title: cell-4

description: single-cell Hi-C sample


title: cell-3

status: Public on Sep 26 2013

type: SRA

city: Rehovot

first: Yaniv

last: Lubling

address: POB 26

country: Israel

institute: Weizmann Institute of Science

description: single-cell Hi-C sample

library_source: genomic

data_processing:
Paired-end reads of each multiplexed lane were paired-up and separated to single cell datasets based on the 3 bp unique identification tags prefixing each read. Read-pairs of each single cell were then processed independently. We mapped read ends separately to the Mus musculus genome (assembly mm9) using the Maq program with standard parameters and retained pairs of reads with unique hits of high quality (q ≥ 30) at both ends. The first RE1 (Bgl II or Dpn II) restriction site downstream of the read was identified and used as the fragment-end (fend) associated with the read. We retained read-pairs that reflect informative ligation events and with both ends mapped near the first RE2 (Alu I) site upstream of RE1 site. We discarded fend-pairs that were covered only once and used the list of unique fend-pairs, ignoring the coverage of each pair. Fend-pairs with problematic fragments (without a RE2 site or with a non-uniquely mapped start) were discarded. Samples that confidently originated from single cell, with substantial number of fend-pairs and with low noise levels were selected for the analysis.
Th1_bgl_pool.txt - Pool of 60 single-cell Hi-C samples
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include the list of unique fend-pairs of the sample (pair of genomic coordinates)

molecule: genomic DNA

organism: Mus musculus

source_name: T-helper cells (Th1)

growth_protocol: CD4+ Th1 cells were prepared from spleens of male C57BL/6 mice by stimulating the single cell suspension from spleen with 1 µg/ml anti-CD3 (eBioscience) for 3 days in RPMI1640 medium with L-glutamine and 5% fetal calf serum, purified using magnetic beads coated with anti-CD4 (Miltenyi Biotec), and further expanded in the presence of 20 ng/ml IL-2 (Sigma).

extract_protocol:
Single cells treated according to the modified Hi-C protocol were isolated in PBS and incubated at 65 degrees C for overnight.
The biotin-labelled DNA from each cell was bound to Dynabeads M-280 streptavidin magnetic beads (Life Technologies), digested with Alu I (New England Biolabs), A-tailed with Klenow Fragment (3'->5' exo-) (New England Biolabs) and dATP, ligated with customised Illumina adapter with T4 DNA ligase (New England Biolabs), then the library was amplified by PCR with library amplification primers, and size-selected between 300 and 700 bp on an agarose gel.

tag: strain

tag: tissue

value: Spleen

tag: restriction enzyme

value: Bgl II

tag: cell type

value: T-helper cells (Th1)


title: cell-5

description: single-cell Hi-C sample


title: JFY-2

status: Public on Sep 27 2013

city: Wuhan

first: Fangyan

last: Jin

state: Hubei

address: No.1, Shizishan Street

country: China

institute: Huazhong Agriculture University

description: Gossypium hirsutum cv. YZ1

library_source: transcriptomic

data_processing:
Millions of raw reads with a length approximate 50bp were generated via Illumina HiSeq™ 2000
Clean reads occupied > 98% of raw reads were produced after filtering dirty raw reads
By using SOAPaligner/soap2, all clean reads were mapped to the reference sequences which were cotton unigenes collected from NCBI, supporting up to 2 bases mismatches in the alignment.
Transcription levels were calculated in RPKM (reads per kilobase of exon model per million mapped reads) which was able to get rid of the disturbance of different gene length and sequencing discrepancy on the calculation of gene expression
Genome_build: Gossypium hirsutum: UniGene Build #11
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Gossypium hirsutum

source_name: zygotic globular-shaped embryos

growth_protocol: The cotton plants (Gossypium hirsutum cv. YZ1), used for zygotic embryos collection, were cultivated in the field under normal farming condition during growing seasons in Wuhan, China. Tissue culture was carried out for somatic embryos collection using hypocotyls excised from germfree seedlings. The explants were cultured on MSB (MS medium plus B5 vitamins) medium supplemented with the combination of 1.0 mg/L IBA plus 0.1 mg/L kinetin. After 40 d of culture, all explants were transferred to fresh MSB medium for induction of embryogenic calli (ECs). The ECs were subcultured monthly on MSB medium, with KNO3 doubled but NH4NO3 removed, and supplemented with 3% (w/v) glucose, 0.25% (w/v) Phytagel, 0.5 mg/L IBA, 0.15 mg/L kinetin, 1.0g/L glutamine and 0.5 g/L asparagines, for embryo maturation. All media were autoclaved at 121°C for 15 min. Cultures were maintained in a room at 28 ± 2 °C under a 14-h photoperiod (irradiance of 135 μmol/m∙s). Different stages of somatic embryos were sampled.

extract_protocol:
Guanidine thiocyanate method was used to extract total RNA
Approximate 20ug of total RNA was sent to Beijing Genomics Institute (Shenzhen, China) where the tag libraries were prepared and sequenced. Before construction of library, RNA quality and quantity were determined by Agilent 2100 with rRNA ratio [28s/18s] > 1.0 and RNA Integrity Number (RIN) > 7. Then mRNA were enriched by using the oligo(dT) magnetic beads, and interrupted by adding the fragmentation buffer to short segments (about 200bp) which were used as templates to synthesize double strand cDNA tags by random hexamer-primer. After purified, washed for end repair and single nucleotide A (adenine) addition, and attached the sequencing adaptors, the library required fragments were enriched by PCR amplification. Millions of raw reads with a length approximate 50bp were generated via Illumina HiSeq™ 2000.

tag: cultivar

value: zygotic embryo

tag: developmental stage

value: globular-shaped stage


title: Th1 ensemble Hi-C

description: ensemble Hi-C


title: cell-1

description: single-cell Hi-C sample


title: batch5_chrom2_LoVo_ZNF83_Rabbit_PassedQC

status: Public on Sep 25 2013

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

description: ChIP-seq that passed automated QC; > 300 peaks, located close to TSS and/or enriched in high complexity motif(s)

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_ZNF83_PassedQC_peaks.txt: hg18

organism: Homo sapiens

source_name: LoVo

growth_protocol: LoVo (ATCC CCL-229) colon adenocarcinoma cells were cultured in DMEM supplemented with penicillin/streptomycin and 10% FBS under standard culture conditions.

extract_protocol:
Cells were cross-linked by 1% formaldehyde, and DNA was sonicated to 200- 400 bp fragments. Antibodies (5 µg) were added and collected using protein G Sepharose (GE). Cross-links were reversed and proteins digested by incubation with proteinase K at 65 °C overnight. DNA was then purified using Qiagen PCR purification kit.
Libraries were constructed according to Illuminas standard protocol. The concentration of the library was determined by Nanodrop spectrophotometer (Thermo Fisher Scientific Inc.) and 10 pmol of the DNA was applied for one flow-cell lane. Sequencing was performed using one lane of Illumina GAIIx, or alternatively, samples were indexed with DNA barcodes and four to six different samples were multiplexed in one library and sequenced using Illumina HiSeq 2000 (single 36 bp reads).

tag: cell line

value: LoVo

value: colon adenocarcinoma

tag: hgn

tag: antibody

value: Abcam :ab128541

tag: control sample

tag: qc successful

value: PassedQC

tag: number of peaks, fdr < 5%

tag: fraction of peaks close to tss

tag: lowest e-value for a high complexity de novo motif


title: batch5_chrom2_LoVo_ZNF581_Rabbit_FailedQC

description: ChIP-seq experiment that failed automated QC; provided for control purposes

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_ZNF581_FailedQC_peaks.txt: hg18

value: Abcam :ab82674

value: FailedQC


title: batch5_chrom2_LoVo_ZNF84_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_ZNF84_PassedQC_peaks.txt: hg18

value: Abcam :ab28719


title: batch5_chrom2_LoVo_ZNF395_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_ZNF395_PassedQC_peaks.txt: hg18

value: Abcam :ab75727


title: batch5_chrom2_LoVo_ZNF280D_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_ZNF280D_PassedQC_peaks.txt: hg18

value: Abcam :ab114972


title: batch5_chrom2_LoVo_ZNF266_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_ZNF266_PassedQC_peaks.txt: hg18

value: Abcam :ab33005


title: batch5_chrom2_LoVo_ZNF143_Mouse_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_ZNF143_PassedQC_peaks.txt: hg18

value: Abcam :ab58168


title: batch5_chrom2_LoVo_ZNF12_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_ZNF12_PassedQC_peaks.txt: hg18

value: Abcam :ab48905


title: batch5_chrom2_LoVo_ZNF263_Mouse_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_ZNF263_PassedQC_peaks.txt: hg18

value: Abcam :ab56831


title: batch5_chrom2_LoVo_ZBTB44_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_ZBTB44_FailedQC_peaks.txt: hg18

value: Abcam :ab81595


title: batch5_chrom2_LoVo_ZNF217_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_ZNF217_FailedQC_peaks.txt: hg18

value: Abcam :ab117798


title: batch5_chrom2_LoVo_YBX1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_YBX1_FailedQC_peaks.txt: hg18

value: Abcam :ab12148


title: batch5_chrom2_LoVo_ZBTB2_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_ZBTB2_FailedQC_peaks.txt: hg18

value: Abcam :ab111404


title: batch5_chrom2_LoVo_ZBTB24_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_ZBTB24_FailedQC_peaks.txt: hg18

value: LoVo

value: Abcam :ab117756


title: batch5_chrom2_LoVo_TSHZ1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_TSHZ1_FailedQC_peaks.txt: hg18

value: colon adenocarcinoma

value: Abcam :ab91230


title: batch5_chrom2_LoVo_WHSC1_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_WHSC1_FailedQC_peaks.txt: hg18

value: Abcam :ab75359


title: batch5_chrom2_LoVo_ZBTB39_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_ZBTB39_FailedQC_peaks.txt: hg18

value: Abcam :ab67878

value: FailedQC


title: batch5_chrom2_LoVo_ZBTB4_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_ZBTB4_FailedQC_peaks.txt: hg18

value: Abcam :ab117775


title: batch5_chrom2_LoVo_TOE1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_TOE1_FailedQC_peaks.txt: hg18

value: Abcam :ab129491


title: T47D, input DNA, treated by hypoxia and glucose deprivation

city: Boston

first: Xiaole

middle: Shirley

last: Liu

state: MA

address: 450 Brookline Avenue, CLS 11007

department: Department of Biostatistics and Computational Biology

country: USA

institute: Dana-Farber Cancer Institute, Harvard School of Public Health

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.7 with the following parameters: bowtie -S -m 1 *.fastq  *.sam.
Sam format files were converted to bed format; mapped reads of treat and input files were randomly sampled to the same depth.
Peaks were called using MACS with p-value cutoff of 1e-7.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files were generated using MACS; scores represent tag pileup over each position.Bed files of peak positions were also generated by MACS.

source_name: breast cancer cells

growth_protocol: All breast cancer cells were cultured according to Neve et al. (Cancer Cell 2006). Following retroviral or lentiviral infection, cells were maintained in the presence of puromycin (2 ug/ml) (Sigma).

extract_protocol:
ChIP was performed as previously described by Chen et al. (Cell 2008).
The ChIP-seq library was prepared using ChIP-Seq DNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: For all hypoxia experiments, cells were maintained in an anaerobic chamber (Coy laboratory) with 0.1% O2. For glucose deprivation experiments, cells were maintained in DMEM without glucose medium (Gibco) with 10% FBS (Gibco) and 50 units/ml of penicillin/streptomycin.

value: ER positive breast cancer cells

tag: chip antibody


title: ribosome footprints for wildtype

city: Stony Brook

first: Ying

last: Cai

state: New York

address: Life Sciences Building Rm 363

department: Molecular Genetics and Microbiology

institute: Stony Brook University

description: ribosome footprints

data_processing:
Basecalls performed using CASAVA version 1.8.2
Tools from fastx were used to trimmed reads to 27 nucleotides and filtered with parameters –Q 33 –q 30 –p 85.
The first 26 nucleotide of the resulted reads were aligned against S288C reference genome R64 using bowtie2 with the end-to-end alignment method and the minimum score was set to -7.  Unaligned reads were recycled for additional alignment using coding region sequence as reference to retrieve exon junction reads.
The position of the 5’ end in the read was used to assign reads to genomic features according to (Ingolia N et al Science 2009) Reads mapped to the rDNA were discarded for following analysis.  Reads per kilo base per Million (RPKM) was calculated to quantify mRNA and ribosomal footprints. Briefly, after removal of genes with less than 7 reads, the count of reads for each gene was normalized by its length (in kb) and the total number of reads (in million).
Genome_build: S288C_reference_genome_R64-1-1
Supplementary_files_format_and_content: RPKM values for each sample

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae cells

growth_protocol: 1 liter of Homozygous diploid wildtype or whi3 cells was grown in 1L YPED to log phase. Upon harvest, culture was pour onto ice and cyclohexamide mixture (the final concentration of cycloheximide was 100 µg/ml) Cells were washed once with ice cold water with 100 µg/ml cycloheximide before RNA extraction.

extract_protocol:
ribosome footprint and small mRNA fragment are prepared using the ARTseq™ Ribosome Profiling Kit (CAT# RPYSC12116) following manufacturer's instructions.
Libraries were prepared using the ARTseq™ Ribosome Profiling Kit (CAT# RPYSC12116) following manufacturer's instructions.

tag: strain background

tag: strain genotype


title: ribosome footprints for whi3

description: ribosome footprints

value: BY4743, whi3::URA3/whi3::URA3


title: mRNA-seq for wildtype

description: poly(A) tail RNA


title: mRNA-seq for whi3

description: poly(A) tail RNA


title: T47D, XBP1_ChIPSeq, treated by hypoxia and glucose deprivation, biological replicate 1

value: XBP1 (Biolegend, 619502)


title: cell-2

description: single-cell Hi-C sample

data_processing:
Paired-end reads of each multiplexed lane were paired-up and separated to single cell datasets based on the 3 bp unique identification tags prefixing each read. Read-pairs of each single cell were then processed independently. We mapped read ends separately to the Mus musculus genome (assembly mm9) using the Maq program with standard parameters and retained pairs of reads with unique hits of high quality (q ≥ 30) at both ends. The first RE1 (Bgl II or Dpn II) restriction site downstream of the read was identified and used as the fragment-end (fend) associated with the read. We retained read-pairs that reflect informative ligation events and with both ends mapped near the first RE2 (Alu I) site upstream of RE1 site. We discarded fend-pairs that were covered only once and used the list of unique fend-pairs, ignoring the coverage of each pair. Fend-pairs with problematic fragments (without a RE2 site or with a non-uniquely mapped start) were discarded. Samples that confidently originated from single cell, with substantial number of fend-pairs and with low noise levels were selected for the analysis.
Th1_bgl_pool.txt - Pool of 60 single-cell Hi-C samples
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include the list of unique fend-pairs of the sample (pair of genomic coordinates)

tag: strain

value: Spleen

value: Bgl II

value: T-helper cells (Th1)


title: batch5_chrom2_LoVo_TFCP2_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_TFCP2_FailedQC_peaks.txt: hg18

value: Abcam :ab80445


title: batch5_chrom2_LoVo_THAP4_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_THAP4_FailedQC_peaks.txt: hg18

value: Abcam :ab68744


title: cDNA from RNAs of Bupleurum chinense roots

city: Beijing

first: Sui

last: Chun

state: Beijing

address: No. 151,Malianwa North Road, Hai Dian District

institute: Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
454 newbler 2.6 software used for basecalling.
A Perl script was written to remove vector sequences and PolyA (T) tail from the original sequences. Reads whose length is less than 100 bp were deemed as low quality and removed before assembly. The rest high quality reads were assembled with MIRA [42] to construct unique consensus sequences. The parameters used by MIRA are as follow: --job=denovo, est, normal, 454 -SK: mnr=yes -SK: rt=2 454_SETTINGS -LR: mxti=no -CL: qc=no.
Supplementary_files_format_and_content: tab-delimited text files include transcript id, length and RPKM values for each Sample.

organism: Bupleurum chinense

source_name: fine roots of two-year old plants

growth_protocol: Plants were naturally grown in Beijing, China, in 2010, sown in Spring and collected in early Autumn in 2011

extract_protocol: Total RNA was isolated using Trizol reagent® according to instructions of manufacturer (Invitrogen, Karlsruhe, Germany) and then mRNA was purified and enriched using the mRNA purification kit (Promega, Fitchburg, USA). The mRNAs were reverse-transcribed using Powerscript™ II (TaKaRa, Japan) with PCR primers SMART IV™ Oligonucleotide (5'-AAGCAGTGGTATCAACGCAGAGTGGCCATTACGGCCGGG-3') and CDS III/3' PCR Primer (5'-ATTCTAGAGGCCGAGGCGGCCGACATG-d(T)30N-1N-3'). Long Distance PCR for double strand cDNA amplification was performed with LA Taq enzyme (TaKaRa, Japan) for 25 cycles (95°C for 30 s, 68°C for 8 min) according to the SMART™ cDNA Library Construction Kit User Manual (Clontech, CA, USA). Finally, double strand cDNAs were purified using DNA purification kit (Qiagen, Venlo, The Netherlands) to generate high quality cDNA. Approximately 10 μg of sheared cDNA were used for GS20-454 sequencing. A total sequencing runs were performed with B. chinense a half and B. scorzonerifolium a half.

value: ‘Zhongchai No. 2’,  a mass-selected cultivar of Bupleurum chinense

tag: tissue

value: fine roots

tag: age

value: two-years old

tag: collection time

value: roots collected at early November in Beijing, the usual harvest time of medicinal materials of Bupleurum


title: cDNA from RNAs of Bupleurum scorzonerifolium roots

organism: Bupleurum scorzonerifolium

tag: cultivar

value: ‘Zhonghongchai No. 1’,  a mass-selected cultivar of  Bupleurum scorzonerifolium


title: batch5_chrom2_LoVo_TCFL5_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_TCFL5_FailedQC_peaks.txt: hg18

value: LoVo

tag: cell type

value: colon adenocarcinoma

value: Abcam :ab69931


title: batch5_chrom2_LoVo_SKI_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_SKI_FailedQC_peaks.txt: hg18

tag: cell line

value: SKI

value: Abcam :ab19864

value: FailedQC


title: batch5_chrom2_LoVo_RCOR1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_RCOR1_FailedQC_peaks.txt: hg18

tag: hgn

value: Abcam :ab32631


title: batch5_chrom2_LoVo_RLF_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_RLF_FailedQC_peaks.txt: hg18

value: RLF

tag: antibody

value: Abcam :ab115154


title: batch5_chrom2_LoVo_PRDM4_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_PRDM4_FailedQC_peaks.txt: hg18

value: Abcam :ab126939

tag: control sample


title: batch5_chrom2_LoVo_RFX7_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_RFX7_FailedQC_peaks.txt: hg18

value: Abcam :ab111988

tag: qc successful


title: batch5_chrom2_LoVo_PCF11_Goat_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_PCF11_PassedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-161998

value: PassedQC

tag: number of peaks, fdr < 5%


title: batch5_chrom2_LoVo_PLAG1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_PLAG1_FailedQC_peaks.txt: hg18

value: Abcam :ab80267

tag: fraction of peaks close to tss


title: batch5_chrom2_LoVo_HOXC13_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_HOXC13_FailedQC_peaks.txt: hg18

value: Abcam :ab55251

tag: lowest e-value for a high complexity de novo motif


title: batch5_chrom2_LoVo_MYBL1_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_MYBL1_FailedQC_peaks.txt: hg18

value: Abcam :ab10934


title: batch5_chrom2_LoVo_HOXC11_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_HOXC11_FailedQC_peaks.txt: hg18

value: Abcam :ab118412


title: batch5_chrom2_LoVo_NFE2L3_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_NFE2L3_FailedQC_peaks.txt: hg18

value: LoVo

value: Abcam :ab111362


title: batch5_chrom2_LoVo_RBPJ_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_RBPJ_FailedQC_peaks.txt: hg18

value: colon adenocarcinoma

value: RBPJ

value: Abcam :ab25949


title: batch5_chrom2_LoVo_NKX2-3_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_NKX2-3_FailedQC_peaks.txt: hg18

value: Abcam :ab66366

value: FailedQC


title: batch5_chrom2_LoVo_MAFK_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_MAFK_PassedQC_peaks.txt: hg18

value: MAFK

value: Abcam :ab50322


title: batch5_chrom2_LoVo_IRX2_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_IRX2_FailedQC_peaks.txt: hg18

value: Abcam :ab72975


title: batch5_chrom2_LoVo_NFIB_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_NFIB_FailedQC_peaks.txt: hg18

value: NFIB

value: Abcam :ab11989


title: batch5_chrom2_LoVo_GRHL1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_GRHL1_FailedQC_peaks.txt: hg18

value: Abcam :ab77762


title: batch5_chrom1_LoVo_SA1_Goat_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_SA1_PassedQC_peaks.txt: hg18

value: Abcam :ab4457

value: PassedQC


title: batch5_chrom2_LoVo_SNAPC4_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_SNAPC4_FailedQC_peaks.txt: hg18

value: Abcam :ab89518


title: batch5_chrom2_LoVo_TEAD4_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_TEAD4_FailedQC_peaks.txt: hg18

value: Abcam :ab58308


title: batch5_chrom1_LoVo_MYNN_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_MYNN_FailedQC_peaks.txt: hg18

value: LoVo

value: MYNN

value: Abcam :ab66273


title: batch5_chrom1_LoVo_SA2_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_SA2_FailedQC_peaks.txt: hg18

value: colon adenocarcinoma

value: Abcam :ab4463


title: batch5_chrom1_LoVo_MEOX2_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_MEOX2_FailedQC_peaks.txt: hg18

value: Abcam :ab55731


title: batch5_chrom1_LoVo_MXI1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_MXI1_FailedQC_peaks.txt: hg18

value: Abcam :ab28740

value: FailedQC


title: batch5_chrom1_LoVo_MAFF_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_MAFF_FailedQC_peaks.txt: hg18

value: MAFF

value: Abcam :ab91486


title: batch5_chrom2_LoVo_PBX3_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_PBX3_FailedQC_peaks.txt: hg18

value: Abcam :ab56239


title: batch5_chrom2_LoVo_CTCF_Goat_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_CTCF_PassedQC_peaks.txt: hg18

value: CTCF

value: Santa Cruz Biotechnology, Inc. :sc-15914 X


title: batch5_chrom1_LoVo_KCMF1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_KCMF1_FailedQC_peaks.txt: hg18

value: Abcam :ab80287


title: batch5_chrom1_LoVo_LCORL_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_LCOR_FailedQC_peaks.txt: hg18

value: LCOR

value: Abcam :ab48339


title: batch5_chrom1_LoVo_IRF9_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_IRF9_FailedQC_peaks.txt: hg18

value: Abcam :ab118791


title: batch5_chrom1_LoVo_HOXD1_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_HOXD1_FailedQC_peaks.txt: hg18

value: LoVo

value: Abcam :ab60715


title: batch5_chrom1_LoVo_HOXB7_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_HOXB7_FailedQC_peaks.txt: hg18

value: Abcam :ab111018


title: batch5_chrom1_LoVo_HOXA9_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_HOXA9_FailedQC_peaks.txt: hg18

value: colon adenocarcinoma

value: Abcam :ab83480


title: batch5_chrom2_LoVo_FOXO4_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom2_LoVo_FOXO4_FailedQC_peaks.txt: hg18

value: Abcam :ab63254


title: batch5_chrom1_LoVo_GRHL2_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_GRHL2_FailedQC_peaks.txt: hg18

value: Abcam :ab86611


title: batch5_chrom1_LoVo_GZF1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_GZF1_FailedQC_peaks.txt: hg18

value: Abcam :ab26163

value: FailedQC


title: batch5_chrom1_LoVo_HNF4G_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_HNF4G_FailedQC_peaks.txt: hg18

value: Abcam :ab66179


title: batch5_chrom1_LoVo_HAND1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_HAND1_FailedQC_peaks.txt: hg18

value: Abcam :ab115256


title: batch5_chrom1_LoVo_FOXJ2_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_FOXJ2_FailedQC_peaks.txt: hg18

value: Abcam :ab22857


title: batch5_chrom1_LoVo_FOXF2_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_FOXF2_FailedQC_peaks.txt: hg18

value: Abcam :ab23306


title: batch5_chrom1_LoVo_FOXC1_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_FOXC1_FailedQC_peaks.txt: hg18

value: Abcam :ab5079


title: batch5_chrom1_LoVo_ELF4_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_ELF4_FailedQC_peaks.txt: hg18

value: Abcam :ab82396


title: batch5_chrom1_LoVo_FOSL1_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_FOSL1_FailedQC_peaks.txt: hg18

value: Abcam :ab117951


title: batch5_chrom1_LoVo_EGR2_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_EGR2_FailedQC_peaks.txt: hg18

value: Abcam :ab43020


title: batch5_chrom1_LoVo_DRAP1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_DRAP1_FailedQC_peaks.txt: hg18

value: LoVo

value: Abcam :ab98034


title: batch5_chrom1_LoVo_DMRT2_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_DMRT2_FailedQC_peaks.txt: hg18

value: Abcam :ab90683


title: batch5_chrom1_LoVo_DDIT3_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_DDIT3_FailedQC_peaks.txt: hg18

value: colon adenocarcinoma

value: Abcam :ab11419


title: batch5_chrom1_LoVo_CREBL2_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_CREBL2_FailedQC_peaks.txt: hg18

value: Abcam :ab67782


title: batch5_chrom1_LoVo_CDC5L_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_CDC5L_FailedQC_peaks.txt: hg18

value: Abcam :ab31779


title: batch5_chrom1_LoVo_CDX1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_CDX1_FailedQC_peaks.txt: hg18

value: Abcam :ab126748


title: batch5_chrom1_LoVo_BRCA1_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_BRCA1_FailedQC_peaks.txt: hg18

value: Abcam :ab16780

value: FailedQC


title: batch5_chrom1_LoVo_BHLHE40_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_BHLHE40_FailedQC_peaks.txt: hg18

value: Abcam :ab70723


title: batch5_chrom1_LoVo_BMI1_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_BMI1_FailedQC_peaks.txt: hg18

value: Abcam :ab14389


title: batch5_chrom1_LoVo_BBX_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_BBX_FailedQC_peaks.txt: hg18

value: BBX

value: Abcam :ab50824


title: batch5_chrom1_LoVo_ADNP2_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_ADNP2_FailedQC_peaks.txt: hg18

value: Abcam :ab105334


title: batch4_chrom3_LoVo_ZNF639_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom3_LoVo_ZNF639_FailedQC_peaks.txt: hg18

value: Abcam :ab114971


title: batch5_chrom1_LoVo_BCL11A_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_BCL11A_FailedQC_peaks.txt: hg18

value: Abcam :ab19489


title: batch5_chrom1_LoVo_ARNTL2_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_ARNTL2_FailedQC_peaks.txt: hg18

value: LoVo

value: Abcam :ab86530


title: batch4_chrom3_LoVo_ZNF3_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom3_LoVo_ZNF3_FailedQC_peaks.txt: hg18

value: Abcam :ab80532


title: batch4_chrom3_LoVo_TFAM_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom3_LoVo_TFAM_FailedQC_peaks.txt: hg18

value: colon adenocarcinoma

value: TFAM

value: Abcam :ab114993


title: batch5_chrom1_LoVo_ASH1L_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_ASH1L_FailedQC_peaks.txt: hg18

value: Abcam :ab50981


title: batch4_chrom3_LoVo_UBP1_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom3_LoVo_UBP1_PassedQC_peaks.txt: hg18

value: Abcam :ab30965

value: PassedQC


title: batch4_chrom3_LoVo_STAT2_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom3_LoVo_STAT2_PassedQC_peaks.txt: hg18

value: Abcam :ab124283


title: batch4_chrom3_LoVo_PBX2_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom3_LoVo_PBX2_FailedQC_peaks.txt: hg18

value: Abcam :ab66942

value: FailedQC


title: batch4_chrom3_LoVo_PBX1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom3_LoVo_PBX1_FailedQC_peaks.txt: hg18

value: Abcam :ab12001


title: batch4_chrom3_LoVo_STAT6_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom3_LoVo_STAT6_FailedQC_peaks.txt: hg18

value: Abcam :ab44718


title: batch4_chrom3_LoVo_ZNF281_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom3_LoVo_ZNF281_PassedQC_peaks.txt: hg18

value: Abcam :ab112047


title: batch4_chrom3_LoVo_ZBTB10_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom3_LoVo_ZBTB10_PassedQC_peaks.txt: hg18

value: Abcam :ab117786


title: batch4_chrom3_LoVo_RFX5_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom3_LoVo_RFX5_FailedQC_peaks.txt: hg18

value: Abcam :ab9255


title: batch4_chrom2_LoVo_ZBTB33_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_ZBTB33_FailedQC_peaks.txt: hg18

value: LoVo

value: Abcam :ab12723


title: batch5_chrom1_LoVo_CTCFL_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_CTCFL_PassedQC_peaks.txt: hg18

value: CTCFL

value: Abcam :ab126778


title: batch4_chrom2_LoVo_TERF2_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_TERF2_FailedQC_peaks.txt: hg18

value: colon adenocarcinoma

value: Abcam :ab13579


title: batch4_chrom2_LoVo_TFAP2_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_TFAP2_PassedQC_peaks.txt: hg18

value: Abcam :ab52222


title: batch4_chrom2_LoVo_TLX1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_TLX1_FailedQC_peaks.txt: hg18

value: Abcam :ab83059


title: batch4_chrom2_LoVo_TERF1_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_TERF1_PassedQC_peaks.txt: hg18

value: Abcam :ab1423

value: PassedQC


title: batch4_chrom2_LoVo_TCF7L1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_TCF7L1_FailedQC_peaks.txt: hg18

value: Abcam :ab82690


title: batch4_chrom2_LoVo_TAL1_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_TAL1_PassedQC_peaks.txt: hg18

value: Abcam :ab75739


title: batch4_chrom2_LoVo_STAT4_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_STAT4_FailedQC_peaks.txt: hg18

value: Abcam :ab28815

value: FailedQC


title: batch5_chrom1_LoVo_RAD21_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_RAD21_PassedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-98784


title: batch4_chrom2_LoVo_STAT5A_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_STAT5A_FailedQC_peaks.txt: hg18

value: Abcam :ab7969


title: batch4_chrom3_LoVo_RAD21_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom3_LoVo_RAD21_PassedQC_peaks.txt: hg18


title: batch4_chrom2_LoVo_SMAD5_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_SMAD5_FailedQC_peaks.txt: hg18

value: Abcam :ab13724


title: batch4_chrom2_LoVo_RXRA_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_RXRA_FailedQC_peaks.txt: hg18

value: LoVo

value: RXRA

value: Santa Cruz Biotechnology, Inc. :sc-46659 X


title: batch4_chrom2_LoVo_RUNX1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_RUNX1_FailedQC_peaks.txt: hg18

value: Abcam :ab23980


title: batch4_chrom2_LoVo_SALL4_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_SALL4_FailedQC_peaks.txt: hg18

value: colon adenocarcinoma

value: Abcam :ab29112


title: batch4_chrom2_LoVo_OVOL2_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_OVOL2_PassedQC_peaks.txt: hg18

value: Abcam :ab83265


title: batch4_chrom2_LoVo_NR1H2_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_NR1H2_FailedQC_peaks.txt: hg18

value: Abcam :ab56237


title: batch4_chrom2_LoVo_NFYB_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_NFYB_FailedQC_peaks.txt: hg18

value: NFYB

value: Abcam :ab6559


title: batch4_chrom2_LoVo_NR1D1_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_NR1D1_FailedQC_peaks.txt: hg18

value: Abcam :ab41939


title: batch4_chrom2_LoVo_NPAT_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_NPAT_PassedQC_peaks.txt: hg18

value: NPAT

value: Abcam :ab99436

value: PassedQC


title: batch4_chrom3_LoVo_CAMTA1_Goat_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom3_LoVo_CAMTA1_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-74355 X

value: FailedQC


title: batch4_chrom2_LoVo_JUND_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_JUND_FailedQC_peaks.txt: hg18

value: JUND

value: Abcam :ab28837


title: batch4_chrom2_LoVo_JUNB_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_JUNB_PassedQC_peaks.txt: hg18

value: LoVo

value: JUNB

value: Abcam :ab31421


title: batch4_chrom2_LoVo_NFYC_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_NFYC_PassedQC_peaks.txt: hg18

value: colon adenocarcinoma

value: NFYC

value: Abcam :ab86237


title: batch4_chrom2_LoVo_JAZF1_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_JAZF1_FailedQC_peaks.txt: hg18

value: Abcam :ab67864


title: batch4_chrom2_LoVo_ID2_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_ID2_FailedQC_peaks.txt: hg18

value: Abcam :ab90055


title: batch4_chrom2_LoVo_ID1_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_ID1_FailedQC_peaks.txt: hg18

value: Abcam :ab66495


title: batch4_chrom2_LoVo_HOXC8_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_HOXC8_FailedQC_peaks.txt: hg18

value: Abcam :ab86236


title: batch4_chrom2_LoVo_HOXB8_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_HOXB8_FailedQC_peaks.txt: hg18

value: Abcam :ab86610


title: batch4_chrom2_LoVo_ID3_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_ID3_FailedQC_peaks.txt: hg18

value: Abcam :ab41834


title: batch5_chrom1_LoVo_LCOR_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch5_chrom1_LoVo_LCORL_FailedQC_peaks.txt: hg18

value: LCORL

value: Abcam :ab49420


title: batch4_chrom2_LoVo_SOX2_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_SOX2_PassedQC_peaks.txt: hg18

value: Abcam :ab59776

value: PassedQC


title: batch4_chrom2_LoVo_STAT1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_STAT1_FailedQC_peaks.txt: hg18

value: Abcam :ab30645

value: FailedQC


title: batch4_chrom2_LoVo_SP1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_SP1_FailedQC_peaks.txt: hg18

value: LoVo

value: Abcam :ab13370


title: batch4_chrom2_LoVo_HOXB6_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_HOXB6_FailedQC_peaks.txt: hg18

value: colon adenocarcinoma

value: Abcam :ab26077


title: batch4_chrom2_LoVo_FOXP1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_FOXP1_FailedQC_peaks.txt: hg18

value: Abcam :ab93807


title: batch4_chrom2_LoVo_GMEB2_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_GMEB2_PassedQC_peaks.txt: hg18

value: Abcam :ab50592


title: batch4_chrom2_LoVo_GATAD1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_GATAD1_FailedQC_peaks.txt: hg18

value: Abcam :ab32825


title: batch4_chrom2_LoVo_ELF2_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_ELF2_PassedQC_peaks.txt: hg18

value: Abcam :ab100916


title: batch4_chrom2_LoVo_E2F2_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_E2F2_FailedQC_peaks.txt: hg18

value: Abcam :ab65222


title: batch4_chrom2_LoVo_E2F8_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_E2F8_PassedQC_peaks.txt: hg18

value: Abcam :ab109596


title: batch4_chrom2_LoVo_CDX2_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_CDX2_FailedQC_peaks.txt: hg18

value: Abcam :ab15258


title: batch4_chrom2_LoVo_CLOCK_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_CLOCK_FailedQC_peaks.txt: hg18

value: CLOCK

value: Abcam :ab3517


title: batch4_chrom2_LoVo_MXD3_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_MXD3_FailedQC_peaks.txt: hg18

value: Abcam :ab108525


title: batch4_chrom2_LoVo_BARX1_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_BARX1_PassedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-99053 X

value: PassedQC


title: batch4_chrom2_LoVo_ARNTL_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_ARNTL_PassedQC_peaks.txt: hg18

value: ARNTL

value: Santa Cruz Biotechnology, Inc. :sc-48790 X


title: batch4_chrom2_LoVo_BACH1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_BACH1_FailedQC_peaks.txt: hg18

value: LoVo

value: Abcam :ab49657

value: FailedQC


title: batch4_chrom2_LoVo_AHCTF1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_AHCTF1_FailedQC_peaks.txt: hg18

value: colon adenocarcinoma

value: Abcam :ab14431


title: batch4_chrom2_LoVo_BCL6_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_BCL6_PassedQC_peaks.txt: hg18

value: Abcam :ab19011


title: batch4_chrom1_LoVo_SOX9_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_SOX9_PassedQC_peaks.txt: hg18

value: Abcam :ab3697


title: batch4_chrom1_LoVo_REST_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_REST_FailedQC_peaks.txt: hg18

value: REST

value: Abcam :ab21635


title: batch4_chrom1_LoVo_RELB_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_RELB_FailedQC_peaks.txt: hg18

value: RELB

value: Abcam :ab33907


title: batch4_chrom1_LoVo_RELA_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_RELA_PassedQC_peaks.txt: hg18

value: RELA

value: Abcam :ab7970


title: batch4_chrom1_LoVo_PPARG_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_PPARG_FailedQC_peaks.txt: hg18

value: PPARG

value: Abcam :ab41928


title: batch4_chrom1_LoVo_NR4A1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_NR4A1_FailedQC_peaks.txt: hg18

value: Abcam :ab13851


title: batch4_chrom1_LoVo_PPARA_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_PPARA_FailedQC_peaks.txt: hg18

value: PPARA

value: Abcam :ab2779


title: batch4_chrom1_LoVo_NR1I2_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_NR1I2_FailedQC_peaks.txt: hg18

value: LoVo

value: Abcam :ab41930


title: batch4_chrom1_LoVo_NFYA_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_NFYA_PassedQC_peaks.txt: hg18

value: colon adenocarcinoma

value: NFYA

value: Abcam :ab6558

value: PassedQC


title: batch4_chrom1_LoVo_NFAT5_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_NFAT5_FailedQC_peaks.txt: hg18

value: Abcam :ab3446

value: FailedQC


title: batch4_chrom1_LoVo_NCOA3_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_NCOA3_FailedQC_peaks.txt: hg18

value: Abcam :ab2782


title: batch4_chrom1_LoVo_NR2E3_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_NR2E3_FailedQC_peaks.txt: hg18

value: Abcam :ab41922


title: batch4_chrom1_LoVo_MYOD1_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_MYOD1_FailedQC_peaks.txt: hg18

value: Abcam :ab16148


title: batch4_chrom1_LoVo_MYC_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_MYC_FailedQC_peaks.txt: hg18

value: MYC

value: Abcam :ab32


title: batch4_chrom2_LoVo_CASP8AP2_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom2_LoVo_CASP8AP2_FailedQC_peaks.txt: hg18

value: Abcam :ab8420


title: batch4_chrom1_LoVo_MLL4_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_MLL4_FailedQC_peaks.txt: hg18

value: Abcam :ab60053


title: batch4_chrom1_LoVo_KLF15_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_KLF15_FailedQC_peaks.txt: hg18

value: Abcam :ab81604


title: batch4_chrom1_LoVo_JUN_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_JUN_PassedQC_peaks.txt: hg18

value: JUN

value: Abcam :ab31419


title: batch4_chrom1_LoVo_IRF2_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_IRF2_FailedQC_peaks.txt: hg18

value: LoVo

value: Abcam :ab55331


title: batch4_chrom1_LoVo_KLF6_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_KLF6_FailedQC_peaks.txt: hg18

value: colon adenocarcinoma

value: Abcam :ab87554


title: batch4_chrom1_LoVo_IRF1_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_IRF1_PassedQC_peaks.txt: hg18

value: Abcam :ab26109

value: PassedQC


title: batch4_chrom1_LoVo_KLF11_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_KLF11_FailedQC_peaks.txt: hg18

value: Abcam :ab61207

value: FailedQC


title: batch4_chrom1_LoVo_HOXD11_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_HOXD11_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-68885 X


title: batch4_chrom1_LoVo_HOXA5_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_HOXA5_PassedQC_peaks.txt: hg18

value: Abcam :ab82645


title: batch4_chrom1_LoVo_HOXA4_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_HOXA4_PassedQC_peaks.txt: hg18

value: Abcam :ab26097


title: batch4_chrom1_LoVo_HOXA13_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_HOXA13_FailedQC_peaks.txt: hg18

value: Abcam :ab26084


title: batch4_chrom1_LoVo_HOXB4_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_HOXB4_FailedQC_peaks.txt: hg18

value: Abcam :ab76093


title: batch4_chrom1_LoVo_HEYL_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_HEYL_FailedQC_peaks.txt: hg18

value: HEYL

value: Abcam :ab26138


title: batch4_chrom1_LoVo_HHEX_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_HHEX_FailedQC_peaks.txt: hg18

value: HHEX

value: Abcam :ab79392


title: batch4_chrom1_LoVo_HES4_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_HES4_FailedQC_peaks.txt: hg18

value: LoVo

value: Abcam :ab66377


title: batch4_chrom1_LoVo_ERM_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_ERM_PassedQC_peaks.txt: hg18

value: colon adenocarcinoma

value: ERM

value: Abcam :ab102010


title: batch4_chrom1_LoVo_EPAS1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_EPAS1_FailedQC_peaks.txt: hg18

value: Abcam :ab199


title: batch4_chrom1_LoVo_E2F3_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_E2F3_PassedQC_peaks.txt: hg18

value: Abcam :ab50917

value: PassedQC


title: batch4_chrom1_LoVo_CREB1_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_CREB1_PassedQC_peaks.txt: hg18

value: Abcam :ab32096


title: batch4_chrom1_LoVo_DR1_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_DR1_FailedQC_peaks.txt: hg18

value: Abcam :ab50783

value: FailedQC


title: batch4_chrom1_LoVo_ATF6_Mouse_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_ATF6_FailedQC_peaks.txt: hg18

value: Abcam :ab11909


title: batch3_chrom2_LoVo_RAD21_Rabbit_PassedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom2_LoVo_RAD21_PassedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-98784


title: batch3_chrom2_LoVo_NR5A2_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom2_LoVo_NR5A2_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-25389 X


title: batch4_chrom1_LoVo_ATF2_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch4_chrom1_LoVo_ATF2_FailedQC_peaks.txt: hg18

value: Abcam :ab28848


title: batch3_chrom2_LoVo_NR3C2_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom2_LoVo_NR3C2_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-11412 X


title: batch3_chrom2_LoVo_NR4A2_Rabbit_FailedQC

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: .txt files generated using MACS 1.4
batch3_chrom2_LoVo_NR4A2_FailedQC_peaks.txt: hg18

value: Santa Cruz Biotechnology, Inc. :sc-5568 X