intensities were all-median normalized, and differentially expressed genes were identified by Analysis of Variance (ANOVA; p < 0.05).

organism: Papio hamadryas

source_name: male IUGR, 7-week High Fat, High Simple Carbohydrates, High Salt Diet, kidney cortex

label_protocol: Complementary RNA (cRNA) was synthesized and biotinylated using the Illumina™ TotalPrep™-96 RNA Amplification Kit (Illumina Inc., San Diego, CA).

growth_protocol: Fed chow diet ad libitum

extract_protocol: Total RNA was isolated from an approximately 5 mg section of each frozen kidney biopsy using a Power Gen Homogenizer (Omni International, Wilmington, DE) and TRI Reagent™ Solution (Invitrogen™, Carlsbad, CA) as previously described in PMID: 17185341. RNA integrity was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA), and RNA concentration was determined by UV-Vis spectrophotometry using a Nanodrop™ 2000 (Thermo Fisher Scientific, Wilmington, DE)

treatment_protocol: Kidney cortex collected by punch biopsy and immediately snap frozen

value: Kidney Cortex


title: SAMPLE 22: IL_IUGR_224_228389_IUGR_HFCS_M_kid


title: SAMPLE 23: IL_IUGR_225_228609_IUGR_HFCS_M_kid


title: 1_E5-Tc8_T

source_name: human pancreatic tumor tissue sample 91


title: SAMPLE 8: IL_IUGR_210_228473_CON_chow_M_kid

source_name: male control, baseline, chow diet, kidney cortex


title: SAMPLE 18: IL_IUGR_220_228392_IUGR_HFCS_F_kid

source_name: female IUGR, 7-week High Fat, High Simple Carbohydrates, High Salt Diet, kidney cortex

value: female


title: SAMPLE 20: IL_IUGR_213_228609_IUGR_chow_M_kid

source_name: male IUGR, baseline, chow diet, kidney cortex


title: NGF3

city: Hamburg

first: Stefan

middle: G

last: Lechner

address: Martinistrasse 52

department: Anaesthesiology

institute: University Medical Center Hamburg-Eppendorf

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequence reads were aligned to the mouse refernce genome GRCm38 and differential gene expression analysis was performed using the BioJupies platform (PMID: 30447998)
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: Dorsal root ganglion

growth_protocol: Digested DRG were grown in medium [DMEM-F12 (Thermo Fisher Scientific) supplemented with L-glutamine (2 µM, Sigma-Aldrich), glucose (8 mg/ml, Sigma-Aldrich), penicillin (200 U/ml)–streptomycin (200 µg/ml) (Thermo Fisher Scientific), 5 % fetal horse serum (Thermo Fischer Scientific)],

extract_protocol:
Samples (20 cells each) were collected by aspiration into fire polished glass pipettes with a tip diameter of ~25 µm that were filled with 2µl of  buffer containing 1µL RNAse inhibitor (Takara #2313A) in 49 µL PBS and RNA was extracted using the SmartSeq2 protocol
Libraries were generated using the Nextera DNA Sample Preparation kit (Illumina) following the manufacturer’s instructions.

treatment_protocol: Samples 1-3 were grown for 24 hours after plating in normal gorwth medium and samples 4-6 were grown in the presence of 50 ng/ml NGF.

tag: cell type

value: CHRNA3-EGFP-positive neurons

tag: treatment

value: 50 ng/ml NGF


title: SAMPLE 14: IL_IUGR_207_228387_IUGR_chow_F_kid

source_name: female IUGR, baseline, chow diet, kidney cortex

tag: tissue

tag: gender


title: SAMPLE 12: IL_IUGR_223_228476_CON_HFCS_M_kid

source_name: male control, 7-week High Fat, High Simple Carbohydrates, High Salt Diet, kidney cortex


title: SAMPLE 7: IL_IUGR_209_228428_CON_chow_M_kid


title: SAMPLE 19: IL_IUGR_212_228389_IUGR_chow_M_kid


title: CTL2

value: untreated


title: NGF1


title: SAMPLE 17: IL_IUGR_219_228387_IUGR_HFCS_F_kid


title: SAMPLE 13: IL_IUGR_206_228369_IUGR_chow_F_kid


title: SAMPLE 10: IL_IUGR_221_228428_CON_HFCS_M_kid

value: male


title: SAMPLE 21: IL_IUGR_214_228742_IUGR_chow_M_kid


title: SAMPLE 15: IL_IUGR_208_228392_IUGR_chow_F_kid


title: SAMPLE 16: IL_IUGR_218_228369_IUGR_HFCS_F_kid


title: SAMPLE 9: IL_IUGR_211_228476_CON_chow_M_kid


title: SAMPLE 11: IL_IUGR_222_228473_CON_HFCS_M_kid


title: NGF2


title: CTL1


title: SAMPLE 5: IL_IUGR_216_228385_CON_HFCS_F_kid

source_name: female control, 7-week High Fat, High Simple Carbohydrates, High Salt Diet, kidney cortex


title: CTL3


title: SAMPLE 3: IL_IUGR_205_228497_CON_chow_F_kid

source_name: female control, baseline, chow diet, kidney cortex


title: SAMPLE 2: IL_IUGR_204_228385_CON_chow_F_kid


title: Stat3C_CD4_mouse6

city: Berlin

first: Francis

last: Baumgartner

address: Hindenburgdamm 30

institute: Charité University Medicine Berlin

data_processing:
Illumina adapter clipping with cutadapt v3.4
Quality trimming with trimmomatic v0.39, mode MAXINFO, target read length 75, strictness 0.5
Transcript quantification with salmon v1.5.2, with gcBias correction, with seqBias correction
Generation of a gene count matrix with tximport v1.20.0, countsFromAbundace = lengthScaledTPM
Minimum expression filtering and normalization with edgeR v3.34.1, filtering with filterByExpr function, TMM normalization with calcNormFactors, conversion to counts per million with cpm function
Assembly: GRCm38, Ensembl release 97
Supplementary files format and content: Tab-delimited text file with isoform identifiers, raw counts and transcripts per million as output by salmon (“quant.sf” file)
Supplementary files format and content: Tab-delimited text file with raw gene counts for each gene per sample
Supplementary files format and content: Tab-delimited text file with normalized gene counts for each gene per sample (counts per million, TMM normalized)

source_name: Spleen

growth_protocol: naive CD4 T-cells were stimulated with 0.25 mg/ml hamster anti-CD3 and 1.0 mg/ml anti-CD28 in goat-anti-hamster coated tissue culture plates in the presence of 2 mg/ml anti-IFNg and 2 mg/ml anti-IL-4 for 2 days

extract_protocol:
RNA was extracted using the Quiagen MicroRNAeasy kit with Dnase I digestion
Automated Illumina TruSeq Stranded mRNA Sample Prep Kit (Cat. No. RS-122-2101) was used with 100ng of input RNA for the construction of sequencing libraries

treatment_protocol: To induce polaization of CD4+ T cells into pathogenic Th17 cells, 20 ng/ml IL-6 (Peprotech), 20 ng/ml IL-1b (Peprotech) and 20 ng/ml IL-23 (eBiosscience) were added to the culture medium.

value: Spleen

tag: age

value: post natal day 35

tag: genotype

value: Stat3CStopfl/fl Cd4-Cre (S3CD4)

tag: stimulation

value: IL6, IL1b, IL23

value: Purified CD4+ T-cells


title: Stat3C_CD4_mouse5

tag: strain


title: Stat3C_CD4_mouse4


title: SAMPLE 4: IL_IUGR_215_227827_CON_HFCS_F_kid


title: SAMPLE 6: IL_IUGR_217_228497_CON_HFCS_F_kid


title: Wt_CD4_mouse3

value: Wildtype


title: SAMPLE 1: IL_IUGR_203_227827_CON_chow_F_kid


title: Wt_CD4_mouse2


title: Lats1/2 KO-rep-2

city: Worcester

first: Junhao

last: Mao

state: MA

address: 55 N Lake Ave

department: MCCB

institute: UMass Medical School

data_processing:
star alignment
featureCount
DESeq2
Genome_build: GRCm38 (annotation ensembl v92)
Supplementary_files_format_and_content: Excel, DESeq2 output

source_name: total small intestine

extract_protocol:
Small intestine tissue was dissected at day8 postnatal. The tissue was wash and flashed with cold PBS and total RNA was harvested using Trizol reagent and RNeasy kit from Qiagen.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: small intestine

value: post natal day 8

value: VilCre+; Lats1/2-/-


title: Control-rep-2

value: VilCre-; Lats1/2-/-


title: Lats1/2 KO-rep-1


title: Wt_CD4_mouse1


title: cerebellum_20w

city: Jerusalem

first: Tal

last: Michaeli

address: Ein Kerem Campus

country: Israel

institute: The Hebrew University

description:
denovo_methylation_Figure_1a_All_samples_with_otherTissues.xls
demethylation_Figure_1a_All_samples_with_otherTissues.xls
Figure_5s_.xls

data_processing:
Quality control applied with trim_galore V0.6.0 deploying cutadapt V1.18 and fastqc v0.11.7.
Paired-end bisulfite treated FASTQ files were aligned by Bismark V0.13.1 deploying Bowtie2 aligner to mm10 assembly.
Methylation calling performed with bismark_methylation_extractor followed by Bismark cov2cytp and a custom AWK script transforming files to methylKit input format.
Differential methylated regions were obtain with methylKit R-package V1.10.0 and earlier consistent versions.
Genome_build: mm10
Supplementary_files_format_and_content: Tables with methylation levels for each sample (columns) in each relevant tile (rows).

source_name: Cerebellum

extract_protocol:
Hindlimb muscles were dissected from mice following euthanization and kept in wash solution (Ham’s F10 media supplemented with 10% horse serum). The muscles were then finely minced with a surgical scalpel and digested in 2 mg/ml Collagenase II (Worthington, 340 U/mg) for 90 min with agitation. Dissociated fibers were washed and further digested with shaking in 100 U/ml Collagenase II and 2 U/ml Dispase (Invitrogen) for 30 min in a volume of 10 ml, passed 10 times through a 20-G needle to release the associated satellite cells and then washed two more times and filtered through a 45-mm cell strainer. Mononuclear cells from each sample were resuspended in 500 ml wash solution, stained with VCAM1-biotin, CD31-APC, CD45- APC and Sca1-Pacific-Blue antibodies (Biolegend) using a 1:100 dilution at 4°C with gentle agitation for 30 min, washed and resuspended in 500 ml and then stained with Streptavidin-PE-Cy7 (1:100) at 4°C with gentle agitation for 15 min. The resulting preparation contains satellite cells (VCAM1+/CD31-/CD45-/Sca-), which can be separated from remaining cells and debris using flow cytometry. DNA was isolated from purified satellite cells, incubated in lysis buffer (25 mM Tris-HCl (pH  8), 2 mM EDTA, 0.2% SDS, 200 mM NaCl) supplemented with 300 μg/ml proteinase K (Roche) followed by phenol:chloroform extraction and ethanol precipitation.
The methylation profile was checked using the RRBS assay [Boyle, 2012]. Briefly, the DNA was digested with the MspI enzyme to yield CpG enriched fragments. Adapter sequences were ligated at both ends, and DNA fragments were then treated with sodium-bisulfite, allowing for easy distinction between methylated and unmethylated bases. The DNA was then amplified by PCR to produce the final libraries.

treatment_protocol: Muscle injury was carried out on hind-limb muscles (tibialis anterior, gastrocnemius, and quadriceps) from 8.5-9 month old mice by piercing multiple times with a 23-gauge needle.

value: Cerebellum tissue

value: NORMAL

value: 20 weeks old


title: Control-rep-1


title: LATS1/2 DKO MEF CP1 4 days repeat1

data_processing:
Paired-end reads were aligned to mm10, with star_2.5.3a, annotated with GENCODE Mouse release 21.
Aligned exon fragments with mapping quality higher than 20 were counted toward gene expression with featureCounts_1.5.2.
TPM (Transcript Per Kilobase Million) values were created from counts.
Genome_build: mm10
Supplementary_files_format_and_content: excel, count and TPM

source_name: Mouse embryonic fibroblasts

growth_protocol: MEF cells are grown in DMEM with 10% FBS + 2mM L-glutamine + 4.5g/L Glucose

extract_protocol:
After treatment the MEF cells were washed with cold PBS and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MEF cells were treated with MGH-CP1 inhibitor at 1uM or control DMSO for 2days or 4 days before total RNA isolation

tag: cell types

value: MEF cells from E13.5 mouse gestation embryo

tag: passage

value: MGH-CP1 1uM in DMSO


title: LATS1/2 DKO MEF DMSO 2 days

value: DMSO


title: liver_1w

source_name: Liver

value: Liver tissue

value: 1 week old


title: LATS1/2 DKO MEF CP1 2 days repeat1


title: LATS1/2 DKO MEF CP1 4 days repeat2


title: WT MEF DMSO 2 days


title: LATS1/2 DKO MEF DMSO 4 days


title: LATS1/2 DKO MEF CP1 2 days repeat2


title: spleen

value: Spleen tissue


title: WT MEF CP1 4 days repeat 2


title: WT MEF DMSO 4 days


title: WT MEF CP1 2 days repeat 2


title: WT MEF CP1 4 days repeat 1


title: spleen_20w


title: PeakMicroglia_MiGS_Sample2

city: Houston

first: Angela

middle: H

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

data_processing:
For MiGS data, reads were aligned to mm10 with bowtie2 (options: -N 1 -L 20 --phred33). Reads with mapping quality (MAPQ) < 10 were discarded. Average coverage in non-overlapping 50bp bins was counted genome-wide using the preprocessing functions of MethylAction (Bhasin, et al., 2015). Chromosomes X and Y were excluded, because the samples are a pool of mice from both sexes.
For RNA-seq data, reads were aligned to mm10 using TopHat (Trapnell, et al., 2009) (options: --library-type fr-firststrand). Read counts were quantified for ENSEMBL mouse genes using featureCounts (Liao, et al., 2014) (options: -F GTF -s 2 -Q 30 -T 20 -p -B -C). FPKM values were computed using edgeR (Robinson, et al., 2010). Chromosomes X and Y were excluded, because the samples are a pool of mice from both sexes.
Genome_build: mm10
Supplementary_files_format_and_content: For MiGS data, a text file has been provided for each sample that contains normalized read counts within the non-overlapping 50bp windows genome wide. Windows with all zero values or all values below a noise cutoff have been removed, so only windows considered to have signal remain. Each row represents one 50bp window. The genomic coordinates (mm10) are provided in the first three columns. The remaining column contains the average coverage of MiGS reads for the window in the sample. For RNA-seq data, reads were counted for ENSEMBL transcription units using featureCounts. The provided CSV file contains one row for each gene, one column containing the raw read counts (no normalization for library size) for each sample, and one column containing the FPKM-normalized read counts for each sample.

source_name: microglia

growth_protocol: C57Bl/6 mice were obtained from the National Cancer Institute. Ccr2rfp/+::Cx3cr1gfp/+ mice were generated by cross breeding Ccr2rfp/rfp::C57Bl/6 mice (Saederup et al., 2010) with Cx3cr1gfp/gfp::C57Bl/6 mice (Jung et al., 2000). Animal experiments were performed according to the protocols approved by the Institutional Animal Care and Use Committee at the Cleveland Clinic following the National Institute of Health guidelines for animal care.

extract_protocol:
The library was constructed by enriching for methylated DNA fragments using MiGS (MBD-isolated Genome Sequencing, Serre 2010). After enrichment, library was prepared using the Illumina ChIP-seq preparation protocol (2007).
Brains and spinal cords were removed and homogenized. Mononuclear cells were separated with a 30% / 70% Percoll (GE Healthcare, NJ, USA) gradient as previously reported (Pino and Cardona, 2011). Single cell suspensions from CNS were stained with anti-F4/80-APC (BM8; eBioscience, CA, USA) and anti-CD45-PerCP (30-F11; BioLegend). Cells were sorted on a BD FACSAria II (BD Biosciences). Data were analyzed with FlowJo software (TreesStar, OR, USA).  Genomic DNA and RNA were extracted from the same samples using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen).

treatment_protocol: EAE was induced in Ccr2rfp/+::Cx3cr1gfp/+ mice of 24-28 weeks of age using myelin-oligodendrocyte-glycoprotein peptide 35-55 (MOG) as described (Huang et al., 2006). All mice were weighed and graded daily for clinical stages as previously reported (Saederup et al., 2010). We defined clinical stage of EAE as follows: onset was the day EAE signs appeared; peak was the second day score didn’t increase after sustained daily worsening; and recovery was the second day score didn’t decrease after a period of sustained daily improvement.

tag: activation

value: peak

tag: background mouse strain


title: IBd-99_Input DNA

city: Wuhan

first: Handong

last: Su

state: Hubei

address: No.1,Shizishan Street · Hongshan District

institute: Huazhong Agricultural University

data_processing:
Basecalls performed using Illumina CASAVA.
Raw reads from ChIP-seq data were mapped to the different Brachypodium genomes using bwa mem with the default parameters.
The mapped reads with MAPQ values >= 20 as uniquely mapping for further analysis.
RPM values were calculated with 1 kb windows along the genome to make it comparable between different samples.
Genome_build: Bdistachyon_314_v3.0; Bhybridum_463_v1.0; Bstacei_316_v1.0
Supplementary_files_format_and_content: BED files contains the positions of mapped reads of the ChIP-seq.

organism: Brachypodium stacei

growth_protocol: Suitable materials were planted in the greenhouse ChIP-seq experiments.

extract_protocol:
Extracted nuclei were digested with micrococcal nuclease (Sigma-Al drich) for ChIP experiments using the maize CENH3 antibody.The ChIP-enriched DNAs of different lines of  Brachypodium species were performed Illumina sequencing. The  CENH3 antibody is a rabbit polyclonal antiserum and was raised against the peptides: KDIQLARRISGHRGY. Keyhole limpet hemocyanin (KLH)-conjugated peptide was used to immunize rabbits.
ChIP libraries were prepared according to standard Illumina's instructions.180-400 bp fragments (contained the joint) were selected by gel extraction.

tag: genotype/variation

value: young leaves

tag: chip antibody


title: PeakMicroglia_MiGS_Sample1


title: NaiveMicroglia_MiGS_Sample2

value: naïve


title: IBd-92_CENH3_ChIPSeq

tag: molecule type

value: ChIPed DNA


title: IBd-99_CENH3_ChIPSeq


title: NaiveMicroglia_MiGS_Sample1


title: CleftProband_349

hyb_protocol: 34 ug of each labeled DNA was co-hybridized to a Roche NimbleGen human whole genome tiling microarray (Human CGH 2.1M Whole-Genome Tiling v2.0D Array)

scan_protocol: Arrays were scanned on a Roche NimbleGen microarray scanner.

data_processing:
532.tif and 635.tif files were analyzed using DEVA software to generate a data_summary.txt file and segMNT.txt file. Data_summary.txt files were analyzed using Nexus 7 Software to generate NexusData.bed files and then compared to the segMNT.txt file using BEDTOOLS 50% reciprocal overlap function. Only calls which shared a reciprocal overlap of 50% or greater were retained for further analysis.
BioDiscovery’s FASST2 Segmentation Algorithm, a Hidden Markov Model (HMM) based approach, was the algorithm used to make copy number calls using Nexus 7 Software. The significance threshold for segmentation was set at 1.0E-6 also requiring a minimum of 3 probes per segment and a maximum probe spacing of 1000 between adjacent probes before breaking a segment. The log ratio thresholds for single copy gain and single copy loss were set at 0.3 and -0.3, respectively. A 3:1 sex chromosome gain threshold was set to 1.2 and a 4:1 sex chromosome gain threshold was set to 1.7. NimbleGen's DEVA segMNT algorithm, which minimizes squared error relative to the segment means, was used as a second algorithm for all copy number calls after data extraction, LOESS spatial correction and background correction. Default parameters were used with the exception of setting the minimum segment difference to 0.3 and requiring a minimum of 3 probes per segment.

source_name: genomic DNA from whole blood

label_protocol: 1 ug of case DNA was labeled with Cy3-coupled nonamers and 1 ug of control DNA (from an unaffected male from the Philippines) was labeled with Cy5-coupled nonamers.

tag: Sex

value: female

tag: syndromic versus non-syndromic

value: non-syndromic

tag: cleft type

value: cleft lip only

tag: cleft laterality

value: right

source_name: DNA from an unaffected male from the Philippines

value: male

value: unaffected


title: CleftProband_350

value: syndromic

value: cleft palate only

value: not applicable


title: CleftProband_348

value: cleft lip and cleft palate

value: bilateral


title: CleftProband_347


title: CleftProband_345


title: CleftProband_344


title: CleftProband_342

value: left


title: CleftProband_339


title: CleftProband_340


title: CleftProband_335


title: CleftProband_338


title: WT MEF CP1 2 days repeat 1

value: MEF cells from E13.5 mouse gestation embryo

tag: treatment

value: MGH-CP1 1uM in DMSO


title: CleftProband_341


title: CleftProband_333


title: CleftProband_337


title: CleftProband_332


title: CleftProband_331


title: CleftProband_330


title: CleftProband_327


title: IBd-92_Input DNA

tag: tissue

value: young leaves


title: CleftProband_328


title: CleftProband_325


title: CleftProband_346


title: CleftProband_322


title: CleftProband_343


title: CleftProband_321


title: CleftProband_319


title: CleftProband_320


title: CleftProband_318


title: CleftProband_315


title: CleftProband_334


title: CleftProband_317


title: CleftProband_313


title: CleftProband_336


title: CleftProband_309


title: CleftProband_310


title: CleftProband_312


title: CleftProband_311


title: CleftProband_308


title: CleftProband_329


title: CleftProband_305


title: CleftProband_326


title: CleftProband_307


title: CleftProband_324


title: CleftProband_323


title: CleftProband_301


title: CleftProband_302


title: CleftProband_304


title: CleftProband_303


title: CleftProband_298


title: CleftProband_299


title: CleftProband_314


title: CleftProband_297


title: CleftProband_300


title: wt_Rad215F_set4_2

city: Daejeon

first: Yoonjung

last: Choi

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: KAIST

data_processing:
ChIP-seq samples were sequenced on either Hiseq2500 with single-end method (50-bp reads) or Novaseq6000 with pair-end method (150-bp reads). S.pombe Hi-C samples were sequenced on Hiseq4000 with pair-end method (100-bp reads).
ChIP-seq reads were aligned to the S.pombe genome (ASM294v2) using NovoAlign (V3.04.04, Novocraft technologies) with default parameters. Aligned reads were converted into BAM and replicates were merged using samtools (v1.10). Significantly enriched peaks were identified using MACS2 (v.2.1.4) and mapped reads were quantified using Deeptools (v3.1.3) and bwtool (v1.0).
For mRNA-seq analysis, raw reads were aligned to S. pombe genome (ASM294v2) using STAR aligner. Strand-specific signal tracks of RNA-seq were generated by using bam2wig.py from RseQC (v3.0.1).
Hi-C data were aligned to the S.pombe genome (ASM294v2) using bowtie2 and normalized using HiC-Pro (v2.11.0-beta). The raw and ICE-normalized matrix was generated at 1-kb and 2.5-kb bin resolution using valid interaction pairs.
Genome_build: S. pombe EF2 genome assembly; ASM294v2
Supplementary_files_format_and_content: ChIP-seq: Yeast ChIP-seq bigwig files were created using deeptools bamCoverage (RPM normalization). In case of calibrated bigWigs for set4 experiments, samtools flagstat was used to count reads that were mapped to s.pombe and s.cerevisiae respectively. The occupancy ratio (OR) was calculated according to the previous publication (Hu, B. et al 2015). Then the calibrated s.pombe ChP (Rad21-5FLAGand notag) bigwigs were created using bamCoverage –scaleFactor option; Hi-C: ICE normalized HiC matrix text files and abs files (in HiC-Pro format); RNA-seq: bigwig files and normalized forward/reverser RPKM test files. The number of mapped reads was further analyzed using HOMER and DESeq.

organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

source_name: S.pombe cells / S.cerevisiae cells

growth_protocol: S. pombe: 1) For Hi-C experiments, yeast cells were grown to mid-log phases at 32 degrees, unless indicated otherwise. 2) For ChIP-seq in tetracycline-regulated system, cells were grown to mid-log phase at 30 degress in YES medium supplied with 2.5 ug/ml of anhydrotetracycline (ahTet). Depletion of rrp6+ was achieved by culturing cells in YES medium that lacks ahTet at indicated times (8, 12hr). Recovery of rrp6+ was achieved by culturing cells at fresh YES medium containing 2.5ug/ml of ahTet. 3) for ChIP-seq experiments, yeast cells were grown to mid-log phases at 30 degrees, unless indicated otherwise.

extract_protocol:
S. pombe (ChIP) : Fixed cells were sonicated twelve times (15 sec on, 180 sec off) using a Fisher Scientific sonic Dismembrator Model 500 sonicator at 30% output. The immunoprecipitated DNA was eluted using SigmaPrep™ spin column and then subjected to protease treatment and cross-linking reversal. Subsequently, the DNA was purified using Qiaquick PCR purification kit (Qiagen).
S. pombe (RNA isolation): DNase-treated mRNA was purified using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB), and subjected to library preparation using NEXTflex™ Rapid Directional mRNA-Seq Kit (BIOO) following the manufacturer’s instructions.
S.pombe (in situ Hi-C): formaldehyde-fixed cells (1.6 x 10^7 cells) were digested with zymolyase. Restriction enzyme digestion (MboI – 4 cutter), filling-in, ligation, crosslink reversal, DNA shearing and library construction were done according to previous publications (Rao, SSP et al 2014) with minor modifications.
ChIP-seq libraries for genome-wide sequencing were prepared using either a NEXTflex™ Illumina ChIP-Seq Library Prep kit (5143-02, BIOO) or Accel-NGS 2S Plus DNA Library Kit (21024, SWIFT). mRNA-seq libraries were made using NEXTflex™ Rapid Directional mRNA-Seq kit (5138-10, BIOO) from purified mRNA.

value: wt

value: ANTI-FLAG M2 antibody (F1804, Sigma)


title: CleftProband_296

value: female


title: wt_Rad215F_set4_1


title: CleftProband_316

value: non-syndromic


title: CleftProband_294


title: CleftProband_293


title: CleftProband_295


title: wt_a-FLAG_notag_set4_2


title: wt_a-FLAG_notag_set4_1


title: CleftProband_292


title: CleftProband_306


title: CleftProband_290


title: wpl1d_a-FLAG_notag_set4_2


title: CleftProband_289

value: cleft lip only


title: CleftProband_291


title: wpl1d_Rad215F_set4_1


title: CleftProband_287


title: CleftProband_288

value: right


title: wpl1d_a-FLAG_notag_set4_1


title: rrp6dwpl1d_a-FLAG_notag_set4_2

description: rrp6dwpl1d_calibrated_aFLAG_notag_rpm.bw


title: rrp6dwpl1d_Rad215F_set4_2

description: rrp6dwpl1d_calibrated_Rad21-5FLAG_rpm.bw


title: CleftProband_286

value: male


title: rrp6dwpl1d_a-FLAG_notag_set4_1


title: rrp6dwpl1d_Rad215F_set4_1


title: CleftProband_285

value: unaffected


title: rrp6d_Rad215F_set4_2


title: CleftProband_284


title: CleftProband_283

value: syndromic


title: wpl1d_Rad215F_set4_2


title: rrp6d_a-FLAG_notag_set4_2


title: rrp6d_Rad215F_set4_1


title: CleftProband_282


title: input_wt_Rad215F_set4_2


title: CleftProband_281


title: CleftProband_280


title: input_wt_notag_set4_2


title: CleftProband_279


title: input_wt_Rad215F_set4_1


title: CleftProband_278


title: input_wt_notag_set4_1


title: CleftProband_277


title: input_wpl1d_Rad215F_set4_1


title: CleftProband_275


title: input_wpl1d_Rad215F_set4_2


title: CleftProband_276


title: input_wpl1d_notag_set4_2


title: CleftProband_274


title: CleftProband_273


title: CleftProband_272


title: input_rrp6dwpl1d_Rad215F_set4_2


title: input_wpl1d_notag_set4_1


title: input_rrp6dwpl1d_Rad215F_set4_1


title: CleftProband_271


title: CleftProband_269


title: CleftProband_270


title: rrp6d_a-FLAG_notag_set4_1


title: input_rrp6d_Rad215F_set4_2


title: input_rrp6dwpl1d_notag_set4_1


title: CleftProband_268


title: input_rrp6dwpl1d_notag_set4_2


title: CleftProband_265


title: CleftProband_267


title: CleftProband_266


title: input_rrp6d_notag_set4_1


title: CleftProband_263


title: input_rrp6d_notag_set4_2


title: CleftProband_264


title: IBd-483_CENH3_ChIPSeq

organism: Brachypodium hybridum

value: ChIPed DNA


title: IBd-163_Input DNA


title: IBd-163_CENH3_ChIPSeq


title: IBd-483_Input DNA


title: CleftProband_262

value: unknown


title: CleftProband_261

value: cleft lip and cleft palate


title: CleftProband_260

value: cleft palate only

value: not applicable


title: CleftProband_259


title: CleftProband_258

value: left


title: CleftProband_257


title: input_rrp6d_Rad215F_set4_1


title: CleftProband_255


title: CleftProband_256


title: CleftProband_254


title: CleftProband_252


title: F4/80+ TAMs isolated from enzyme-digested 4T1 tumors, rep4

city: London

first: JONATHAN

last: CARON

state: Greater London

address: New Hunt's House, Newcomen St

department: Cancer Studies

institute: KING'S COLLEGE LONDON

description: 4T1 TAM 4

hyb_protocol: As recommended by the array manufacturer with the following exception: NuGEN recommended hybridization temperature of 48°C. Staining with Cy3-Streptavidin.

scan_protocol: Image BeadChip on the iScan System

data_processing: Raw fluorescence signals were collected using GenomeStudio (Illumina), and imported into Partek Genomics Suite (PGS) for further analysis. Background was subtracted from the raw data and fluorescence signals were normalized using the quantiles method.

source_name: TAM

label_protocol: mRNA was converted to cDNA, amplified using the Ovation® PicoSL WTA system V2 (NuGEN), biotinylated using the Encore® BiotinIL Module (NuGEN)

growth_protocol: RPMI 10% FCS, penicillin/streptomycin, 50ng/ml M-CSF

extract_protocol: According to the manufacturers’ protocol, PureLink RNA Mini Kit

treatment_protocol: Miltenyi magnetic beads

value: Balb/c

tag: gender

value: Female

tag: disease state

value: 4T1 mouse model of breast cancer

value: tumor from 4T1-bearing mouse

tag: cell type

value: tumor-associated macrophage (TAM)


title: CleftProband_253

value: non-syndromic


title: CleftProband_249


title: F4/80+ TAMs isolated from enzyme-digested 4T1 tumors, rep1

description: 4T1 TAM 1

tag: strain


title: F4/80+ TAMs isolated from enzyme-digested 4T1 tumors, rep3

description: 4T1 TAM 3


title: CleftProband_248

value: bilateral


title: CleftProband_247


title: splenic-derived macrophage, no extra-cytokine, 72h, rep2

value: spleen from 4T1-bearing mouse

value: in-vitro-polarized macrophage, M0

value: no extra-cytokine